Warning: Permanently added '54.172.163.73' (ED25519) to the list of known hosts. Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1767087424.501667 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.13.7, NVR = mock-6.6-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1767087424.501667 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator/percolator.spec) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1767087424.501667/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-9d08b767-7b82-4e8f-be13-3594351e03de INFO: Checking that 7052f52ff1de7967d92f840a7db25c815686a1f31067551f67570b2bb8b7b5eb image matches host's architecture INFO: Copy content of container 7052f52ff1de7967d92f840a7db25c815686a1f31067551f67570b2bb8b7b5eb to /var/lib/mock/fedora-rawhide-i686-bootstrap-1767087424.501667/root INFO: mounting 7052f52ff1de7967d92f840a7db25c815686a1f31067551f67570b2bb8b7b5eb with podman image mount INFO: image 7052f52ff1de7967d92f840a7db25c815686a1f31067551f67570b2bb8b7b5eb as /var/lib/containers/storage/overlay/6769e0d543b4e42d648a0e3c6c6dc3a7cd922687bf21fe4c4c3c48d04183880c/merged INFO: umounting image 7052f52ff1de7967d92f840a7db25c815686a1f31067551f67570b2bb8b7b5eb (/var/lib/containers/storage/overlay/6769e0d543b4e42d648a0e3c6c6dc3a7cd922687bf21fe4c4c3c48d04183880c/merged) with podman image umount INFO: Removing image mock-bootstrap-9d08b767-7b82-4e8f-be13-3594351e03de INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1767087424.501667/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-1.fc44.x86_64 rpm-sequoia-1.10.0-1.fc44.x86_64 dnf5-5.3.0.0-3.fc44.x86_64 dnf5-plugins-5.3.0.0-3.fc44.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 17.3 MiB/s | 12.4 MiB | 00m01s local 100% | 15.9 MiB/s | 12.5 MiB | 00m01s Copr repository 100% | 5.7 MiB/s | 5.3 MiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash i686 0:5.3.0-2.fc44 copr_base 8.6 MiB bzip2 i686 0:1.0.8-21.fc44 copr_base 85.4 KiB coreutils i686 0:9.9-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 5.3 MiB cpio i686 0:2.15-6.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.1 MiB diffutils i686 0:3.12-3.fc44 copr_base 1.6 MiB fedora-release noarch 0:44-0.10 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 0.0 B findutils i686 1:4.10.0-6.fc44 copr_base 1.9 MiB gawk i686 0:5.3.2-2.fc44 copr_base 1.8 MiB glibc-minimal-langpack i686 0:2.42.9000-17.fc44 copr_base 0.0 B grep i686 0:3.12-2.fc44 copr_base 1.0 MiB gzip i686 0:1.14-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 396.8 KiB info i686 0:7.2-7.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 360.3 KiB patch i686 0:2.8-3.fc44 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https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 956.8 KiB rpm-plugin-selinux i686 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 11.1 KiB rpm-sequoia i686 0:1.10.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.7 MiB rpm-sign-libs i686 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 30.9 KiB rust-srpm-macros noarch 0:28.4-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 5.5 KiB selinux-policy noarch 0:42.19-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 32.0 KiB selinux-policy-targeted noarch 0:42.19-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 18.7 MiB setup noarch 0:2.15.0-27.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 724.9 KiB sqlite-libs i686 0:3.51.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.6 MiB systemd-libs i686 0:259-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.3 MiB systemd-standalone-sysusers i686 0:259-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 292.7 KiB tpm2-tss i686 0:4.1.3-8.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.6 MiB tree-sitter-srpm-macros noarch 0:0.4.2-1.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 8.3 KiB util-linux-core i686 0:2.41.3-8.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.4 MiB xxhash-libs i686 0:0.8.3-3.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 113.5 KiB xz-libs i686 1:5.8.1-4.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 233.3 KiB zig-srpm-macros noarch 0:1-5.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.1 KiB zip i686 0:3.0-44.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 694.3 KiB zlib-ng-compat i686 0:2.3.2-2.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 184.9 KiB zstd i686 0:1.5.7-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 519.0 KiB Installing groups: build Transaction Summary: Installing: 183 packages Total size of inbound packages is 68 MiB. Need to download 68 MiB. After this operation, 218 MiB extra will be used (install 218 MiB, remove 0 B). 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1.6 MiB | 00m00s [ 28/183] libgcc-0:16.0.0-0.3.fc44.i686 100% | 7.4 MiB/s | 128.5 KiB | 00m00s [ 29/183] mpfr-0:4.2.2-2.fc44.i686 100% | 129.5 MiB/s | 397.9 KiB | 00m00s [ 30/183] gmp-1:6.3.0-4.fc44.i686 100% | 16.9 MiB/s | 312.3 KiB | 00m00s [ 31/183] readline-0:8.3-2.fc43.i686 100% | 14.0 MiB/s | 230.1 KiB | 00m00s [ 32/183] bzip2-libs-0:1.0.8-21.fc44.i6 100% | 20.8 MiB/s | 42.7 KiB | 00m00s [ 33/183] setup-0:2.15.0-27.fc44.noarch 100% | 9.2 MiB/s | 151.3 KiB | 00m00s [ 34/183] libselinux-0:3.9-5.fc44.i686 100% | 6.3 MiB/s | 102.5 KiB | 00m00s [ 35/183] audit-libs-0:4.1.2-2.fc44.i68 100% | 8.8 MiB/s | 143.7 KiB | 00m00s [ 36/183] ncurses-libs-0:6.5-8.20250614 100% | 20.2 MiB/s | 352.3 KiB | 00m00s [ 37/183] xz-libs-1:5.8.1-4.fc44.i686 100% | 6.7 MiB/s | 123.5 KiB | 00m00s [ 38/183] libblkid-0:2.41.3-8.fc44.i686 100% | 8.8 MiB/s | 135.3 KiB | 00m00s [ 39/183] libcap-ng-0:0.8.5-8.fc44.i686 100% | 1.8 MiB/s | 32.8 KiB | 00m00s [ 40/183] libfdisk-0:2.41.3-8.fc44.i686 100% | 8.8 MiB/s | 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246.0 KiB | 00m00s [ 67/183] R-srpm-macros-0:1.3.0-1.fc44. 100% | 513.3 KiB/s | 10.3 KiB | 00m00s [ 68/183] ansible-srpm-macros-0:1-18.1. 100% | 948.0 KiB/s | 19.9 KiB | 00m00s [ 69/183] dwz-0:0.16-2.fc44.i686 100% | 46.2 MiB/s | 142.1 KiB | 00m00s [ 70/183] build-reproducibility-srpm-ma 100% | 676.7 KiB/s | 12.9 KiB | 00m00s [ 71/183] filesystem-srpm-macros-0:3.18 100% | 12.9 MiB/s | 26.4 KiB | 00m00s [ 72/183] cmake-srpm-macros-0:3.31.10-3 100% | 517.7 KiB/s | 10.4 KiB | 00m00s [ 73/183] fonts-srpm-macros-1:5.0.0-1.f 100% | 1.5 MiB/s | 27.3 KiB | 00m00s [ 74/183] efi-srpm-macros-0:6-5.fc44.no 100% | 1.0 MiB/s | 22.5 KiB | 00m00s [ 75/183] forge-srpm-macros-0:0.4.0-3.f 100% | 1.3 MiB/s | 20.1 KiB | 00m00s [ 76/183] gap-srpm-macros-0:2-1.fc44.no 100% | 754.5 KiB/s | 9.1 KiB | 00m00s [ 77/183] fpc-srpm-macros-0:1.3-15.fc43 100% | 526.1 KiB/s | 7.9 KiB | 00m00s [ 78/183] ghc-srpm-macros-0:1.9.2-3.fc4 100% | 672.8 KiB/s | 8.7 KiB | 00m00s [ 79/183] gnat-srpm-macros-0:6-8.fc43.n 100% | 707.2 KiB/s | 8.5 KiB | 00m00s [ 80/183] go-srpm-macros-0:3.8.0-1.fc44 100% | 1.8 MiB/s | 28.3 KiB | 00m00s [ 81/183] java-srpm-macros-0:1-7.fc43.n 100% | 661.9 KiB/s | 7.9 KiB | 00m00s [ 82/183] kernel-srpm-macros-0:1.0-27.f 100% | 495.6 KiB/s | 8.9 KiB | 00m00s [ 83/183] lua-srpm-macros-0:1-16.fc43.n 100% | 583.8 KiB/s | 8.8 KiB | 00m00s [ 84/183] ocaml-srpm-macros-0:11-2.fc43 100% | 712.4 KiB/s | 9.3 KiB | 00m00s [ 85/183] openblas-srpm-macros-0:2-20.f 100% | 474.7 KiB/s | 7.6 KiB | 00m00s [ 86/183] perl-srpm-macros-0:1-60.fc43. 100% | 637.6 KiB/s | 8.3 KiB | 00m00s [ 87/183] package-notes-srpm-macros-0:0 100% | 561.6 KiB/s | 9.0 KiB | 00m00s [ 88/183] pyproject-srpm-macros-0:1.18. 100% | 1.0 MiB/s | 13.3 KiB | 00m00s [ 89/183] python-srpm-macros-0:3.14-9.f 100% | 1.9 MiB/s | 23.8 KiB | 00m00s [ 90/183] qt5-srpm-macros-0:5.15.18-1.f 100% | 614.5 KiB/s | 8.6 KiB | 00m00s [ 91/183] qt6-srpm-macros-0:6.10.1-1.fc 100% | 623.8 KiB/s | 9.4 KiB | 00m00s [ 92/183] rust-srpm-macros-0:28.4-1.fc4 100% | 725.8 KiB/s | 10.9 KiB | 00m00s [ 93/183] tree-sitter-srpm-macros-0:0.4 100% | 890.0 KiB/s | 13.4 KiB | 00m00s [ 94/183] zig-srpm-macros-0:1-5.fc43.no 100% | 648.8 KiB/s | 8.4 KiB | 00m00s [ 95/183] zip-0:3.0-44.fc43.i686 100% | 17.2 MiB/s | 264.9 KiB | 00m00s [ 96/183] pkgconf-0:2.3.0-3.fc43.i686 100% | 2.7 MiB/s | 44.7 KiB | 00m00s [ 97/183] pkgconf-m4-0:2.3.0-3.fc43.noa 100% | 869.4 KiB/s | 13.9 KiB | 00m00s [ 98/183] libpkgconf-0:2.3.0-3.fc43.i68 100% | 2.4 MiB/s | 41.0 KiB | 00m00s [ 99/183] pcre2-syntax-0:10.47-1.fc44.n 100% | 8.0 MiB/s | 164.7 KiB | 00m00s [100/183] ed-0:1.22.3-1.fc44.i686 100% | 3.4 MiB/s | 83.4 KiB | 00m00s [101/183] libattr-0:2.5.2-6.fc43.i686 100% | 794.8 KiB/s | 18.3 KiB | 00m00s [102/183] libsepol-0:3.9-2.fc44.i686 100% | 119.9 MiB/s | 368.3 KiB | 00m00s [103/183] ncurses-base-0:6.5-8.20250614 100% | 3.0 MiB/s | 63.5 KiB | 00m00s [104/183] libatomic-0:16.0.0-0.3.fc44.i 100% | 1.2 MiB/s | 18.4 KiB | 00m00s [105/183] sqlite-libs-0:3.51.0-1.fc44.i 100% | 44.0 MiB/s | 811.5 KiB | 00m00s [106/183] lz4-libs-0:1.10.0-3.fc44.i686 100% | 75.0 MiB/s | 76.8 KiB | 00m00s [107/183] libxml2-0:2.12.10-5.fc44.i686 100% | 32.5 MiB/s | 733.1 KiB | 00m00s [108/183] libzstd-0:1.5.7-3.fc44.i686 100% | 21.9 MiB/s | 359.5 KiB | 00m00s [109/183] fedora-release-common-0:44-0. 100% | 1.9 MiB/s | 24.7 KiB | 00m00s [110/183] file-libs-0:5.46-8.fc44.i686 100% | 38.1 MiB/s | 857.7 KiB | 00m00s [111/183] openssl-libs-1:3.5.4-1.fc44.i 100% | 81.6 MiB/s | 2.6 MiB | 00m00s [112/183] elfutils-debuginfod-client-0: 100% | 3.3 MiB/s | 47.6 KiB | 00m00s [113/183] elfutils-libs-0:0.194-2.fc44. 100% | 17.5 MiB/s | 305.1 KiB | 00m00s [114/183] libcap-0:2.77-1.fc44.i686 100% | 5.8 MiB/s | 89.1 KiB | 00m00s [115/183] coreutils-common-0:9.9-1.fc44 100% | 90.3 MiB/s | 2.1 MiB | 00m00s [116/183] linkdupes-0:0.7.2-2.fc44.i686 100% | 23.3 MiB/s | 381.2 KiB | 00m00s [117/183] add-determinism-0:0.7.2-2.fc4 100% | 42.4 MiB/s | 912.6 KiB | 00m00s [118/183] jansson-0:2.14-3.fc44.i686 100% | 46.8 MiB/s | 47.9 KiB | 00m00s [119/183] alternatives-0:1.33-3.fc44.i6 100% | 2.7 MiB/s | 41.3 KiB | 00m00s [120/183] lua-libs-0:5.4.8-4.fc44.i686 100% | 9.2 MiB/s | 150.4 KiB | 00m00s [121/183] libgomp-0:16.0.0-0.3.fc44.i68 100% | 21.4 MiB/s | 372.5 KiB | 00m00s [122/183] rpm-sequoia-0:1.10.0-1.fc44.i 100% | 35.1 MiB/s | 1.0 MiB | 00m00s [123/183] rpm-sign-libs-0:6.0.1-1.fc44. 100% | 1.6 MiB/s | 28.5 KiB | 00m00s [124/183] ca-certificates-0:2025.2.80_v 100% | 41.3 MiB/s | 973.8 KiB | 00m00s [125/183] crypto-policies-0:20251128-1. 100% | 3.8 MiB/s | 74.7 KiB | 00m00s [126/183] fedora-release-identity-basic 100% | 679.8 KiB/s | 14.3 KiB | 00m00s [127/183] json-c-0:0.18-7.fc44.i686 100% | 24.1 MiB/s | 49.3 KiB | 00m00s [128/183] fedora-repos-0:44-0.1.noarch 100% | 453.7 KiB/s | 9.1 KiB | 00m00s [129/183] elfutils-default-yama-scope-0 100% | 618.9 KiB/s | 11.8 KiB | 00m00s [130/183] gnulib-l10n-0:20241231-1.fc44 100% | 6.6 MiB/s | 143.0 KiB | 00m00s [131/183] libffi-0:3.5.2-1.fc44.i686 100% | 2.2 MiB/s | 39.0 KiB | 00m00s [132/183] p11-kit-0:0.25.8-1.fc44.i686 100% | 27.2 MiB/s | 501.8 KiB | 00m00s [133/183] gnupg2-0:2.4.8-4.fc44.i686 100% | 237.9 MiB/s | 1.7 MiB | 00m00s [134/183] gnupg2-dirmngr-0:2.4.8-4.fc44 100% | 58.1 MiB/s | 297.5 KiB | 00m00s [135/183] gnupg2-gpg-agent-0:2.4.8-4.fc 100% | 95.9 MiB/s | 294.5 KiB | 00m00s [136/183] p11-kit-trust-0:0.25.8-1.fc44 100% | 8.3 MiB/s | 144.6 KiB | 00m00s [137/183] gnupg2-gpgconf-0:2.4.8-4.fc44 100% | 39.5 MiB/s | 121.4 KiB | 00m00s [138/183] gnupg2-keyboxd-0:2.4.8-4.fc44 100% | 48.7 MiB/s | 99.7 KiB | 00m00s [139/183] gnupg2-verify-0:2.4.8-4.fc44. 100% | 58.5 MiB/s | 179.8 KiB | 00m00s [140/183] libfsverity-0:1.6-3.fc44.i686 100% | 9.7 MiB/s | 19.8 KiB | 00m00s [141/183] libtasn1-0:4.20.0-2.fc44.i686 100% | 25.2 MiB/s | 77.4 KiB | 00m00s [142/183] ima-evm-utils-libs-0:1.6.2-7. 100% | 1.7 MiB/s | 29.9 KiB | 00m00s [143/183] fedora-gpg-keys-0:44-0.1.noar 100% | 8.3 MiB/s | 127.7 KiB | 00m00s [144/183] libassuan-0:2.5.7-4.fc44.i686 100% | 34.7 MiB/s | 71.1 KiB | 00m00s [145/183] tpm2-tss-0:4.1.3-8.fc43.i686 100% | 18.1 MiB/s | 369.7 KiB | 00m00s [146/183] fedora-repos-rawhide-0:44-0.1 100% | 665.2 KiB/s | 8.6 KiB | 00m00s [147/183] npth-0:1.8-3.fc44.i686 100% | 12.6 MiB/s | 25.8 KiB | 00m00s [148/183] libksba-0:1.6.7-4.fc44.i686 100% | 82.6 MiB/s | 169.2 KiB | 00m00s [149/183] gnutls-0:3.8.11-8.fc44.i686 100% | 230.9 MiB/s | 1.4 MiB | 00m00s [150/183] libgcrypt-0:1.11.2-1.fc44.i68 100% | 29.8 MiB/s | 549.5 KiB | 00m00s [151/183] libgpg-error-0:1.58-1.fc44.i6 100% | 12.1 MiB/s | 248.2 KiB | 00m00s [152/183] gpgverify-0:2.2-3.fc43.noarch 100% | 925.3 KiB/s | 11.1 KiB | 00m00s [153/183] openldap-0:2.6.10-4.fc44.i686 100% | 15.0 MiB/s | 277.4 KiB | 00m00s [154/183] libusb1-0:1.0.29-4.fc44.i686 100% | 5.1 MiB/s | 83.4 KiB | 00m00s [155/183] libevent-0:2.1.12-16.fc44.i68 100% | 148.5 MiB/s | 304.1 KiB | 00m00s [156/183] gdbm-libs-1:1.23-10.fc44.i686 100% | 20.0 MiB/s | 61.4 KiB | 00m00s [157/183] libidn2-0:2.3.8-2.fc44.i686 100% | 83.3 MiB/s | 170.7 KiB | 00m00s [158/183] libunistring-0:1.1-10.fc44.i6 100% | 134.9 MiB/s | 552.5 KiB | 00m00s [159/183] cyrus-sasl-lib-0:2.1.28-33.fc 100% | 41.9 MiB/s | 857.7 KiB | 00m00s [160/183] nettle-0:3.10.1-2.fc44.i686 100% | 144.5 MiB/s | 444.0 KiB | 00m00s [161/183] libtool-ltdl-0:2.5.4-9.fc44.i 100% | 2.5 MiB/s | 38.6 KiB | 00m00s [162/183] xxhash-libs-0:0.8.3-3.fc43.i6 100% | 2.0 MiB/s | 47.4 KiB | 00m00s [163/183] libcurl-0:8.18.0~rc2-1.fc44.i 100% | 18.2 MiB/s | 465.5 KiB | 00m00s [164/183] policycoreutils-0:3.9-5.fc44. 100% | 5.3 MiB/s | 191.1 KiB | 00m00s [165/183] gdb-minimal-0:16.3-6.fc44.i68 100% | 48.7 MiB/s | 4.8 MiB | 00m00s [166/183] selinux-policy-0:42.19-1.fc44 100% | 1.7 MiB/s | 65.4 KiB | 00m00s [167/183] selinux-policy-targeted-0:42. 100% | 75.8 MiB/s | 6.6 MiB | 00m00s [168/183] systemd-standalone-sysusers-0 100% | 5.2 MiB/s | 147.9 KiB | 00m00s [169/183] rpm-plugin-selinux-0:6.0.1-1. 100% | 663.0 KiB/s | 19.2 KiB | 00m00s [170/183] libselinux-utils-0:3.9-5.fc44 100% | 4.7 MiB/s | 110.5 KiB | 00m00s [171/183] krb5-libs-0:1.21.3-10.fc44.i6 100% | 34.2 MiB/s | 805.9 KiB | 00m00s [172/183] libnghttp3-0:1.14.0-1.fc44.i6 100% | 39.8 MiB/s | 81.6 KiB | 00m00s [173/183] libbrotli-0:1.2.0-1.fc44.i686 100% | 13.3 MiB/s | 339.6 KiB | 00m00s [174/183] libpsl-0:0.21.5-6.fc44.i686 100% | 64.1 MiB/s | 65.7 KiB | 00m00s [175/183] libnghttp2-0:1.68.0-2.fc44.i6 100% | 3.2 MiB/s | 77.7 KiB | 00m00s [176/183] ngtcp2-0:1.18.0-1.fc44.i686 100% | 7.1 MiB/s | 173.6 KiB | 00m00s [177/183] libssh-0:0.11.3-1.fc44.i686 100% | 9.4 MiB/s | 250.8 KiB | 00m00s [178/183] keyutils-libs-0:1.6.3-6.fc44. 100% | 31.1 MiB/s | 31.8 KiB | 00m00s [179/183] ngtcp2-crypto-ossl-0:1.18.0-1 100% | 1.1 MiB/s | 27.7 KiB | 00m00s [180/183] publicsuffix-list-dafsa-0:202 100% | 2.3 MiB/s | 59.2 KiB | 00m00s [181/183] libverto-0:0.3.2-11.fc43.i686 100% | 809.7 KiB/s | 21.1 KiB | 00m00s [182/183] libcom_err-0:1.47.3-3.fc44.i6 100% | 1.0 MiB/s | 27.3 KiB | 00m00s [183/183] libssh-config-0:0.11.3-1.fc44 100% | 364.5 KiB/s | 9.1 KiB | 00m00s -------------------------------------------------------------------------------- [183/183] Total 100% | 56.1 MiB/s | 68.2 MiB | 00m01s Running transaction [ 1/185] Verify package files 100% | 639.0 B/s | 183.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-51.fc44.i686 >>> Finished %pretrans scriptlet: filesystem-0:3.18-51.fc44.i686 >>> [RPM] /var/lib/mock/fedora-rawhide-i686-1767087424.501667/root/var/cache/dnf/copr_base-7e55b3bc06c2f1cc/packages/bash-5.3.0-2.fc44.i686.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 52ac7d71d4a9769d: NOKEY [ 2/185] Prepare transaction 100% | 3.4 KiB/s | 183.0 B | 00m00s [ 3/185] Installing libgcc-0:16.0.0-0. 100% | 292.4 MiB/s | 299.4 KiB | 00m00s [ 4/185] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/185] Installing publicsuffix-list- 100% | 0.0 B/s | 69.8 KiB | 00m00s [ 6/185] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 7/185] Installing coreutils-common-0 100% | 387.2 MiB/s | 11.2 MiB | 00m00s [ 8/185] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 9/185] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 10/185] Installing fedora-gpg-keys-0: 100% | 43.7 MiB/s | 179.0 KiB | 00m00s [ 11/185] Installing fedora-repos-0:44- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 12/185] Installing fedora-release-com 100% | 24.3 MiB/s | 24.9 KiB | 00m00s [ 13/185] Installing fedora-release-0:4 100% | 15.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/185] Installing setup-0:2.15.0-27. 100% | 51.0 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/185] Installing filesystem-0:3.18- 100% | 2.8 MiB/s | 212.3 KiB | 00m00s [ 16/185] Installing ncurses-base-0:6.5 100% | 86.3 MiB/s | 353.5 KiB | 00m00s [ 17/185] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB | 00m00s [ 18/185] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 19/185] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [ 20/185] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [ 21/185] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [ 22/185] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [ 23/185] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [ 24/185] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [ 25/185] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [ 26/185] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [ 27/185] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [ 28/185] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [ 29/185] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [ 30/185] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [ 31/185] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [ 32/185] Installing bash-0:5.3.0-2.fc4 100% | 268.5 MiB/s | 8.6 MiB | 00m00s [ 33/185] Installing glibc-common-0:2.4 100% | 63.7 MiB/s | 1.0 MiB | 00m00s [ 34/185] Installing glibc-gconv-extra- 100% | 272.3 MiB/s | 6.8 MiB | 00m00s [ 35/185] Installing glibc-0:2.42.9000- 100% | 164.1 MiB/s | 5.7 MiB | 00m00s [ 36/185] Installing ncurses-libs-0:6.5 100% | 233.4 MiB/s | 956.1 KiB | 00m00s [ 37/185] Installing glibc-minimal-lang 100% | 20.2 KiB/s | 124.0 B | 00m00s [ 38/185] Installing crypto-policies-0: 100% | 38.5 MiB/s | 157.7 KiB | 00m00s [ 39/185] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [ 40/185] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [ 41/185] Installing zlib-ng-compat-0:2 100% | 181.3 MiB/s | 185.6 KiB | 00m00s [ 42/185] Installing bzip2-libs-0:1.0.8 100% | 0.0 B/s | 80.8 KiB | 00m00s [ 43/185] Installing libgpg-error-0:1.5 100% | 57.5 MiB/s | 941.8 KiB | 00m00s [ 44/185] Installing libassuan-0:2.5.7- 100% | 164.9 MiB/s | 168.9 KiB | 00m00s [ 45/185] Installing libgcrypt-0:1.11.2 100% | 312.5 MiB/s | 1.3 MiB | 00m00s [ 46/185] Installing readline-0:8.3-2.f 100% | 237.4 MiB/s | 486.1 KiB | 00m00s [ 47/185] Installing gmp-1:6.3.0-4.fc44 100% | 359.6 MiB/s | 736.5 KiB | 00m00s [ 48/185] Installing xz-libs-1:5.8.1-4. 100% | 228.9 MiB/s | 234.4 KiB | 00m00s [ 49/185] Installing libuuid-0:2.41.3-8 100% | 0.0 B/s | 41.6 KiB | 00m00s [ 50/185] Installing popt-0:1.19-9.fc43 100% | 69.5 MiB/s | 142.4 KiB | 00m00s [ 51/185] Installing libzstd-0:1.5.7-3. 100% | 299.9 MiB/s | 921.2 KiB | 00m00s [ 52/185] Installing elfutils-libelf-0: 100% | 376.1 MiB/s | 1.1 MiB | 00m00s [ 53/185] Installing npth-0:1.8-3.fc44. 100% | 0.0 B/s | 49.9 KiB | 00m00s [ 54/185] Installing elfutils-libs-0:0. 100% | 359.2 MiB/s | 735.7 KiB | 00m00s [ 55/185] Installing libblkid-0:2.41.3- 100% | 279.6 MiB/s | 286.3 KiB | 00m00s [ 56/185] Installing systemd-libs-0:259 100% | 334.1 MiB/s | 2.3 MiB | 00m00s [ 57/185] Installing libxcrypt-0:4.5.2- 100% | 292.4 MiB/s | 299.4 KiB | 00m00s [ 58/185] Installing libsepol-0:3.9-2.f 100% | 438.7 MiB/s | 898.4 KiB | 00m00s [ 59/185] Installing sqlite-libs-0:3.51 100% | 322.1 MiB/s | 1.6 MiB | 00m00s [ 60/185] Installing gnupg2-gpgconf-0:2 100% | 20.8 MiB/s | 255.8 KiB | 00m00s [ 61/185] Installing pcre2-0:10.47-1.fc 100% | 345.0 MiB/s | 706.5 KiB | 00m00s [ 62/185] Installing libselinux-0:3.9-5 100% | 208.6 MiB/s | 213.6 KiB | 00m00s [ 63/185] Installing grep-0:3.12-2.fc44 100% | 67.0 MiB/s | 1.0 MiB | 00m00s [ 64/185] Installing findutils-1:4.10.0 100% | 117.5 MiB/s | 1.9 MiB | 00m00s [ 65/185] Installing libattr-0:2.5.2-6. 100% | 0.0 B/s | 24.6 KiB | 00m00s [ 66/185] Installing libacl-0:2.3.2-4.f 100% | 0.0 B/s | 35.9 KiB | 00m00s [ 67/185] Installing sed-0:4.9-6.fc44.i 100% | 56.6 MiB/s | 868.6 KiB | 00m00s [ 68/185] Installing libtasn1-0:4.20.0- 100% | 177.0 MiB/s | 181.3 KiB | 00m00s [ 69/185] Installing libunistring-0:1.1 100% | 347.5 MiB/s | 1.7 MiB | 00m00s [ 70/185] Installing libidn2-0:2.3.8-2. 100% | 182.9 MiB/s | 561.8 KiB | 00m00s [ 71/185] Installing xz-1:5.8.1-4.fc44. 100% | 78.7 MiB/s | 1.3 MiB | 00m00s [ 72/185] Installing libmount-0:2.41.3- 100% | 403.2 MiB/s | 412.9 KiB | 00m00s [ 73/185] Installing gnupg2-verify-0:2. 100% | 27.7 MiB/s | 368.6 KiB | 00m00s [ 74/185] Installing dwz-0:0.16-2.fc44. 100% | 25.2 MiB/s | 310.3 KiB | 00m00s [ 75/185] Installing mpfr-0:4.2.2-2.fc4 100% | 322.0 MiB/s | 989.3 KiB | 00m00s [ 76/185] Installing gawk-0:5.3.2-2.fc4 100% | 107.6 MiB/s | 1.8 MiB | 00m00s [ 77/185] Installing libksba-0:1.6.7-4. 100% | 398.7 MiB/s | 408.3 KiB | 00m00s [ 78/185] Installing unzip-0:6.0-68.fc4 100% | 30.0 MiB/s | 399.3 KiB | 00m00s [ 79/185] Installing file-libs-0:5.46-8 100% | 659.4 MiB/s | 11.9 MiB | 00m00s [ 80/185] Installing file-0:5.46-8.fc44 100% | 7.9 MiB/s | 96.7 KiB | 00m00s [ 81/185] Installing diffutils-0:3.12-3 100% | 98.1 MiB/s | 1.6 MiB | 00m00s [ 82/185] Installing libcap-ng-0:0.8.5- 100% | 67.6 MiB/s | 69.2 KiB | 00m00s [ 83/185] Installing audit-libs-0:4.1.2 100% | 193.0 MiB/s | 395.2 KiB | 00m00s [ 84/185] Installing libsemanage-0:3.9- 100% | 314.2 MiB/s | 321.7 KiB | 00m00s [ 85/185] Installing libsmartcols-0:2.4 100% | 184.3 MiB/s | 188.7 KiB | 00m00s [ 86/185] Installing libeconf-0:0.7.9-2 100% | 64.2 MiB/s | 65.7 KiB | 00m00s [ 87/185] Installing pam-libs-0:1.7.1-3 100% | 127.5 MiB/s | 130.6 KiB | 00m00s [ 88/185] Installing libcap-0:2.77-1.fc 100% | 14.9 MiB/s | 198.9 KiB | 00m00s [ 89/185] Installing alternatives-0:1.3 100% | 5.6 MiB/s | 62.9 KiB | 00m00s [ 90/185] Installing lua-libs-0:5.4.8-4 100% | 303.6 MiB/s | 310.9 KiB | 00m00s [ 91/185] Installing json-c-0:0.18-7.fc 100% | 85.1 MiB/s | 87.1 KiB | 00m00s [ 92/185] Installing libffi-0:3.5.2-1.f 100% | 78.4 MiB/s | 80.3 KiB | 00m00s [ 93/185] Installing p11-kit-0:0.25.8-1 100% | 127.3 MiB/s | 2.4 MiB | 00m00s [ 94/185] Installing p11-kit-trust-0:0. 100% | 19.4 MiB/s | 398.3 KiB | 00m00s [ 95/185] Installing ngtcp2-0:1.18.0-1. 100% | 183.2 MiB/s | 375.2 KiB | 00m00s [ 96/185] Installing openssl-libs-1:3.5 100% | 364.6 MiB/s | 7.3 MiB | 00m00s [ 97/185] Installing coreutils-0:9.9-1. 100% | 168.3 MiB/s | 5.4 MiB | 00m00s [ 98/185] Installing ca-certificates-0: 100% | 1.6 MiB/s | 2.5 MiB | 00m02s [ 99/185] Installing gzip-0:1.14-1.fc44 100% | 28.1 MiB/s | 402.4 KiB | 00m00s [100/185] Installing rpm-sequoia-0:1.10 100% | 392.3 MiB/s | 2.7 MiB | 00m00s [101/185] Installing libfsverity-0:1.6- 100% | 0.0 B/s | 28.7 KiB | 00m00s [102/185] Installing libevent-0:2.1.12- 100% | 340.7 MiB/s | 1.0 MiB | 00m00s [103/185] Installing ngtcp2-crypto-ossl 100% | 46.7 MiB/s | 47.8 KiB | 00m00s [104/185] Installing util-linux-core-0: 100% | 76.9 MiB/s | 1.4 MiB | 00m00s [105/185] Installing zip-0:3.0-44.fc43. 100% | 48.7 MiB/s | 698.2 KiB | 00m00s [106/185] Installing gnupg2-keyboxd-0:2 100% | 28.1 MiB/s | 201.2 KiB | 00m00s [107/185] Installing libpsl-0:0.21.5-6. 100% | 74.9 MiB/s | 76.7 KiB | 00m00s [108/185] Installing tar-2:1.35-6.fc43. 100% | 142.8 MiB/s | 3.0 MiB | 00m00s [109/185] Installing linkdupes-0:0.7.2- 100% | 57.4 MiB/s | 822.5 KiB | 00m00s [110/185] Installing libselinux-utils-0 100% | 20.9 MiB/s | 278.2 KiB | 00m00s [111/185] Installing liblastlog2-0:2.41 100% | 6.6 MiB/s | 34.0 KiB | 00m00s [112/185] Installing systemd-standalone 100% | 20.5 MiB/s | 293.2 KiB | 00m00s [113/185] Installing libusb1-0:1.0.29-4 100% | 25.1 MiB/s | 180.2 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.i686 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.i686 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [114/185] Installing tpm2-tss-0:4.1.3-8 100% | 271.8 MiB/s | 1.6 MiB | 00m00s [115/185] Installing gnupg2-gpg-agent-0 100% | 35.8 MiB/s | 696.2 KiB | 00m00s [116/185] Installing ima-evm-utils-libs 100% | 51.9 MiB/s | 53.2 KiB | 00m00s [117/185] Installing libfdisk-0:2.41.3- 100% | 207.4 MiB/s | 424.7 KiB | 00m00s [118/185] Installing util-linux-0:2.41. 100% | 98.5 MiB/s | 3.3 MiB | 00m00s [119/185] Installing policycoreutils-0: 100% | 27.8 MiB/s | 683.6 KiB | 00m00s [120/185] Installing selinux-policy-0:4 100% | 1.7 MiB/s | 33.6 KiB | 00m00s [121/185] Installing selinux-policy-tar 100% | 193.7 MiB/s | 14.9 MiB | 00m00s [122/185] Installing libxml2-0:2.12.10- 100% | 100.1 MiB/s | 1.8 MiB | 00m00s [123/185] Installing nettle-0:3.10.1-2. 100% | 256.3 MiB/s | 787.5 KiB | 00m00s [124/185] Installing gnutls-0:3.8.11-8. 100% | 387.1 MiB/s | 3.9 MiB | 00m00s [125/185] Installing bzip2-0:1.0.8-21.f 100% | 7.3 MiB/s | 89.9 KiB | 00m00s [126/185] Installing add-determinism-0: 100% | 127.3 MiB/s | 2.2 MiB | 00m00s [127/185] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [128/185] Installing cpio-0:2.15-6.fc43 100% | 73.7 MiB/s | 1.1 MiB | 00m00s [129/185] Installing libpkgconf-0:2.3.0 100% | 75.9 MiB/s | 77.7 KiB | 00m00s [130/185] Installing pkgconf-0:2.3.0-3. 100% | 6.9 MiB/s | 85.4 KiB | 00m00s [131/185] Installing pkgconf-pkg-config 100% | 160.5 KiB/s | 1.8 KiB | 00m00s [132/185] Installing ed-0:1.22.3-1.fc44 100% | 12.2 MiB/s | 150.0 KiB | 00m00s [133/185] Installing patch-0:2.8-3.fc44 100% | 19.1 MiB/s | 235.2 KiB | 00m00s [134/185] Installing libatomic-0:16.0.0 100% | 0.0 B/s | 28.4 KiB | 00m00s [135/185] Installing libstdc++-0:16.0.0 100% | 365.9 MiB/s | 2.9 MiB | 00m00s [136/185] Installing rpm-libs-0:6.0.1-1 100% | 312.0 MiB/s | 958.3 KiB | 00m00s [137/185] Installing zstd-0:1.5.7-3.fc4 100% | 39.3 MiB/s | 522.6 KiB | 00m00s [138/185] Installing lz4-libs-0:1.10.0- 100% | 150.0 MiB/s | 153.6 KiB | 00m00s [139/185] Installing libarchive-0:3.8.4 100% | 334.9 MiB/s | 1.0 MiB | 00m00s [140/185] Installing jansson-0:2.14-3.f 100% | 87.5 MiB/s | 89.6 KiB | 00m00s [141/185] Installing libgomp-0:16.0.0-0 100% | 280.9 MiB/s | 575.3 KiB | 00m00s [142/185] Installing libtool-ltdl-0:2.5 100% | 72.6 MiB/s | 74.4 KiB | 00m00s [143/185] Installing gdbm-libs-1:1.23-1 100% | 130.7 MiB/s | 133.9 KiB | 00m00s [144/185] Installing cyrus-sasl-lib-0:2 100% | 137.4 MiB/s | 2.5 MiB | 00m00s [145/185] Installing openldap-0:2.6.10- 100% | 220.3 MiB/s | 676.8 KiB | 00m00s [146/185] Installing gnupg2-dirmngr-0:2 100% | 32.2 MiB/s | 660.4 KiB | 00m00s [147/185] Installing gnupg2-0:2.4.8-4.f 100% | 226.4 MiB/s | 6.6 MiB | 00m00s [148/185] Installing gpgverify-0:2.2-3. 100% | 0.0 B/s | 9.4 KiB | 00m00s [149/185] Installing rpm-sign-libs-0:6. 100% | 0.0 B/s | 31.8 KiB | 00m00s [150/185] Installing rpm-build-libs-0:6 100% | 261.6 MiB/s | 267.9 KiB | 00m00s [151/185] Installing xxhash-libs-0:0.8. 100% | 112.2 MiB/s | 114.9 KiB | 00m00s [152/185] Installing libbrotli-0:1.2.0- 100% | 277.8 MiB/s | 853.4 KiB | 00m00s [153/185] Installing libnghttp2-0:1.68. 100% | 158.8 MiB/s | 162.6 KiB | 00m00s [154/185] Installing libnghttp3-0:1.14. 100% | 160.6 MiB/s | 164.4 KiB | 00m00s [155/185] Installing keyutils-libs-0:1. 100% | 53.5 MiB/s | 54.8 KiB | 00m00s [156/185] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 63.4 KiB | 00m00s [157/185] Installing libverto-0:0.3.2-1 100% | 25.8 MiB/s | 26.5 KiB | 00m00s [158/185] Installing krb5-libs-0:1.21.3 100% | 290.1 MiB/s | 2.3 MiB | 00m00s [159/185] Installing libssh-0:0.11.3-1. 100% | 300.3 MiB/s | 615.1 KiB | 00m00s [160/185] Installing libcurl-0:8.18.0~r 100% | 332.0 MiB/s | 1.0 MiB | 00m00s [161/185] Installing elfutils-debuginfo 100% | 5.8 MiB/s | 76.6 KiB | 00m00s [162/185] Installing binutils-0:2.45.50 100% | 334.9 MiB/s | 27.5 MiB | 00m00s [163/185] Installing elfutils-0:0.194-2 100% | 136.6 MiB/s | 2.6 MiB | 00m00s [164/185] Installing gdb-minimal-0:16.3 100% | 294.7 MiB/s | 13.9 MiB | 00m00s [165/185] Installing debugedit-0:5.2-3. 100% | 16.7 MiB/s | 221.9 KiB | 00m00s [166/185] Installing curl-0:8.18.0~rc2- 100% | 22.4 MiB/s | 481.4 KiB | 00m00s [167/185] Installing rpm-0:6.0.1-1.fc44 100% | 79.1 MiB/s | 2.5 MiB | 00m00s [168/185] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [169/185] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.2 KiB | 00m00s [170/185] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [171/185] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [172/185] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.3 KiB | 00m00s [173/185] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [174/185] Installing redhat-rpm-config- 100% | 92.7 MiB/s | 189.9 KiB | 00m00s [175/185] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [176/185] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [177/185] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [178/185] Installing R-srpm-macros-0:1. 100% | 0.0 B/s | 4.0 KiB | 00m00s [179/185] Installing python-srpm-macros 100% | 51.7 MiB/s | 52.9 KiB | 00m00s [180/185] Installing rpm-build-0:6.0.1- 100% | 19.3 MiB/s | 276.5 KiB | 00m00s [181/185] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [182/185] Installing rpm-plugin-selinux 100% | 0.0 B/s | 12.2 KiB | 00m00s [183/185] Installing which-0:2.23-3.fc4 100% | 4.6 MiB/s | 80.3 KiB | 00m00s [184/185] Installing shadow-utils-2:4.1 100% | 140.6 MiB/s | 3.9 MiB | 00m00s [185/185] Installing info-0:7.2-7.fc44. 100% | 52.3 KiB/s | 360.7 KiB | 00m07s Warning: skipped OpenPGP checks for 183 packages from repositories: copr_base, https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.0-1.fc44.noarch add-determinism-0.7.2-2.fc44.i686 alternatives-1.33-3.fc44.i686 ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.2-2.fc44.i686 bash-5.3.0-2.fc44.i686 binutils-2.45.50-12.fc44.i686 build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch bzip2-1.0.8-21.fc44.i686 bzip2-libs-1.0.8-21.fc44.i686 ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch cmake-srpm-macros-3.31.10-3.fc44.noarch coreutils-9.9-1.fc44.i686 coreutils-common-9.9-1.fc44.i686 cpio-2.15-6.fc43.i686 crypto-policies-20251128-1.git19878fe.fc44.noarch curl-8.18.0~rc2-1.fc44.i686 cyrus-sasl-lib-2.1.28-33.fc44.i686 debugedit-5.2-3.fc44.i686 diffutils-3.12-3.fc44.i686 dwz-0.16-2.fc44.i686 ed-1.22.3-1.fc44.i686 efi-srpm-macros-6-5.fc44.noarch elfutils-0.194-2.fc44.i686 elfutils-debuginfod-client-0.194-2.fc44.i686 elfutils-default-yama-scope-0.194-2.fc44.noarch elfutils-libelf-0.194-2.fc44.i686 elfutils-libs-0.194-2.fc44.i686 fedora-gpg-keys-44-0.1.noarch fedora-release-44-0.10.noarch fedora-release-common-44-0.10.noarch fedora-release-identity-basic-44-0.10.noarch fedora-repos-44-0.1.noarch fedora-repos-rawhide-44-0.1.noarch file-5.46-8.fc44.i686 file-libs-5.46-8.fc44.i686 filesystem-3.18-51.fc44.i686 filesystem-srpm-macros-3.18-51.fc44.noarch findutils-4.10.0-6.fc44.i686 fonts-srpm-macros-5.0.0-1.fc44.noarch forge-srpm-macros-0.4.0-3.fc43.noarch fpc-srpm-macros-1.3-15.fc43.noarch gap-srpm-macros-2-1.fc44.noarch gawk-5.3.2-2.fc44.i686 gdb-minimal-16.3-6.fc44.i686 gdbm-libs-1.23-10.fc44.i686 ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42.9000-17.fc44.i686 glibc-common-2.42.9000-17.fc44.i686 glibc-gconv-extra-2.42.9000-17.fc44.i686 glibc-minimal-langpack-2.42.9000-17.fc44.i686 gmp-6.3.0-4.fc44.i686 gnat-srpm-macros-6-8.fc43.noarch gnulib-l10n-20241231-1.fc44.noarch gnupg2-2.4.8-4.fc44.i686 gnupg2-dirmngr-2.4.8-4.fc44.i686 gnupg2-gpg-agent-2.4.8-4.fc44.i686 gnupg2-gpgconf-2.4.8-4.fc44.i686 gnupg2-keyboxd-2.4.8-4.fc44.i686 gnupg2-verify-2.4.8-4.fc44.i686 gnutls-3.8.11-8.fc44.i686 go-srpm-macros-3.8.0-1.fc44.noarch gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc44.i686 gzip-1.14-1.fc44.i686 ima-evm-utils-libs-1.6.2-7.fc44.i686 info-7.2-7.fc44.i686 jansson-2.14-3.fc44.i686 java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc44.i686 kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc44.i686 krb5-libs-1.21.3-10.fc44.i686 libacl-2.3.2-4.fc44.i686 libarchive-3.8.4-1.fc44.i686 libassuan-2.5.7-4.fc44.i686 libatomic-16.0.0-0.3.fc44.i686 libattr-2.5.2-6.fc43.i686 libblkid-2.41.3-8.fc44.i686 libbrotli-1.2.0-1.fc44.i686 libcap-2.77-1.fc44.i686 libcap-ng-0.8.5-8.fc44.i686 libcom_err-1.47.3-3.fc44.i686 libcurl-8.18.0~rc2-1.fc44.i686 libeconf-0.7.9-2.fc44.i686 libevent-2.1.12-16.fc44.i686 libfdisk-2.41.3-8.fc44.i686 libffi-3.5.2-1.fc44.i686 libfsverity-1.6-3.fc44.i686 libgcc-16.0.0-0.3.fc44.i686 libgcrypt-1.11.2-1.fc44.i686 libgomp-16.0.0-0.3.fc44.i686 libgpg-error-1.58-1.fc44.i686 libidn2-2.3.8-2.fc44.i686 libksba-1.6.7-4.fc44.i686 liblastlog2-2.41.3-8.fc44.i686 libmount-2.41.3-8.fc44.i686 libnghttp2-1.68.0-2.fc44.i686 libnghttp3-1.14.0-1.fc44.i686 libpkgconf-2.3.0-3.fc43.i686 libpsl-0.21.5-6.fc44.i686 libselinux-3.9-5.fc44.i686 libselinux-utils-3.9-5.fc44.i686 libsemanage-3.9-4.fc44.i686 libsepol-3.9-2.fc44.i686 libsmartcols-2.41.3-8.fc44.i686 libssh-0.11.3-1.fc44.i686 libssh-config-0.11.3-1.fc44.noarch libstdc++-16.0.0-0.3.fc44.i686 libtasn1-4.20.0-2.fc44.i686 libtool-ltdl-2.5.4-9.fc44.i686 libunistring-1.1-10.fc44.i686 libusb1-1.0.29-4.fc44.i686 libuuid-2.41.3-8.fc44.i686 libverto-0.3.2-11.fc43.i686 libxcrypt-4.5.2-2.fc44.i686 libxml2-2.12.10-5.fc44.i686 libzstd-1.5.7-3.fc44.i686 linkdupes-0.7.2-2.fc44.i686 lua-libs-5.4.8-4.fc44.i686 lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc44.i686 mpfr-4.2.2-2.fc44.i686 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rpm-build-6.0.1-1.fc44.i686 rpm-build-libs-6.0.1-1.fc44.i686 rpm-libs-6.0.1-1.fc44.i686 rpm-plugin-selinux-6.0.1-1.fc44.i686 rpm-sequoia-1.10.0-1.fc44.i686 rpm-sign-libs-6.0.1-1.fc44.i686 rust-srpm-macros-28.4-1.fc44.noarch sed-4.9-6.fc44.i686 selinux-policy-42.19-1.fc44.noarch selinux-policy-targeted-42.19-1.fc44.noarch setup-2.15.0-27.fc44.noarch shadow-utils-4.18.0-7.fc44.i686 sqlite-libs-3.51.0-1.fc44.i686 systemd-libs-259-1.fc44.i686 systemd-standalone-sysusers-259-1.fc44.i686 tar-1.35-6.fc43.i686 tpm2-tss-4.1.3-8.fc43.i686 tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-68.fc44.i686 util-linux-2.41.3-8.fc44.i686 util-linux-core-2.41.3-8.fc44.i686 which-2.23-3.fc43.i686 xxhash-libs-0.8.3-3.fc43.i686 xz-5.8.1-4.fc44.i686 xz-libs-5.8.1-4.fc44.i686 zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.i686 zlib-ng-compat-2.3.2-2.fc44.i686 zstd-1.5.7-3.fc44.i686 Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-i686-1767087424.501667/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-bynv2nwo/percolator/percolator.spec) Config(child) 0 minutes 26 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/percolator-3.08-1.fc44.src.rpm) Config(fedora-rawhide-i686) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1767087424.501667/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1767087424.501667/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1767087424.501667/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-1.fc44.x86_64 rpm-sequoia-1.10.0-1.fc44.x86_64 dnf5-5.3.0.0-3.fc44.x86_64 dnf5-plugins-5.3.0.0-3.fc44.x86_64 Finish: chroot init Start: build phase for percolator-3.08-1.fc44.src.rpm Start: build setup for percolator-3.08-1.fc44.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 74.4 KiB/s | 3.5 KiB | 00m00s local 100% | 74.4 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 32.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: boost-devel i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 143.0 MiB boost-static i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 260.0 MiB bzip2-devel i686 0:1.0.8-21.fc44 copr_base 309.8 KiB cmake i686 0:3.31.10-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 35.4 MiB eigen3-devel noarch 0:5.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 9.5 MiB gcc i686 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 123.4 MiB gcc-c++ i686 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 49.0 MiB gtest-devel i686 0:1.17.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.1 MiB libtirpc-devel i686 0:1.3.7-1.fc44 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99.2 KiB annobin-plugin-gcc i686 0:13.04-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 698.6 KiB boost i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.3 KiB boost-atomic i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 16.0 KiB boost-chrono i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 32.7 KiB boost-container i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 64.6 KiB boost-context i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 11.7 KiB boost-contract i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 102.3 KiB boost-coroutine i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 16.2 KiB boost-date-time i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 11.5 KiB boost-fiber i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 77.9 KiB boost-filesystem i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 142.8 KiB boost-graph i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 361.9 KiB boost-iostreams i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 85.8 KiB boost-json i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 344.2 KiB boost-locale i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 628.7 KiB boost-log i686 0:1.83.0-17.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.5 MiB boost-math i686 0:1.83.0-17.fc44 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0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 513.2 KiB libquadmath-devel i686 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 22.1 KiB libstdc++-devel i686 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 29.8 MiB libtirpc i686 0:1.3.7-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 211.5 KiB libubsan i686 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 563.1 KiB libuv i686 1:1.51.0-2.fc44 copr_base 582.1 KiB libxcrypt-devel i686 0:4.5.2-2.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 31.0 KiB mpdecimal i686 0:4.0.1-2.fc44 copr_base 220.2 KiB openblas i686 0:0.3.29-2.fc44 copr_base 111.7 KiB openblas-openmp i686 0:0.3.29-2.fc44 copr_base 25.7 MiB pyproject-rpm-macros noarch 0:1.18.6-1.fc44 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https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 81.7 KiB python3-rpm-macros noarch 0:3.14-9.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 6.5 KiB rhash i686 0:1.4.5-3.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 394.5 KiB sqlite i686 0:3.51.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.0 MiB tokyocabinet i686 0:1.4.48-29.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.5 MiB tzdata noarch 0:2025c-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.2 MiB vim-filesystem noarch 2:9.1.1972-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 40.0 B xerces-c i686 0:3.3.0-8.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 3.7 MiB Transaction Summary: Installing: 95 packages Total size of inbound packages is 213 MiB. Need to download 213 MiB. After this operation, 926 MiB extra will be used (install 926 MiB, remove 0 B). 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libicu-0:77.1-1.fc44.i686 100% | 355.5 MiB/s | 11.0 MiB | 00m00s [41/95] libquadmath-devel-0:16.0.0-0.3. 100% | 848.4 KiB/s | 22.1 KiB | 00m00s [42/95] libcutl-0:1.10.0-33.fc44.i686 100% | 977.0 KiB/s | 364.4 KiB | 00m00s [43/95] boost-chrono-0:1.83.0-17.fc44.i 100% | 1.7 MiB/s | 24.7 KiB | 00m00s [44/95] boost-container-0:1.83.0-17.fc4 100% | 2.9 MiB/s | 38.1 KiB | 00m00s [45/95] boost-atomic-0:1.83.0-17.fc44.i 100% | 1.0 MiB/s | 17.1 KiB | 00m00s [46/95] boost-context-0:1.83.0-17.fc44. 100% | 1.0 MiB/s | 14.5 KiB | 00m00s [47/95] boost-contract-0:1.83.0-17.fc44 100% | 3.2 MiB/s | 45.8 KiB | 00m00s [48/95] boost-coroutine-0:1.83.0-17.fc4 100% | 1.1 MiB/s | 18.2 KiB | 00m00s [49/95] boost-date-time-0:1.83.0-17.fc4 100% | 940.9 KiB/s | 13.2 KiB | 00m00s [50/95] boost-fiber-0:1.83.0-17.fc44.i6 100% | 3.2 MiB/s | 43.2 KiB | 00m00s [51/95] boost-filesystem-0:1.83.0-17.fc 100% | 4.4 MiB/s | 72.9 KiB | 00m00s [52/95] boost-iostreams-0:1.83.0-17.fc4 100% | 3.1 MiB/s | 41.8 KiB | 00m00s 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MiB/s | 145.8 MiB | 00m01s [84/97] Installing libtirpc-0:1.3.7-1.f 100% | 208.5 MiB/s | 213.5 KiB | 00m00s [85/97] Installing sqlite-0:3.51.0-1.fc 100% | 109.5 MiB/s | 2.0 MiB | 00m00s [86/97] Installing tokyocabinet-0:1.4.4 100% | 90.3 MiB/s | 1.5 MiB | 00m00s [87/97] Installing tokyocabinet-devel-0 100% | 452.2 MiB/s | 463.1 KiB | 00m00s [88/97] Installing sqlite-devel-0:3.51. 100% | 339.2 MiB/s | 694.7 KiB | 00m00s [89/97] Installing libtirpc-devel-0:1.3 100% | 128.5 MiB/s | 263.1 KiB | 00m00s [90/97] Installing boost-static-0:1.83. 100% | 449.1 MiB/s | 260.1 MiB | 00m01s [91/97] Installing python3-devel-0:3.14 100% | 90.7 MiB/s | 2.0 MiB | 00m00s [92/97] Installing gtest-devel-0:1.17.0 100% | 212.9 MiB/s | 1.1 MiB | 00m00s [93/97] Installing xerces-c-devel-0:3.3 100% | 280.7 MiB/s | 4.2 MiB | 00m00s [94/97] Installing gcc-c++-0:16.0.0-0.3 100% | 366.1 MiB/s | 49.1 MiB | 00m00s [95/97] Installing annobin-plugin-gcc-0 100% | 52.6 MiB/s | 700.3 KiB | 00m00s [96/97] Installing gcc-plugin-annobin-0 100% | 4.6 MiB/s | 61.5 KiB | 00m00s [97/97] Installing xsd-0:4.1.0-0.18.a11 100% | 27.6 MiB/s | 4.8 MiB | 00m00s Warning: skipped OpenPGP checks for 95 packages from repositories: copr_base, https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch Complete! Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 64.7 KiB/s | 3.5 KiB | 00m00s local 100% | 64.7 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 28.5 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Nothing to do. Package "boost-devel-1.83.0-17.fc44.i686" is already installed. Package "boost-static-1.83.0-17.fc44.i686" is already installed. Package "bzip2-devel-1.0.8-21.fc44.i686" is already installed. Package "cmake-3.31.10-3.fc44.i686" is already installed. Package "eigen3-devel-5.0.1-1.fc44.noarch" is already installed. Package "gcc-16.0.0-0.3.fc44.i686" is already installed. Package "gcc-c++-16.0.0-0.3.fc44.i686" is already installed. Package "gtest-devel-1.17.0-1.fc44.i686" is already installed. Package "make-1:4.4.1-11.fc44.i686" is already installed. Package "libtirpc-devel-1.3.7-1.fc44.i686" is already installed. Package "sqlite-devel-3.51.0-1.fc44.i686" is already installed. Package "tokyocabinet-devel-1.4.48-29.fc44.i686" is already installed. Package "xerces-c-devel-3.3.0-8.fc43.i686" is already installed. Package "python3-devel-3.14.2-1.fc44.i686" is already installed. Package "xsd-4.1.0-0.18.a11.fc43.i686" is already installed. Package "zlib-ng-compat-devel-2.3.2-2.fc44.i686" is already installed. Finish: build setup for percolator-3.08-1.fc44.src.rpm Start: rpmbuild percolator-3.08-1.fc44.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1753228800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.Eyj25t Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.n6owHq + umask 022 + cd /builddir/build/BUILD/percolator-3.08-build + cd /builddir/build/BUILD/percolator-3.08-build + rm -rf percolator-rel-3-08 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-08.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd percolator-rel-3-08 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (percolator-unbundle_eigen_gtest.patch):' Patch #0 (percolator-unbundle_eigen_gtest.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file src/CMakeLists.txt patching file tests/unit_tests/percolator/CMakeLists.txt + find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';' + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.xx' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec chmod 0644 '{}' ';' + rm -rf 'percolator/_deps/*' + chmod a-x src/converters/MSToolkit/RAMP/README + mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README + mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt + sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.HAmRZY + umask 022 + cd /builddir/build/BUILD/percolator-3.08-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-08 + export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu' + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu' + mkdir -p percolator + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu ' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B redhat-linux-build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -B percolator -S ./ -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=ON -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=i386 -- The C compiler identification is GNU 16.0.0 -- The CXX compiler identification is GNU 16.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "5.2") -- Found OpenMP_CXX: -fopenmp (found version "5.2") -- Found OpenMP: TRUE (found version "5.2") -- -- ------------------------------------------------------------------------------- -- Building PERCOLATOR: -- change a configuration variable with: cmake -D= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- CMAKE_PREFIX_PATH = ../ -- XML_SUPPORT = ON -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = i386 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Xerces-C: /usr/lib/libxerces-c.so -- : /usr/include -- Version: 3.3.0 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Locating CodeSynthesis library with XSDDIR set to -- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx -- RPC found, will include headers from: /usr/include/tirpc -- and libraries from : /usr/lib/libtirpc.so -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system -- Finding GoogleTest... -- Found GTest: /usr/lib/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_TESTING CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_INSTALL_FULL_SBINDIR CMAKE_INSTALL_SBINDIR CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator + xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd + /usr/bin/cmake --build percolator -j4 --verbose Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4 /usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' /usr/bin/gmake -f src/CMakeFiles/generate_xsd.dir/build.make src/CMakeFiles/generate_xsd.dir/depend /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/generate_xsd.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' /usr/bin/gmake -f src/CMakeFiles/generate_xsd.dir/build.make src/CMakeFiles/generate_xsd.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' [ 1%] Generating percolator_out.* from XSD [ 2%] Generating percolator_in.* from XSD cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --std c++11 --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_out.xsd cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --std c++11 --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_in.xsd [ 3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o [ 4%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c [ 5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp [ 7%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' [ 7%] Built target generate_xsd [ 8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp [ 9%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c [ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c [ 11%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' [ 13%] Linking C static library libdblas.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake [ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/percolator_in.cxx cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1 a - CMakeFiles/dblas.dir/daxpy.c.o a - CMakeFiles/dblas.dir/ddot.c.o a - CMakeFiles/dblas.dir/dgemv.c.o a - CMakeFiles/dblas.dir/dnrm2.c.o a - CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ranlib libdblas.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' [ 14%] Built target dblas [ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp [ 16%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/percolator_out.cxx [ 17%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:109:35: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder] 109 | std::unique_ptr gp_; // (new XMLGrammarPoolImpl (mm)); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:104:22: warning: ‘xercesc_3_3::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder] 104 | DOMImplementation& dom_impl_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:147:1: warning: when initialized here [-Wreorder] 147 | parser_impl::parser_impl() : clean_(true), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In member function ‘std::unique_ptr parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:182:14: warning: unused variable ‘n’ [-Wunused-variable] 182 | size_t n(s.size()); | ^ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:174:9: warning: unused variable ‘i’ [-Wunused-variable] 174 | int i(1); | ^ [ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ 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-I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/serializer.cxx [ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp [ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation] 986 | strncpy(protein_field_tail, protein_id, protein_field_free); | ^ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here 977 | size_t protein_id_len = strlen(protein_id); | ~~~~~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp [ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp [ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp [ 29%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp [ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 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src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp [ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp [ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp [ 35%] Linking CXX static library libpicked_protein.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1 /usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o /usr/bin/ranlib libpicked_protein.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator' [ 35%] Built target picked_protein [ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder] 119 | bool reportUniquePeptides_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning: ‘bool XMLInterface::printDecoys_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder] 120 | bool reportPepXML_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning: ‘bool XMLInterface::printExpMass_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp: In member function ‘int XMLInterface::readAndScorePin(std::istream&, std::vector&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:239:32: warning: unused variable ‘numFeatures’ [-Wunused-variable] 239 | const unsigned int numFeatures = FeatureNames::getNumFeatures(); | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:255:22: warning: variable ‘numProteins’ set but not used [-Wunused-but-set-variable=] 255 | unsigned numProteins = 0; | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable=] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ [ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp [ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized] 1577 | f.rho = si.rho; | ~~~^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here 1538 | Solver::SolutionInfo si; | ^~ [ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp [ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable] 122 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable] 118 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable] 168 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable] 157 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ [ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder] 114 | bool trainBestPositive_; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning: ‘unsigned int CrossValidation::numThreads_’ [-Wreorder] 102 | unsigned int numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning: when initialized here [-Wreorder] 27 | CrossValidation::CrossValidation(bool quickValidation, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 154 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 344 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder] 102 | useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning: ‘bool Caller::xmlPrintDecoys_’ [-Wreorder] 86 | bool xmlPrintDecoys_, xmlPrintExpMass_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder] 100 | bool reportEachIteration_, quickValidation_, trainBestPositive_, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning: ‘unsigned int Caller::numThreads_’ [-Wreorder] 98 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ [ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp [ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp [ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ [ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder] 87 | bool concatenatedSearch_; | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning: ‘double SanityCheck::test_fdr_’ [-Wreorder] 72 | double test_fdr_, initial_train_fdr_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder] 31 | SanityCheck::SanityCheck() : | ^~~~~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp [ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector >)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 103 | for (int k = 1; k < numStrings; ++k) { | ~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp [ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp [ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp [ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning: ‘double ProteinProbEstimator::pi0_’ [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder] 242 | unsigned int numberTargetProteins_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning: ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder] 237 | bool usePi0_; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder] 243 | std::string decoyPattern_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning: ‘double ProteinProbEstimator::fdr_’ [-Wreorder] 240 | double fdr_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp [ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map&, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable] 161 | unsigned int native_id = scan - 1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable] 165 | double RT = pPSM->getRetentionTime(); | ^~ [ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp [ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 142 | for (int k=0; k::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp [ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp [ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp [ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp [ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp [ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder] 108 | bool isDecoy_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning: ‘int ProteinScoreHolder::groupId_’ [-Wreorder] 106 | int groupId_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder] 20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide, | ^~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder] 86 | double maxPeptidePval_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning: ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning: ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder] 83 | ProteinInferenceMethod protInferenceMethod_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 167 | if (total_non_enzymatic_flanks > peptideScores.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual void PickedProteinInterface::computeProbabilities(const std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:345:16: warning: variable ‘fisher’ set but not used [-Wunused-but-set-variable=] 345 | double fisher = 0.0; | ^~~~~~ [ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp [ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array&, const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 385 | for (int k=0; k& operator*=(Array&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 395 | for (int k=0; k operator-(const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 533 | for (int k=0; k= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- CMAKE_PREFIX_PATH = ../ -- XML_SUPPORT = OFF -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = i386 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system -- Finding GoogleTest... -- Found GTest: /usr/lib/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_TESTING CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_INSTALL_FULL_SBINDIR CMAKE_INSTALL_SBINDIR CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR TokyoCabinet_INCLUDE_DIR TokyoCabinet_LIBRARY -- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido + /usr/bin/cmake --build src/fido -j4 --verbose Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4 /usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 1%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o [ 2%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c [ 3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp [ 6%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection 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/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c [ 9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c [ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c [ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp [ 13%] Linking C static library libdblas.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1 a - CMakeFiles/dblas.dir/daxpy.c.o a - CMakeFiles/dblas.dir/ddot.c.o a - CMakeFiles/dblas.dir/dgemv.c.o a - CMakeFiles/dblas.dir/dnrm2.c.o a - CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ranlib libdblas.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 13%] Built target dblas [ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 15%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp [ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp [ 18%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp [ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp [ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp [ 22%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder] 119 | bool reportUniquePeptides_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning: ‘bool XMLInterface::printDecoys_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder] 120 | bool reportPepXML_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning: ‘bool XMLInterface::printExpMass_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ [ 23%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp [ 25%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation] 986 | strncpy(protein_field_tail, protein_id, protein_field_free); | ^ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here 977 | size_t protein_id_len = strlen(protein_id); | ~~~~~~^~~~~~~~~~~~ [ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable=] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ [ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp [ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp [ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp [ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp [ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp [ 34%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp [ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp [ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized] 1577 | f.rho = si.rho; | ~~~^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here 1538 | Solver::SolutionInfo si; | ^~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable] 122 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable] 118 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable] 168 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable] 157 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder] 102 | useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning: ‘bool Caller::xmlPrintDecoys_’ [-Wreorder] 86 | bool xmlPrintDecoys_, xmlPrintExpMass_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder] 100 | bool reportEachIteration_, quickValidation_, trainBestPositive_, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning: ‘unsigned int Caller::numThreads_’ [-Wreorder] 98 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ [ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp [ 39%] Linking CXX static library libpicked_protein.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1 /usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o /usr/bin/ranlib libpicked_protein.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 39%] Built target picked_protein [ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder] 114 | bool trainBestPositive_; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning: ‘unsigned int CrossValidation::numThreads_’ [-Wreorder] 102 | unsigned int numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning: when initialized here [-Wreorder] 27 | CrossValidation::CrossValidation(bool quickValidation, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 154 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 344 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp [ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp [ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp [ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp [ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder] 87 | bool concatenatedSearch_; | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning: ‘double SanityCheck::test_fdr_’ [-Wreorder] 72 | double test_fdr_, initial_train_fdr_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder] 31 | SanityCheck::SanityCheck() : | ^~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp [ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector >)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 103 | for (int k = 1; k < numStrings; ++k) { | ~~^~~~~~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp [ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp [ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp [ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning: ‘double ProteinProbEstimator::pi0_’ [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder] 242 | unsigned int numberTargetProteins_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning: ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder] 237 | bool usePi0_; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder] 243 | std::string decoyPattern_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning: ‘double ProteinProbEstimator::fdr_’ [-Wreorder] 240 | double fdr_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp [ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map&, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable] 161 | unsigned int native_id = scan - 1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable] 165 | double RT = pPSM->getRetentionTime(); | ^~ [ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp [ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp [ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 142 | for (int k=0; k::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp [ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp [ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp [ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder] 108 | bool isDecoy_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning: ‘int ProteinScoreHolder::groupId_’ [-Wreorder] 106 | int groupId_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder] 20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide, | ^~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp [ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder] 86 | double maxPeptidePval_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning: ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning: ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder] 83 | ProteinInferenceMethod protInferenceMethod_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 167 | if (total_non_enzymatic_flanks > peptideScores.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual void PickedProteinInterface::computeProbabilities(const std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:345:16: warning: variable ‘fisher’ set but not used [-Wunused-but-set-variable=] 345 | double fisher = 0.0; | ^~~~~~ [ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp [ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp [ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp [ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array&, const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 385 | for (int k=0; k& operator*=(Array&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 395 | for (int k=0; k operator-(const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 533 | for (int k=0; k::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 82%] Linking CXX static library libperclibrary.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1 /usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o /usr/bin/ranlib libperclibrary.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 82%] Built target perclibrary /usr/bin/gmake -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend /usr/bin/gmake -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend /usr/bin/gmake -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality 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"--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/gmake -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build /usr/bin/gmake -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 85%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o [ 85%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp [ 86%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp [ 88%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 89%] Linking CXX executable qvality cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1 [ 90%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 92%] Linking CXX executable percolator cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1 [ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ [ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 65 | if (n > 0) | ^ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp [ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src ../libperclibrary.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [ 97%] Built target qvality [ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable] 143 | int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm, | ^~~~~~~ [100%] Linking CXX executable gtest_unit cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a -lstdc++ /usr/lib/libboost_filesystem.a /usr/lib/libboost_system.a /usr/lib/libboost_atomic.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [100%] Built target percolator /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit /usr/lib/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib/libgtest.so.1.17.0 gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' [100%] Built target gtest_unit gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles 0 + mkdir -p src/converters + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu ' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B src/fido -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -B src/converters -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=i386 -DBUILD_TESTING:BOOL=ON -- The C compiler identification is GNU 16.0.0 -- The CXX compiler identification is GNU 16.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "5.2") -- Found OpenMP_CXX: -fopenmp (found version "5.2") -- Found OpenMP: TRUE (found version "5.2") -- -- ------------------------------------------------------------------------------- -- Building PERCOLATOR: -- change a configuration variable with: cmake -D= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- CMAKE_PREFIX_PATH = ../ -- XML_SUPPORT = OFF -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = i386 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system -- Finding GoogleTest... -- Found GTest: /usr/lib/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_TESTING CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_INSTALL_FULL_SBINDIR CMAKE_INSTALL_SBINDIR CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR PERCOLATOR-CONVERTERS_BINARY_DIR SERIALIZE SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR TokyoCabinet_INCLUDE_DIR TokyoCabinet_LIBRARY -- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns src/xml/mzIdentML1.1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/gaml_tandem1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/tandem2011.12.01.1.xsd + /usr/bin/cmake --build src/converters -j4 --verbose Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4 /usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' /usr/bin/gmake -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build /usr/bin/gmake -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' [ 2%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o [ 2%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c [ 3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp [ 5%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp [ 6%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp [ 7%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c [ 9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c [ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c [ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp [ 13%] Linking C static library libdblas.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1 a - CMakeFiles/dblas.dir/daxpy.c.o a - CMakeFiles/dblas.dir/ddot.c.o a - CMakeFiles/dblas.dir/dgemv.c.o a - CMakeFiles/dblas.dir/dnrm2.c.o a - CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o /usr/bin/ranlib libdblas.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' [ 13%] Built target dblas [ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 15%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp [ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp [ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp [ 19%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp [ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp [ 22%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder] 119 | bool reportUniquePeptides_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning: ‘bool XMLInterface::printDecoys_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder] 120 | bool reportPepXML_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning: ‘bool XMLInterface::printExpMass_’ [-Wreorder] 112 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning: when initialized here [-Wreorder] 59 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ [ 23%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp [ 25%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation] 986 | strncpy(protein_field_tail, protein_id, protein_field_free); | ^ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here 977 | size_t protein_id_len = strlen(protein_id); | ~~~~~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable=] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ [ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp [ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp [ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp [ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp [ 31%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp [ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp [ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp [ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp [ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized] 1577 | f.rho = si.rho; | ~~~^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here 1538 | Solver::SolutionInfo si; | ^~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable] 122 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable] 118 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable] 168 | auto& peptide = peptideToScores.first; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable] 157 | auto& composition = compositionToPeptides.first; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder] 102 | useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning: ‘bool Caller::xmlPrintDecoys_’ [-Wreorder] 86 | bool xmlPrintDecoys_, xmlPrintExpMass_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder] 100 | bool reportEachIteration_, quickValidation_, trainBestPositive_, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning: ‘unsigned int Caller::numThreads_’ [-Wreorder] 98 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning: when initialized here [-Wreorder] 42 | Caller::Caller() | ^~~~~~ [ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ [ 39%] Linking CXX static library libpicked_protein.a cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1 /usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o /usr/bin/ranlib libpicked_protein.a gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters' [ 39%] Built target picked_protein [ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder] 114 | bool trainBestPositive_; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning: ‘unsigned int CrossValidation::numThreads_’ [-Wreorder] 102 | unsigned int numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning: when initialized here [-Wreorder] 27 | CrossValidation::CrossValidation(bool quickValidation, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 154 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 344 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp [ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp [ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp [ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp [ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder] 87 | bool concatenatedSearch_; | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning: ‘double SanityCheck::test_fdr_’ [-Wreorder] 72 | double test_fdr_, initial_train_fdr_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder] 31 | SanityCheck::SanityCheck() : | ^~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp [ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector >)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 103 | for (int k = 1; k < numStrings; ++k) { | ~~^~~~~~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp [ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp [ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp [ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning: ‘double ProteinProbEstimator::pi0_’ [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder] 242 | unsigned int numberTargetProteins_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning: ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder] 237 | bool usePi0_; | ^~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder] 243 | std::string decoyPattern_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning: ‘double ProteinProbEstimator::fdr_’ [-Wreorder] 240 | double fdr_; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp [ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map&, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable] 161 | unsigned int native_id = scan - 1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable] 165 | double RT = pPSM->getRetentionTime(); | ^~ [ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp [ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp [ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 142 | for (int k=0; k::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp [ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp [ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp [ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ [ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder] 108 | bool isDecoy_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning: ‘int ProteinScoreHolder::groupId_’ [-Wreorder] 106 | int groupId_; | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder] 20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide, | ^~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp [ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder] 86 | double maxPeptidePval_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning: ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning: ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder] 83 | ProteinInferenceMethod protInferenceMethod_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 167 | if (total_non_enzymatic_flanks > peptideScores.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual void PickedProteinInterface::computeProbabilities(const std::string&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:345:16: warning: variable ‘fisher’ set but not used [-Wunused-but-set-variable=] 345 | double fisher = 0.0; | ^~~~~~ [ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp [ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp [ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp [ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -mtls-dialect=gnu -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning: when initialized here [-Wreorder] 40 | ScoreHolder() | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 38 | LabelType label; | ^~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 37 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning: when initialized here [-Wreorder] 47 | ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7, from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=] 171 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note: by ‘void Set::add(int)’ 13 | void add(int el); | ^~~ /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array&, const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 385 | for (int k=0; k& operator*=(Array&, double)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 395 | for (int k=0; k operator-(const Array&)’: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 533 | for (int k=0; k