Warning: Permanently added '44.214.91.244' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-67rlswa4/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-67rlswa4/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759573086.662618 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.3 starting (python version = 3.13.7, NVR = mock-6.3-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-67rlswa4/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-67rlswa4/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759573086.662618 -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-67rlswa4/percolator/percolator.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.3 INFO: Mock Version: 6.3 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759573086.662618/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-2c39aefa-5050-46cd-af61-b4f25a90cc4e INFO: Checking that 19b5ed24160aec7bdee8c95283d653b8c67f85e67219910873fdc355ac0c4112 image matches host's architecture INFO: Copy content of container 19b5ed24160aec7bdee8c95283d653b8c67f85e67219910873fdc355ac0c4112 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759573086.662618/root INFO: mounting 19b5ed24160aec7bdee8c95283d653b8c67f85e67219910873fdc355ac0c4112 with podman image mount INFO: image 19b5ed24160aec7bdee8c95283d653b8c67f85e67219910873fdc355ac0c4112 as /var/lib/containers/storage/overlay/5c0a70c285a2fdab7d3bb7870b0996f39c685eb0aa3440c4c444e76d6ac756c6/merged INFO: umounting image 19b5ed24160aec7bdee8c95283d653b8c67f85e67219910873fdc355ac0c4112 (/var/lib/containers/storage/overlay/5c0a70c285a2fdab7d3bb7870b0996f39c685eb0aa3440c4c444e76d6ac756c6/merged) with podman image umount INFO: Removing image mock-bootstrap-2c39aefa-5050-46cd-af61-b4f25a90cc4e 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-x86_64-1759573086.662618/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-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 dnf5-5.2.17.0-2.fc44.x86_64 dnf5-plugins-5.2.17.0-2.fc44.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 32.5 KiB/s | 1.5 KiB | 00m00s fedora 100% | 83.4 KiB/s | 29.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.3.0-2.fc43 fedora 8.4 MiB bzip2 x86_64 1.0.8-21.fc43 fedora 95.3 KiB coreutils x86_64 9.8-3.fc44 fedora 5.4 MiB cpio x86_64 2.15-6.fc43 fedora 1.1 MiB diffutils x86_64 3.12-3.fc43 fedora 1.6 MiB fedora-release-common noarch 44-0.3 fedora 20.6 KiB findutils x86_64 1:4.10.0-6.fc43 fedora 1.8 MiB gawk x86_64 5.3.2-2.fc43 fedora 1.8 MiB glibc-minimal-langpack x86_64 2.42.9000-5.fc44 fedora 0.0 B grep x86_64 3.12-2.fc43 fedora 1.0 MiB gzip x86_64 1.14-1.fc44 fedora 397.8 KiB info x86_64 7.2-6.fc43 fedora 353.9 KiB patch x86_64 2.8-2.fc43 fedora 222.8 KiB redhat-rpm-config noarch 343-14.fc44 fedora 183.3 KiB rpm-build x86_64 6.0.0-1.fc44 fedora 287.4 KiB sed x86_64 4.9-5.fc43 fedora 857.3 KiB shadow-utils x86_64 2:4.18.0-3.fc43 fedora 3.9 MiB tar x86_64 2:1.35-6.fc43 fedora 2.9 MiB unzip x86_64 6.0-68.fc44 fedora 390.3 KiB util-linux x86_64 2.41.1-17.fc44 fedora 3.5 MiB which x86_64 2.23-3.fc43 fedora 83.5 KiB xz x86_64 1:5.8.1-2.fc43 fedora 1.3 MiB Installing dependencies: add-determinism x86_64 0.7.2-2.fc44 fedora 2.3 MiB alternatives x86_64 1.33-2.fc43 fedora 62.2 KiB ansible-srpm-macros noarch 1-18.1.fc43 fedora 35.7 KiB audit-libs x86_64 4.1.2-2.fc44 fedora 378.8 KiB binutils x86_64 2.45.50-4.fc44 fedora 27.3 MiB build-reproducibility-srpm-macros noarch 0.7.2-2.fc44 fedora 1.2 KiB bzip2-libs x86_64 1.0.8-21.fc43 fedora 80.6 KiB ca-certificates noarch 2025.2.80_v9.0.304-2.fc44 fedora 2.7 MiB coreutils-common x86_64 9.8-3.fc44 fedora 11.1 MiB crypto-policies noarch 20250714-5.gitcd6043a.fc44 fedora 146.9 KiB curl x86_64 8.16.0-1.fc44 fedora 475.3 KiB cyrus-sasl-lib x86_64 2.1.28-33.fc44 fedora 2.3 MiB debugedit x86_64 5.2-3.fc44 fedora 214.0 KiB dwz x86_64 0.16-2.fc43 fedora 287.1 KiB ed x86_64 1.22.2-1.fc44 fedora 148.1 KiB efi-srpm-macros noarch 6-4.fc43 fedora 40.1 KiB elfutils x86_64 0.193-3.fc43 fedora 2.9 MiB elfutils-debuginfod-client x86_64 0.193-3.fc43 fedora 83.9 KiB elfutils-default-yama-scope noarch 0.193-3.fc43 fedora 1.8 KiB elfutils-libelf x86_64 0.193-3.fc43 fedora 1.2 MiB elfutils-libs x86_64 0.193-3.fc43 fedora 683.4 KiB fedora-gpg-keys noarch 44-0.1 fedora 131.2 KiB fedora-release noarch 44-0.3 fedora 0.0 B fedora-release-identity-basic noarch 44-0.3 fedora 664.0 B fedora-repos noarch 44-0.1 fedora 4.9 KiB fedora-repos-rawhide noarch 44-0.1 fedora 2.2 KiB file x86_64 5.46-8.fc44 fedora 100.2 KiB file-libs x86_64 5.46-8.fc44 fedora 11.9 MiB filesystem x86_64 3.18-50.fc43 fedora 112.0 B filesystem-srpm-macros noarch 3.18-50.fc43 fedora 38.2 KiB fonts-srpm-macros noarch 1:5.0.0-1.fc44 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-3.fc43 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-15.fc43 fedora 144.0 B gap-srpm-macros noarch 2-1.fc44 fedora 2.1 KiB gdb-minimal x86_64 16.3-6.fc44 fedora 13.3 MiB gdbm-libs x86_64 1:1.23-10.fc43 fedora 129.9 KiB ghc-srpm-macros noarch 1.9.2-3.fc43 fedora 779.0 B glibc x86_64 2.42.9000-5.fc44 fedora 6.7 MiB glibc-common x86_64 2.42.9000-5.fc44 fedora 1.0 MiB glibc-gconv-extra x86_64 2.42.9000-5.fc44 fedora 7.2 MiB gmp x86_64 1:6.3.0-4.fc44 fedora 815.3 KiB gnat-srpm-macros noarch 6-8.fc43 fedora 1.0 KiB gnulib-l10n noarch 20241231-1.fc44 fedora 655.0 KiB gnupg2 x86_64 2.4.8-4.fc43 fedora 6.5 MiB gnupg2-dirmngr x86_64 2.4.8-4.fc43 fedora 618.4 KiB gnupg2-gpg-agent x86_64 2.4.8-4.fc43 fedora 671.4 KiB gnupg2-gpgconf x86_64 2.4.8-4.fc43 fedora 250.0 KiB gnupg2-keyboxd x86_64 2.4.8-4.fc43 fedora 201.4 KiB gnupg2-verify x86_64 2.4.8-4.fc43 fedora 348.5 KiB gnutls x86_64 3.8.10-5.fc44 fedora 3.8 MiB go-srpm-macros noarch 3.8.0-1.fc44 fedora 61.9 KiB gpgverify noarch 2.2-3.fc43 fedora 8.7 KiB ima-evm-utils-libs x86_64 1.6.2-6.fc43 fedora 60.7 KiB jansson x86_64 2.14-3.fc43 fedora 89.1 KiB java-srpm-macros noarch 1-7.fc43 fedora 870.0 B json-c x86_64 0.18-7.fc43 fedora 82.7 KiB kernel-srpm-macros noarch 1.0-27.fc43 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-6.fc43 fedora 54.3 KiB krb5-libs x86_64 1.21.3-8.fc44 fedora 2.3 MiB libacl x86_64 2.3.2-4.fc43 fedora 35.9 KiB libarchive x86_64 3.8.1-3.fc43 fedora 951.1 KiB libassuan x86_64 2.5.7-4.fc43 fedora 163.8 KiB libattr x86_64 2.5.2-6.fc43 fedora 24.4 KiB libblkid x86_64 2.41.1-17.fc44 fedora 262.4 KiB libbrotli x86_64 1.1.0-10.fc44 fedora 833.3 KiB libcap x86_64 2.76-3.fc44 fedora 209.1 KiB libcap-ng x86_64 0.8.5-8.fc44 fedora 68.9 KiB libcom_err x86_64 1.47.3-2.fc43 fedora 63.1 KiB libcurl x86_64 8.16.0-1.fc44 fedora 919.5 KiB libeconf x86_64 0.7.9-2.fc43 fedora 64.9 KiB libevent x86_64 2.1.12-16.fc43 fedora 883.1 KiB libfdisk x86_64 2.41.1-17.fc44 fedora 380.4 KiB libffi x86_64 3.5.2-1.fc44 fedora 83.8 KiB libfsverity x86_64 1.6-3.fc43 fedora 28.5 KiB libgcc x86_64 15.2.1-2.fc44 fedora 266.6 KiB libgcrypt x86_64 1.11.1-2.fc43 fedora 1.6 MiB libgomp x86_64 15.2.1-2.fc44 fedora 541.1 KiB libgpg-error x86_64 1.55-2.fc43 fedora 915.3 KiB libidn2 x86_64 2.3.8-2.fc43 fedora 552.5 KiB libksba x86_64 1.6.7-4.fc43 fedora 398.5 KiB liblastlog2 x86_64 2.41.1-17.fc44 fedora 33.9 KiB libmount x86_64 2.41.1-17.fc44 fedora 372.7 KiB libnghttp2 x86_64 1.67.1-1.fc44 fedora 162.2 KiB libpkgconf x86_64 2.3.0-3.fc43 fedora 78.1 KiB libpsl x86_64 0.21.5-6.fc43 fedora 76.4 KiB libselinux x86_64 3.9-5.fc44 fedora 193.1 KiB libselinux-utils x86_64 3.9-5.fc44 fedora 309.0 KiB libsemanage x86_64 3.9-4.fc44 fedora 308.5 KiB libsepol x86_64 3.9-2.fc43 fedora 822.0 KiB libsmartcols x86_64 2.41.1-17.fc44 fedora 180.5 KiB libssh x86_64 0.11.3-1.fc44 fedora 567.1 KiB libssh-config noarch 0.11.3-1.fc44 fedora 277.0 B libstdc++ x86_64 15.2.1-2.fc44 fedora 2.8 MiB libtasn1 x86_64 4.20.0-2.fc43 fedora 176.3 KiB libtool-ltdl x86_64 2.5.4-7.fc43 fedora 70.1 KiB libunistring x86_64 1.1-10.fc43 fedora 1.7 MiB libusb1 x86_64 1.0.29-4.fc44 fedora 171.3 KiB libuuid x86_64 2.41.1-17.fc44 fedora 37.4 KiB libverto x86_64 0.3.2-11.fc43 fedora 25.4 KiB libxcrypt x86_64 4.4.38-9.fc44 fedora 284.4 KiB libxml2 x86_64 2.12.10-5.fc44 fedora 1.7 MiB libzstd x86_64 1.5.7-3.fc44 fedora 940.3 KiB linkdupes x86_64 0.7.2-2.fc44 fedora 838.7 KiB lua-libs x86_64 5.4.8-2.fc43 fedora 280.8 KiB lua-srpm-macros noarch 1-16.fc43 fedora 1.3 KiB lz4-libs x86_64 1.10.0-3.fc43 fedora 161.4 KiB mpfr x86_64 4.2.2-2.fc43 fedora 832.8 KiB ncurses-base noarch 6.5-7.20250614.fc43 fedora 328.1 KiB ncurses-libs x86_64 6.5-7.20250614.fc43 fedora 946.3 KiB nettle x86_64 3.10.1-2.fc43 fedora 790.6 KiB npth x86_64 1.8-3.fc43 fedora 49.6 KiB ocaml-srpm-macros noarch 11-2.fc43 fedora 1.9 KiB openblas-srpm-macros noarch 2-20.fc43 fedora 112.0 B openldap x86_64 2.6.10-4.fc44 fedora 659.8 KiB openssl-libs x86_64 1:3.5.1-3.fc44 fedora 9.2 MiB p11-kit x86_64 0.25.8-1.fc44 fedora 2.3 MiB p11-kit-trust x86_64 0.25.8-1.fc44 fedora 446.5 KiB package-notes-srpm-macros noarch 0.5-14.fc43 fedora 1.6 KiB pam-libs x86_64 1.7.1-3.fc43 fedora 126.8 KiB pcre2 x86_64 10.46-1.fc44 fedora 697.7 KiB pcre2-syntax noarch 10.46-1.fc44 fedora 275.3 KiB perl-srpm-macros noarch 1-60.fc43 fedora 861.0 B pkgconf x86_64 2.3.0-3.fc43 fedora 88.5 KiB pkgconf-m4 noarch 2.3.0-3.fc43 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-3.fc43 fedora 989.0 B policycoreutils x86_64 3.9-5.fc44 fedora 683.5 KiB popt x86_64 1.19-9.fc43 fedora 132.8 KiB publicsuffix-list-dafsa noarch 20250616-2.fc43 fedora 69.1 KiB pyproject-srpm-macros noarch 1.18.4-1.fc44 fedora 1.9 KiB python-srpm-macros noarch 3.14-8.fc44 fedora 51.6 KiB qt5-srpm-macros noarch 5.15.17-2.fc43 fedora 500.0 B qt6-srpm-macros noarch 6.10.0~rc-1.fc44 fedora 464.0 B readline x86_64 8.3-2.fc43 fedora 511.7 KiB rpm x86_64 6.0.0-1.fc44 fedora 3.1 MiB rpm-build-libs x86_64 6.0.0-1.fc44 fedora 268.4 KiB rpm-libs x86_64 6.0.0-1.fc44 fedora 933.8 KiB rpm-plugin-selinux x86_64 6.0.0-1.fc44 fedora 12.0 KiB rpm-sequoia x86_64 1.9.0-2.fc43 fedora 2.5 MiB rpm-sign-libs x86_64 6.0.0-1.fc44 fedora 39.7 KiB rust-srpm-macros noarch 26.4-1.fc44 fedora 4.8 KiB selinux-policy noarch 42.11-2.fc44 fedora 31.9 KiB selinux-policy-targeted noarch 42.11-2.fc44 fedora 18.7 MiB setup noarch 2.15.0-26.fc43 fedora 725.0 KiB sqlite-libs x86_64 3.50.4-1.fc44 fedora 1.5 MiB systemd-libs x86_64 258-1.fc44 fedora 2.3 MiB systemd-standalone-sysusers x86_64 258-1.fc44 fedora 293.5 KiB tpm2-tss x86_64 4.1.3-8.fc43 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0.4.2-1.fc43 fedora 8.3 KiB util-linux-core x86_64 2.41.1-17.fc44 fedora 1.5 MiB xxhash-libs x86_64 0.8.3-3.fc43 fedora 90.2 KiB xz-libs x86_64 1:5.8.1-2.fc43 fedora 217.8 KiB zig-srpm-macros noarch 1-5.fc43 fedora 1.1 KiB zip x86_64 3.0-44.fc43 fedora 694.5 KiB zlib-ng-compat x86_64 2.2.5-2.fc44 fedora 137.6 KiB zstd x86_64 1.5.7-3.fc44 fedora 506.2 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 177 packages Total size of inbound packages is 66 MiB. Need to download 0 B. After this operation, 219 MiB extra will be used (install 219 MiB, remove 0 B). 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Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. [ 1/179] Verify package files 100% | 665.0 B/s | 177.0 B | 00m00s [ 2/179] Prepare transaction 100% | 3.3 KiB/s | 177.0 B | 00m00s [ 3/179] Installing libgcc-0:15.2.1-2. 100% | 262.0 MiB/s | 268.3 KiB | 00m00s [ 4/179] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/179] Installing publicsuffix-list- 100% | 0.0 B/s | 69.8 KiB | 00m00s [ 6/179] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 7/179] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 8/179] Installing fedora-gpg-keys-0: 100% | 43.7 MiB/s | 179.0 KiB | 00m00s [ 9/179] Installing fedora-repos-0:44- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/179] Installing fedora-release-com 100% | 24.3 MiB/s | 24.9 KiB | 00m00s [ 11/179] Installing fedora-release-0:4 100% | 17.3 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-26.fc43.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. >>> [ 12/179] Installing setup-0:2.15.0-26. 100% | 47.6 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/179] Installing filesystem-0:3.18- 100% | 2.7 MiB/s | 212.8 KiB | 00m00s [ 14/179] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 15/179] Installing pcre2-syntax-0:10. 100% | 271.2 MiB/s | 277.8 KiB | 00m00s [ 16/179] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 17/179] Installing coreutils-common-0 100% | 372.5 MiB/s | 11.2 MiB | 00m00s [ 18/179] Installing ncurses-base-0:6.5 100% | 86.3 MiB/s | 353.5 KiB | 00m00s [ 19/179] Installing bash-0:5.3.0-2.fc4 100% | 263.4 MiB/s | 8.4 MiB | 00m00s [ 20/179] Installing glibc-common-0:2.4 100% | 60.0 MiB/s | 1.0 MiB | 00m00s [ 21/179] Installing glibc-gconv-extra- 100% | 281.2 MiB/s | 7.3 MiB | 00m00s [ 22/179] Installing glibc-0:2.42.9000- 100% | 181.0 MiB/s | 6.7 MiB | 00m00s [ 23/179] Installing ncurses-libs-0:6.5 100% | 232.6 MiB/s | 952.8 KiB | 00m00s [ 24/179] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 25/179] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB | 00m00s [ 26/179] Installing bzip2-libs-0:1.0.8 100% | 79.8 MiB/s | 81.7 KiB | 00m00s [ 27/179] Installing libgpg-error-0:1.5 100% | 60.0 MiB/s | 921.1 KiB | 00m00s [ 28/179] Installing libstdc++-0:15.2.1 100% | 406.3 MiB/s | 2.8 MiB | 00m00s [ 29/179] Installing libassuan-0:2.5.7- 100% | 161.7 MiB/s | 165.6 KiB | 00m00s [ 30/179] Installing libgcrypt-0:1.11.1 100% | 393.8 MiB/s | 1.6 MiB | 00m00s [ 31/179] Installing readline-0:8.3-2.f 100% | 250.9 MiB/s | 513.9 KiB | 00m00s [ 32/179] Installing gmp-1:6.3.0-4.fc44 100% | 399.2 MiB/s | 817.5 KiB | 00m00s [ 33/179] Installing xz-libs-1:5.8.1-2. 100% | 213.8 MiB/s | 218.9 KiB | 00m00s [ 34/179] Installing libuuid-0:2.41.1-1 100% | 37.6 MiB/s | 38.5 KiB | 00m00s [ 35/179] Installing popt-0:1.19-9.fc43 100% | 68.1 MiB/s | 139.4 KiB | 00m00s [ 36/179] Installing libzstd-0:1.5.7-3. 100% | 306.5 MiB/s | 941.6 KiB | 00m00s [ 37/179] Installing elfutils-libelf-0: 100% | 388.8 MiB/s | 1.2 MiB | 00m00s [ 38/179] Installing npth-0:1.8-3.fc43. 100% | 0.0 B/s | 50.7 KiB | 00m00s [ 39/179] Installing libblkid-0:2.41.1- 100% | 257.3 MiB/s | 263.5 KiB | 00m00s [ 40/179] Installing libxcrypt-0:4.4.38 100% | 280.4 MiB/s | 287.1 KiB | 00m00s [ 41/179] Installing libsepol-0:3.9-2.f 100% | 401.8 MiB/s | 822.9 KiB | 00m00s [ 42/179] Installing sqlite-libs-0:3.50 100% | 379.1 MiB/s | 1.5 MiB | 00m00s [ 43/179] Installing gnupg2-gpgconf-0:2 100% | 18.9 MiB/s | 252.0 KiB | 00m00s [ 44/179] Installing libattr-0:2.5.2-6. 100% | 0.0 B/s | 25.4 KiB | 00m00s [ 45/179] Installing libacl-0:2.3.2-4.f 100% | 0.0 B/s | 36.8 KiB | 00m00s [ 46/179] Installing pcre2-0:10.46-1.fc 100% | 341.4 MiB/s | 699.1 KiB | 00m00s [ 47/179] Installing libselinux-0:3.9-5 100% | 189.8 MiB/s | 194.4 KiB | 00m00s [ 48/179] Installing grep-0:3.12-2.fc43 100% | 62.7 MiB/s | 1.0 MiB | 00m00s [ 49/179] Installing sed-0:4.9-5.fc43.x 100% | 56.3 MiB/s | 865.5 KiB | 00m00s [ 50/179] Installing findutils-1:4.10.0 100% | 109.3 MiB/s | 1.9 MiB | 00m00s [ 51/179] Installing libtasn1-0:4.20.0- 100% | 173.9 MiB/s | 178.1 KiB | 00m00s [ 52/179] Installing libunistring-0:1.1 100% | 345.3 MiB/s | 1.7 MiB | 00m00s [ 53/179] Installing libidn2-0:2.3.8-2. 100% | 60.6 MiB/s | 558.7 KiB | 00m00s [ 54/179] Installing crypto-policies-0: 100% | 33.6 MiB/s | 172.0 KiB | 00m00s [ 55/179] Installing xz-1:5.8.1-2.fc43. 100% | 74.0 MiB/s | 1.3 MiB | 00m00s [ 56/179] Installing libmount-0:2.41.1- 100% | 365.0 MiB/s | 373.8 KiB | 00m00s [ 57/179] Installing gnupg2-verify-0:2. 100% | 26.3 MiB/s | 349.9 KiB | 00m00s [ 58/179] Installing dwz-0:0.16-2.fc43. 100% | 21.7 MiB/s | 288.5 KiB | 00m00s [ 59/179] Installing mpfr-0:4.2.2-2.fc4 100% | 271.6 MiB/s | 834.4 KiB | 00m00s [ 60/179] Installing gawk-0:5.3.2-2.fc4 100% | 100.9 MiB/s | 1.8 MiB | 00m00s [ 61/179] Installing libksba-0:1.6.7-4. 100% | 195.8 MiB/s | 401.1 KiB | 00m00s [ 62/179] Installing unzip-0:6.0-68.fc4 100% | 29.6 MiB/s | 393.8 KiB | 00m00s [ 63/179] Installing file-libs-0:5.46-8 100% | 658.7 MiB/s | 11.9 MiB | 00m00s [ 64/179] Installing file-0:5.46-8.fc44 100% | 8.3 MiB/s | 101.7 KiB | 00m00s [ 65/179] Installing diffutils-0:3.12-3 100% | 91.8 MiB/s | 1.6 MiB | 00m00s [ 66/179] Installing libeconf-0:0.7.9-2 100% | 65.0 MiB/s | 66.5 KiB | 00m00s [ 67/179] Installing libcap-ng-0:0.8.5- 100% | 69.2 MiB/s | 70.8 KiB | 00m00s [ 68/179] Installing audit-libs-0:4.1.2 100% | 186.3 MiB/s | 381.5 KiB | 00m00s [ 69/179] Installing pam-libs-0:1.7.1-3 100% | 126.0 MiB/s | 129.0 KiB | 00m00s [ 70/179] Installing libcap-0:2.76-3.fc 100% | 16.1 MiB/s | 214.3 KiB | 00m00s [ 71/179] Installing systemd-libs-0:258 100% | 332.1 MiB/s | 2.3 MiB | 00m00s [ 72/179] Installing libsemanage-0:3.9- 100% | 303.0 MiB/s | 310.2 KiB | 00m00s [ 73/179] Installing libsmartcols-0:2.4 100% | 177.3 MiB/s | 181.6 KiB | 00m00s [ 74/179] Installing lua-libs-0:5.4.8-2 100% | 275.3 MiB/s | 281.9 KiB | 00m00s [ 75/179] Installing json-c-0:0.18-7.fc 100% | 82.0 MiB/s | 84.0 KiB | 00m00s [ 76/179] Installing libffi-0:3.5.2-1.f 100% | 83.2 MiB/s | 85.2 KiB | 00m00s [ 77/179] Installing p11-kit-0:0.25.8-1 100% | 114.5 MiB/s | 2.3 MiB | 00m00s [ 78/179] Installing alternatives-0:1.3 100% | 5.2 MiB/s | 63.8 KiB | 00m00s [ 79/179] Installing p11-kit-trust-0:0. 100% | 21.9 MiB/s | 448.3 KiB | 00m00s [ 80/179] Installing openssl-libs-1:3.5 100% | 384.2 MiB/s | 9.2 MiB | 00m00s [ 81/179] Installing coreutils-0:9.8-3. 100% | 161.0 MiB/s | 5.5 MiB | 00m00s [ 82/179] Installing ca-certificates-0: 100% | 2.1 MiB/s | 2.5 MiB | 00m01s [ 83/179] Installing gzip-0:1.14-1.fc44 100% | 26.3 MiB/s | 403.3 KiB | 00m00s [ 84/179] Installing rpm-sequoia-0:1.9. 100% | 354.1 MiB/s | 2.5 MiB | 00m00s [ 85/179] Installing libfsverity-0:1.6- 100% | 28.8 MiB/s | 29.5 KiB | 00m00s [ 86/179] Installing libevent-0:2.1.12- 100% | 288.7 MiB/s | 886.8 KiB | 00m00s [ 87/179] Installing util-linux-core-0: 100% | 82.2 MiB/s | 1.5 MiB | 00m00s [ 88/179] Installing libusb1-0:1.0.29-4 100% | 21.1 MiB/s | 172.9 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [ 89/179] Installing tpm2-tss-0:4.1.3-8 100% | 262.0 MiB/s | 1.6 MiB | 00m00s [ 90/179] Installing ima-evm-utils-libs 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [ 91/179] Installing gnupg2-gpg-agent-0 100% | 31.4 MiB/s | 675.4 KiB | 00m00s [ 92/179] Installing systemd-standalone 100% | 22.1 MiB/s | 294.1 KiB | 00m00s [ 93/179] Installing rpm-libs-0:6.0.0-1 100% | 304.5 MiB/s | 935.3 KiB | 00m00s [ 94/179] Installing zip-0:3.0-44.fc43. 100% | 48.7 MiB/s | 698.4 KiB | 00m00s [ 95/179] Installing gnupg2-keyboxd-0:2 100% | 33.0 MiB/s | 202.7 KiB | 00m00s [ 96/179] Installing libpsl-0:0.21.5-6. 100% | 75.7 MiB/s | 77.5 KiB | 00m00s [ 97/179] Installing tar-2:1.35-6.fc43. 100% | 140.9 MiB/s | 3.0 MiB | 00m00s [ 98/179] Installing linkdupes-0:0.7.2- 100% | 58.6 MiB/s | 840.1 KiB | 00m00s [ 99/179] Installing libselinux-utils-0 100% | 22.6 MiB/s | 323.4 KiB | 00m00s [100/179] Installing liblastlog2-0:2.41 100% | 7.0 MiB/s | 35.9 KiB | 00m00s [101/179] Installing libfdisk-0:2.41.1- 100% | 124.2 MiB/s | 381.4 KiB | 00m00s [102/179] Installing util-linux-0:2.41. 100% | 99.2 MiB/s | 3.6 MiB | 00m00s [103/179] Installing policycoreutils-0: 100% | 29.0 MiB/s | 711.8 KiB | 00m00s [104/179] Installing selinux-policy-0:4 100% | 1.8 MiB/s | 33.5 KiB | 00m00s [105/179] Installing selinux-policy-tar 100% | 191.1 MiB/s | 14.9 MiB | 00m00s [106/179] Installing zstd-0:1.5.7-3.fc4 100% | 31.1 MiB/s | 509.8 KiB | 00m00s [107/179] Installing libxml2-0:2.12.10- 100% | 100.3 MiB/s | 1.7 MiB | 00m00s [108/179] Installing nettle-0:3.10.1-2. 100% | 258.4 MiB/s | 793.7 KiB | 00m00s [109/179] Installing gnutls-0:3.8.10-5. 100% | 349.4 MiB/s | 3.8 MiB | 00m00s [110/179] Installing bzip2-0:1.0.8-21.f 100% | 7.5 MiB/s | 99.8 KiB | 00m00s [111/179] Installing add-determinism-0: 100% | 128.0 MiB/s | 2.3 MiB | 00m00s [112/179] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [113/179] Installing cpio-0:2.15-6.fc43 100% | 68.7 MiB/s | 1.1 MiB | 00m00s [114/179] Installing ed-0:1.22.2-1.fc44 100% | 12.2 MiB/s | 150.4 KiB | 00m00s [115/179] Installing patch-0:2.8-2.fc43 100% | 16.9 MiB/s | 224.3 KiB | 00m00s [116/179] Installing lz4-libs-0:1.10.0- 100% | 158.6 MiB/s | 162.5 KiB | 00m00s [117/179] Installing libarchive-0:3.8.1 100% | 310.2 MiB/s | 953.1 KiB | 00m00s [118/179] Installing libgomp-0:15.2.1-2 100% | 264.9 MiB/s | 542.5 KiB | 00m00s [119/179] Installing libtool-ltdl-0:2.5 100% | 69.6 MiB/s | 71.2 KiB | 00m00s [120/179] Installing gdbm-libs-1:1.23-1 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [121/179] Installing cyrus-sasl-lib-0:2 100% | 127.8 MiB/s | 2.3 MiB | 00m00s [122/179] Installing openldap-0:2.6.10- 100% | 216.0 MiB/s | 663.6 KiB | 00m00s [123/179] Installing gnupg2-dirmngr-0:2 100% | 30.3 MiB/s | 621.1 KiB | 00m00s [124/179] Installing gnupg2-0:2.4.8-4.f 100% | 218.4 MiB/s | 6.6 MiB | 00m00s [125/179] Installing rpm-sign-libs-0:6. 100% | 39.6 MiB/s | 40.6 KiB | 00m00s [126/179] Installing gpgverify-0:2.2-3. 100% | 0.0 B/s | 9.4 KiB | 00m00s [127/179] Installing jansson-0:2.14-3.f 100% | 88.3 MiB/s | 90.5 KiB | 00m00s [128/179] Installing libpkgconf-0:2.3.0 100% | 77.4 MiB/s | 79.2 KiB | 00m00s [129/179] Installing pkgconf-0:2.3.0-3. 100% | 6.8 MiB/s | 91.0 KiB | 00m00s [130/179] Installing pkgconf-pkg-config 100% | 147.8 KiB/s | 1.8 KiB | 00m00s [131/179] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [132/179] Installing libbrotli-0:1.1.0- 100% | 272.0 MiB/s | 835.6 KiB | 00m00s [133/179] Installing libnghttp2-0:1.67. 100% | 159.5 MiB/s | 163.4 KiB | 00m00s [134/179] Installing keyutils-libs-0:1. 100% | 54.4 MiB/s | 55.7 KiB | 00m00s [135/179] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 64.2 KiB | 00m00s [136/179] Installing libverto-0:0.3.2-1 100% | 26.6 MiB/s | 27.2 KiB | 00m00s [137/179] Installing krb5-libs-0:1.21.3 100% | 287.5 MiB/s | 2.3 MiB | 00m00s [138/179] Installing libssh-0:0.11.3-1. 100% | 277.9 MiB/s | 569.2 KiB | 00m00s [139/179] Installing libcurl-0:8.16.0-1 100% | 299.7 MiB/s | 920.6 KiB | 00m00s [140/179] Installing curl-0:8.16.0-1.fc 100% | 20.3 MiB/s | 478.1 KiB | 00m00s [141/179] Installing rpm-0:6.0.0-1.fc44 100% | 80.5 MiB/s | 2.6 MiB | 00m00s [142/179] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.1 KiB | 00m00s [143/179] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [144/179] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [145/179] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.3 KiB | 00m00s [146/179] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [147/179] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [148/179] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [149/179] Installing elfutils-libs-0:0. 100% | 223.1 MiB/s | 685.2 KiB | 00m00s [150/179] Installing elfutils-debuginfo 100% | 6.0 MiB/s | 86.2 KiB | 00m00s [151/179] Installing elfutils-0:0.193-3 100% | 145.9 MiB/s | 2.9 MiB | 00m00s [152/179] Installing binutils-0:2.45.50 100% | 322.0 MiB/s | 27.4 MiB | 00m00s [153/179] Installing gdb-minimal-0:16.3 100% | 276.2 MiB/s | 13.3 MiB | 00m00s [154/179] Installing debugedit-0:5.2-3. 100% | 16.3 MiB/s | 217.3 KiB | 00m00s [155/179] Installing rpm-build-libs-0:6 100% | 262.9 MiB/s | 269.2 KiB | 00m00s [156/179] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [157/179] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [158/179] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [159/179] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [160/179] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [161/179] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [162/179] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [163/179] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [164/179] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [165/179] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [166/179] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [167/179] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [168/179] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [169/179] Installing rpm-build-0:6.0.0- 100% | 20.7 MiB/s | 296.5 KiB | 00m00s [170/179] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [171/179] Installing redhat-rpm-config- 100% | 92.5 MiB/s | 189.5 KiB | 00m00s [172/179] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [173/179] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [174/179] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [175/179] Installing python-srpm-macros 100% | 10.3 MiB/s | 52.9 KiB | 00m00s [176/179] Installing rpm-plugin-selinux 100% | 0.0 B/s | 13.0 KiB | 00m00s [177/179] Installing which-0:2.23-3.fc4 100% | 6.0 MiB/s | 85.7 KiB | 00m00s [178/179] Installing shadow-utils-2:4.1 100% | 141.8 MiB/s | 4.0 MiB | 00m00s [179/179] Installing info-0:7.2-6.fc43. 100% | 49.0 KiB/s | 354.3 KiB | 00m07s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.7.2-2.fc44.x86_64 alternatives-1.33-2.fc43.x86_64 ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.2-2.fc44.x86_64 bash-5.3.0-2.fc43.x86_64 binutils-2.45.50-4.fc44.x86_64 build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch bzip2-1.0.8-21.fc43.x86_64 bzip2-libs-1.0.8-21.fc43.x86_64 ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch coreutils-9.8-3.fc44.x86_64 coreutils-common-9.8-3.fc44.x86_64 cpio-2.15-6.fc43.x86_64 crypto-policies-20250714-5.gitcd6043a.fc44.noarch curl-8.16.0-1.fc44.x86_64 cyrus-sasl-lib-2.1.28-33.fc44.x86_64 debugedit-5.2-3.fc44.x86_64 diffutils-3.12-3.fc43.x86_64 dwz-0.16-2.fc43.x86_64 ed-1.22.2-1.fc44.x86_64 efi-srpm-macros-6-4.fc43.noarch elfutils-0.193-3.fc43.x86_64 elfutils-debuginfod-client-0.193-3.fc43.x86_64 elfutils-default-yama-scope-0.193-3.fc43.noarch elfutils-libelf-0.193-3.fc43.x86_64 elfutils-libs-0.193-3.fc43.x86_64 fedora-gpg-keys-44-0.1.noarch fedora-release-44-0.3.noarch fedora-release-common-44-0.3.noarch fedora-release-identity-basic-44-0.3.noarch fedora-repos-44-0.1.noarch fedora-repos-rawhide-44-0.1.noarch file-5.46-8.fc44.x86_64 file-libs-5.46-8.fc44.x86_64 filesystem-3.18-50.fc43.x86_64 filesystem-srpm-macros-3.18-50.fc43.noarch findutils-4.10.0-6.fc43.x86_64 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.fc43.x86_64 gdb-minimal-16.3-6.fc44.x86_64 gdbm-libs-1.23-10.fc43.x86_64 ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42.9000-5.fc44.x86_64 glibc-common-2.42.9000-5.fc44.x86_64 glibc-gconv-extra-2.42.9000-5.fc44.x86_64 glibc-minimal-langpack-2.42.9000-5.fc44.x86_64 gmp-6.3.0-4.fc44.x86_64 gnat-srpm-macros-6-8.fc43.noarch gnulib-l10n-20241231-1.fc44.noarch gnupg2-2.4.8-4.fc43.x86_64 gnupg2-dirmngr-2.4.8-4.fc43.x86_64 gnupg2-gpg-agent-2.4.8-4.fc43.x86_64 gnupg2-gpgconf-2.4.8-4.fc43.x86_64 gnupg2-keyboxd-2.4.8-4.fc43.x86_64 gnupg2-verify-2.4.8-4.fc43.x86_64 gnutls-3.8.10-5.fc44.x86_64 go-srpm-macros-3.8.0-1.fc44.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc43.x86_64 gzip-1.14-1.fc44.x86_64 ima-evm-utils-libs-1.6.2-6.fc43.x86_64 info-7.2-6.fc43.x86_64 jansson-2.14-3.fc43.x86_64 java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc43.x86_64 kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc43.x86_64 krb5-libs-1.21.3-8.fc44.x86_64 libacl-2.3.2-4.fc43.x86_64 libarchive-3.8.1-3.fc43.x86_64 libassuan-2.5.7-4.fc43.x86_64 libattr-2.5.2-6.fc43.x86_64 libblkid-2.41.1-17.fc44.x86_64 libbrotli-1.1.0-10.fc44.x86_64 libcap-2.76-3.fc44.x86_64 libcap-ng-0.8.5-8.fc44.x86_64 libcom_err-1.47.3-2.fc43.x86_64 libcurl-8.16.0-1.fc44.x86_64 libeconf-0.7.9-2.fc43.x86_64 libevent-2.1.12-16.fc43.x86_64 libfdisk-2.41.1-17.fc44.x86_64 libffi-3.5.2-1.fc44.x86_64 libfsverity-1.6-3.fc43.x86_64 libgcc-15.2.1-2.fc44.x86_64 libgcrypt-1.11.1-2.fc43.x86_64 libgomp-15.2.1-2.fc44.x86_64 libgpg-error-1.55-2.fc43.x86_64 libidn2-2.3.8-2.fc43.x86_64 libksba-1.6.7-4.fc43.x86_64 liblastlog2-2.41.1-17.fc44.x86_64 libmount-2.41.1-17.fc44.x86_64 libnghttp2-1.67.1-1.fc44.x86_64 libpkgconf-2.3.0-3.fc43.x86_64 libpsl-0.21.5-6.fc43.x86_64 libselinux-3.9-5.fc44.x86_64 libselinux-utils-3.9-5.fc44.x86_64 libsemanage-3.9-4.fc44.x86_64 libsepol-3.9-2.fc43.x86_64 libsmartcols-2.41.1-17.fc44.x86_64 libssh-0.11.3-1.fc44.x86_64 libssh-config-0.11.3-1.fc44.noarch libstdc++-15.2.1-2.fc44.x86_64 libtasn1-4.20.0-2.fc43.x86_64 libtool-ltdl-2.5.4-7.fc43.x86_64 libunistring-1.1-10.fc43.x86_64 libusb1-1.0.29-4.fc44.x86_64 libuuid-2.41.1-17.fc44.x86_64 libverto-0.3.2-11.fc43.x86_64 libxcrypt-4.4.38-9.fc44.x86_64 libxml2-2.12.10-5.fc44.x86_64 libzstd-1.5.7-3.fc44.x86_64 linkdupes-0.7.2-2.fc44.x86_64 lua-libs-5.4.8-2.fc43.x86_64 lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc43.x86_64 mpfr-4.2.2-2.fc43.x86_64 ncurses-base-6.5-7.20250614.fc43.noarch ncurses-libs-6.5-7.20250614.fc43.x86_64 nettle-3.10.1-2.fc43.x86_64 npth-1.8-3.fc43.x86_64 ocaml-srpm-macros-11-2.fc43.noarch openblas-srpm-macros-2-20.fc43.noarch openldap-2.6.10-4.fc44.x86_64 openssl-libs-3.5.1-3.fc44.x86_64 p11-kit-0.25.8-1.fc44.x86_64 p11-kit-trust-0.25.8-1.fc44.x86_64 package-notes-srpm-macros-0.5-14.fc43.noarch pam-libs-1.7.1-3.fc43.x86_64 patch-2.8-2.fc43.x86_64 pcre2-10.46-1.fc44.x86_64 pcre2-syntax-10.46-1.fc44.noarch perl-srpm-macros-1-60.fc43.noarch pkgconf-2.3.0-3.fc43.x86_64 pkgconf-m4-2.3.0-3.fc43.noarch pkgconf-pkg-config-2.3.0-3.fc43.x86_64 policycoreutils-3.9-5.fc44.x86_64 popt-1.19-9.fc43.x86_64 publicsuffix-list-dafsa-20250616-2.fc43.noarch pyproject-srpm-macros-1.18.4-1.fc44.noarch python-srpm-macros-3.14-8.fc44.noarch qt5-srpm-macros-5.15.17-2.fc43.noarch qt6-srpm-macros-6.10.0~rc-1.fc44.noarch readline-8.3-2.fc43.x86_64 redhat-rpm-config-343-14.fc44.noarch rpm-6.0.0-1.fc44.x86_64 rpm-build-6.0.0-1.fc44.x86_64 rpm-build-libs-6.0.0-1.fc44.x86_64 rpm-libs-6.0.0-1.fc44.x86_64 rpm-plugin-selinux-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 rpm-sign-libs-6.0.0-1.fc44.x86_64 rust-srpm-macros-26.4-1.fc44.noarch sed-4.9-5.fc43.x86_64 selinux-policy-42.11-2.fc44.noarch selinux-policy-targeted-42.11-2.fc44.noarch setup-2.15.0-26.fc43.noarch shadow-utils-4.18.0-3.fc43.x86_64 sqlite-libs-3.50.4-1.fc44.x86_64 systemd-libs-258-1.fc44.x86_64 systemd-standalone-sysusers-258-1.fc44.x86_64 tar-1.35-6.fc43.x86_64 tpm2-tss-4.1.3-8.fc43.x86_64 tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-68.fc44.x86_64 util-linux-2.41.1-17.fc44.x86_64 util-linux-core-2.41.1-17.fc44.x86_64 which-2.23-3.fc43.x86_64 xxhash-libs-0.8.3-3.fc43.x86_64 xz-5.8.1-2.fc43.x86_64 xz-libs-5.8.1-2.fc43.x86_64 zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.x86_64 zlib-ng-compat-2.2.5-2.fc44.x86_64 zstd-1.5.7-3.fc44.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 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-x86_64-1759573086.662618/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-67rlswa4/percolator/percolator.spec) Config(child) 0 minutes 17 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-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759573086.662618/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759573086.662618/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-x86_64-1759573086.662618/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-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 dnf5-5.2.17.0-2.fc44.x86_64 dnf5-plugins-5.2.17.0-2.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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm Updating and loading repositories: Copr repository 100% | 117.3 KiB/s | 1.5 KiB | 00m00s fedora 100% | 104.0 KiB/s | 29.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: boost-devel x86_64 1.83.0-17.fc44 fedora 143.0 MiB boost-static x86_64 1.83.0-17.fc44 fedora 383.3 MiB bzip2-devel x86_64 1.0.8-21.fc43 fedora 309.8 KiB cmake x86_64 3.31.6-4.fc43 fedora 34.5 MiB eigen3-devel noarch 3.4.0-18.fc43 fedora 8.4 MiB gcc x86_64 15.2.1-2.fc44 fedora 111.9 MiB gcc-c++ x86_64 15.2.1-2.fc44 fedora 41.4 MiB gtest-devel x86_64 1.17.0-1.fc44 copr_base 1.1 MiB libtirpc-devel x86_64 1.3.7-0.fc44 fedora 251.6 KiB make x86_64 1:4.4.1-11.fc43 fedora 1.8 MiB python3-devel x86_64 3.14.0~rc3-1.fc44 fedora 1.9 MiB sqlite-devel x86_64 3.50.4-1.fc44 fedora 684.1 KiB tokyocabinet-devel x86_64 1.4.48-28.fc43 fedora 460.2 KiB xerces-c-devel x86_64 3.3.0-8.fc43 fedora 4.1 MiB xsd x86_64 4.1.0-0.18.a11.fc43 fedora 5.0 MiB zlib-ng-compat-devel x86_64 2.2.5-2.fc44 fedora 107.0 KiB Installing dependencies: annobin-docs noarch 12.99-1.fc43 fedora 98.9 KiB annobin-plugin-gcc x86_64 12.99-1.fc43 fedora 1.0 MiB boost x86_64 1.83.0-17.fc44 fedora 1.3 KiB boost-atomic x86_64 1.83.0-17.fc44 fedora 20.9 KiB boost-chrono x86_64 1.83.0-17.fc44 fedora 37.5 KiB boost-container x86_64 1.83.0-17.fc44 fedora 65.4 KiB boost-context x86_64 1.83.0-17.fc44 fedora 12.4 KiB boost-contract x86_64 1.83.0-17.fc44 fedora 99.1 KiB boost-coroutine x86_64 1.83.0-17.fc44 fedora 21.1 KiB boost-date-time x86_64 1.83.0-17.fc44 fedora 12.2 KiB boost-fiber x86_64 1.83.0-17.fc44 fedora 78.7 KiB boost-filesystem x86_64 1.83.0-17.fc44 fedora 143.6 KiB boost-graph x86_64 1.83.0-17.fc44 fedora 363.1 KiB boost-iostreams x86_64 1.83.0-17.fc44 fedora 90.6 KiB boost-json x86_64 1.83.0-17.fc44 fedora 333.1 KiB boost-locale x86_64 1.83.0-17.fc44 fedora 617.7 KiB boost-log x86_64 1.83.0-17.fc44 fedora 1.5 MiB boost-math x86_64 1.83.0-17.fc44 fedora 642.6 KiB boost-nowide x86_64 1.83.0-17.fc44 fedora 20.8 KiB boost-numpy3 x86_64 1.83.0-17.fc44 fedora 57.6 KiB boost-program-options x86_64 1.83.0-17.fc44 fedora 280.8 KiB boost-python3 x86_64 1.83.0-17.fc44 fedora 258.2 KiB boost-random x86_64 1.83.0-17.fc44 fedora 29.6 KiB boost-regex x86_64 1.83.0-17.fc44 fedora 291.2 KiB boost-serialization x86_64 1.83.0-17.fc44 fedora 441.6 KiB boost-stacktrace x86_64 1.83.0-17.fc44 fedora 59.8 KiB boost-system x86_64 1.83.0-17.fc44 fedora 12.2 KiB boost-test x86_64 1.83.0-17.fc44 fedora 647.2 KiB boost-thread x86_64 1.83.0-17.fc44 fedora 132.7 KiB boost-timer x86_64 1.83.0-17.fc44 fedora 21.0 KiB boost-type_erasure x86_64 1.83.0-17.fc44 fedora 54.1 KiB boost-wave x86_64 1.83.0-17.fc44 fedora 868.3 KiB cmake-data noarch 3.31.6-4.fc43 fedora 8.5 MiB cmake-filesystem x86_64 3.31.6-4.fc43 fedora 0.0 B cmake-rpm-macros noarch 3.31.6-4.fc43 fedora 7.7 KiB cpp x86_64 15.2.1-2.fc44 fedora 37.9 MiB emacs-filesystem noarch 1:30.0-5.fc43 fedora 0.0 B expat x86_64 2.7.2-1.fc44 fedora 298.6 KiB flexiblas x86_64 3.4.5-5.fc44 fedora 50.4 KiB flexiblas-netlib x86_64 3.4.5-5.fc44 fedora 10.9 MiB flexiblas-openblas-openmp x86_64 3.4.5-5.fc44 fedora 39.2 KiB gcc-plugin-annobin x86_64 15.2.1-2.fc44 fedora 57.1 KiB glibc-devel x86_64 2.42.9000-5.fc44 fedora 2.3 MiB gmock x86_64 1.17.0-1.fc44 copr_base 131.0 KiB gtest x86_64 1.17.0-1.fc44 copr_base 505.8 KiB jsoncpp x86_64 1.9.6-2.fc43 fedora 257.6 KiB kernel-headers x86_64 6.17.0-63.fc44 fedora 6.7 MiB libcutl x86_64 1.10.0-33.fc43 fedora 1.1 MiB libgfortran x86_64 15.2.1-2.fc44 fedora 3.4 MiB libicu x86_64 77.1-1.fc43 fedora 36.4 MiB libicu-devel x86_64 77.1-1.fc43 fedora 5.0 MiB libmpc x86_64 1.3.1-8.fc43 fedora 160.6 KiB libquadmath x86_64 15.2.1-2.fc44 fedora 317.9 KiB libquadmath-devel x86_64 15.2.1-2.fc44 fedora 22.2 KiB libstdc++-devel x86_64 15.2.1-2.fc44 fedora 37.3 MiB libtirpc x86_64 1.3.7-0.fc44 fedora 198.9 KiB libuv x86_64 1:1.51.0-2.fc43 fedora 570.2 KiB libxcrypt-devel x86_64 4.4.38-9.fc44 fedora 30.8 KiB mpdecimal x86_64 4.0.1-2.fc43 fedora 217.2 KiB openblas x86_64 0.3.29-2.fc43 fedora 111.7 KiB openblas-openmp x86_64 0.3.29-2.fc43 fedora 43.7 MiB pyproject-rpm-macros noarch 1.18.4-1.fc44 fedora 114.9 KiB python-pip-wheel noarch 25.2-4.fc44 fedora 1.2 MiB python-rpm-macros noarch 3.14-8.fc44 fedora 27.6 KiB python3 x86_64 3.14.0~rc3-1.fc44 fedora 28.9 KiB python3-libs x86_64 3.14.0~rc3-1.fc44 fedora 43.0 MiB python3-numpy x86_64 1:2.3.3-2.fc44 fedora 41.3 MiB python3-numpy-f2py x86_64 1:2.3.3-2.fc44 fedora 2.1 MiB python3-packaging noarch 25.0-7.fc44 fedora 607.4 KiB python3-rpm-generators noarch 14-13.fc43 fedora 81.7 KiB python3-rpm-macros noarch 3.14-8.fc44 fedora 6.5 KiB rhash x86_64 1.4.5-3.fc43 fedora 351.1 KiB sqlite x86_64 3.50.4-1.fc44 fedora 1.8 MiB tokyocabinet x86_64 1.4.48-28.fc43 fedora 1.5 MiB tzdata noarch 2025b-3.fc43 fedora 1.6 MiB vim-filesystem noarch 2:9.1.1818-1.fc44 fedora 40.0 B xerces-c x86_64 3.3.0-8.fc43 fedora 3.8 MiB Transaction Summary: Installing: 93 packages Total size of inbound packages is 209 MiB. Need to download 55 MiB. After this operation, 1 GiB extra will be used (install 1 GiB, remove 0 B). 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Finish: build setup for percolator-3.08-1.fc44.src.rpm Start: rpmbuild percolator-3.08-1.fc44.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1753228800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.9FNnOk Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.v9uLV6 + 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.n68Z7z + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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/lib64: + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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/lib64: + 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/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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=x86_64 -- The C compiler identification is GNU 15.2.1 -- The CXX compiler identification is GNU 15.2.1 -- 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 "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- -- ------------------------------------------------------------------------------- -- 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 = x86_64 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Xerces-C: /usr/lib64/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/lib64/libtirpc.so -- Found Boost: /usr/lib64/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/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.0s) -- 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 LIB_SUFFIX 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/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]: 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]: 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/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build /usr/bin/gmake -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.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_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_in/13=percolatorInNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_in.xsd [ 2%] Generating percolator_out.* 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 [ 4%] 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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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%] Built target generate_xsd [ 8%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 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' [ 13%] Built target dblas [ 14%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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' [ 15%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 16%] 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++ -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 17%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 19%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^ [ 20%] 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 -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 21%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ~~~~~~^~~~~~~~~~~~ [ 22%] 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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 25%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 26%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 32%] Building CXX object 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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%] 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' [ 34%] Built target picked_protein [ 35%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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/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; | ^~~~~ 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(); | ^~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) | ^~~~~~~~~~~ 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; | ^~~~~~~~~~~ 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 ‘long unsigned int’} [-Wsign-compare] 344 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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() | ^~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang 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-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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() : | ^~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) | ^~~~~~~~~~~ /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 ‘long 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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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(); | ^~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 ‘long 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 ‘long 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 ‘long 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 ‘long 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 = x86_64 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Boost: /usr/lib64/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/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.0s) -- 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 LIB_SUFFIX 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 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/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 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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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o [ 5%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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-mno-omit-leaf-frame-pointer -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 [ 7%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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%] 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 [ 13%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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) | ^~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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() | ^~~~~~ 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; | ^~~~~~~~~~~ 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 ‘long unsigned int’} [-Wsign-compare] 344 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 ‘long 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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/Scores.cpp:31: /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/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 ‘long 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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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; | ^~~~~ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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 ‘long 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 ‘long 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 ‘long 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 = x86_64 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Boost: /usr/lib64/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/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") -- Configuring done (1.0s) -- 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 LIB_SUFFIX 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 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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/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' [ 1%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o [ 2%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 3%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 C object src/dblas/CMakeFiles/dblas.dir/ddot.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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 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) | ^~~~~~~~ [ 14%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 17%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 18%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 21%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 22%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ~~~~~~^~~~~~~~~~~~ [ 23%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 25%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 26%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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); | ^~~ 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; | ^~~~~ /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, | ^~~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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) | ^~~~~~~~~~~ [ 36%] 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 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' [ 36%] Built target picked_protein [ 38%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 39%] 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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() | ^~~~~~ 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) | ^~~~~~~~~~~ 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) | ^~~~~~~~~~~ /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; | ^~~~~~~~~~~ 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 ‘long 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) | ^~~~~~~~~~~ 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() : | ^~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) | ^~~~~~~~~~~ /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 ‘long 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/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); | ^~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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); | ^~~ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 ‘long 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] 533 | for (int k=0; k