Warning: Permanently added '34.230.5.70' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/7358077-fedora-40-x86_64 --chroot fedora-40-x86_64


Version: 0.72
PID: 10151
Logging PID: 10152
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'bootstrap': 'off',
 'build_id': 7358077,
 'buildroot_pkgs': [],
 'chroot': 'fedora-40-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '1475f66085495f4f5fc845ae4aace3979959e4b6',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/iucar/cran/R-CRAN-castor',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'R-CRAN-castor',
 'package_version': '1.8.0-1.copr7358077',
 'project_dirname': 'cran',
 'project_name': 'cran',
 'project_owner': 'iucar',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/iucar/cran/fedora-40-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'iucar/cran--iucar',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'iucar',
 'tags': [],
 'task_id': '7358077-fedora-40-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/iucar/cran/R-CRAN-castor /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/iucar/cran/R-CRAN-castor', '/var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor'...

Running: git checkout 1475f66085495f4f5fc845ae4aace3979959e4b6 --

cmd: ['git', 'checkout', '1475f66085495f4f5fc845ae4aace3979959e4b6', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor
rc: 0
stdout: 
stderr: Note: switching to '1475f66085495f4f5fc845ae4aace3979959e4b6'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 1475f66 automatic import of R-CRAN-castor

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading castor_1.8.0.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o castor_1.8.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/iucar/cran/R-CRAN-castor/castor_1.8.0.tar.gz/md5/b240641eb72d741cf7bb9675de9572b3/castor_1.8.0.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  887k  100  887k    0     0  9623k      0 --:--:-- --:--:-- --:--:-- 9649k
INFO: Reading stdout from command: md5sum castor_1.8.0.tar.gz

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor/R-CRAN-castor.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714166301.082308 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.5 starting (python version = 3.12.1, NVR = mock-5.5-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor/R-CRAN-castor.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714166301.082308 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
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-56a7s7da/R-CRAN-castor/R-CRAN-castor.spec)  Config(fedora-40-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.5
INFO: Mock Version: 5.5
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-1714166301.082308/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 (fallback)
INFO: Buildroot is handled by package management from host and used with --installroot:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.19.2-1.fc39.noarch
  python3-dnf-plugins-core-4.6.0-1.fc39.noarch
  yum-4.19.2-1.fc39.noarch
  dnf5-5.1.17-1.fc39.x86_64
  dnf5-plugins-5.1.17-1.fc39.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 updates                                100% |  70.0 KiB/s |  21.5 KiB |  00m00s
 fedora                                 100% | 134.2 KiB/s |  22.7 KiB |  00m00s
 Copr repository                        100% |  59.2 KiB/s |   1.5 KiB |  00m00s
 Copr repository                        100% | 172.0 MiB/s |  12.9 MiB |  00m00s
Repositories loaded.
Package                           Arch   Version                    Repository      Size
Installing group/module packages:                                                       
 bash                             x86_64 5.2.26-3.fc40              fedora       8.1 MiB
 bzip2                            x86_64 1.0.8-18.fc40              fedora      91.7 KiB
 coreutils                        x86_64 9.4-6.fc40                 fedora       5.8 MiB
 cpio                             x86_64 2.15-1.fc40                fedora       1.1 MiB
 diffutils                        x86_64 3.10-5.fc40                fedora       1.6 MiB
 fedora-release-common            noarch 40-39                      updates     19.1 KiB
 findutils                        x86_64 1:4.9.0-8.fc40             fedora       1.5 MiB
 gawk                             x86_64 5.3.0-3.fc40               fedora       1.7 MiB
 glibc-minimal-langpack           x86_64 2.39-8.fc40                updates      0.0   B
 grep                             x86_64 3.11-7.fc40                fedora       1.0 MiB
 gzip                             x86_64 1.13-1.fc40                fedora     385.0 KiB
 info                             x86_64 7.1-2.fc40                 fedora     357.8 KiB
 patch                            x86_64 2.7.6-24.fc40              fedora     262.8 KiB
 redhat-rpm-config                noarch 286-1.fc40                 fedora     185.2 KiB
 rpm-build                        x86_64 4.19.1.1-1.fc40            fedora     173.7 KiB
 sed                              x86_64 4.9-1.fc40                 fedora     861.5 KiB
 shadow-utils                     x86_64 2:4.15.1-2.fc40            updates      4.1 MiB
 tar                              x86_64 2:1.35-3.fc40              fedora       2.9 MiB
 unzip                            x86_64 6.0-63.fc40                fedora     382.8 KiB
 util-linux                       x86_64 2.40-13.fc40               updates      3.7 MiB
 which                            x86_64 2.21-41.fc40               fedora      80.2 KiB
 xz                               x86_64 1:5.4.6-3.fc40             fedora       2.0 MiB
Installing dependencies:                                                                
 alternatives                     x86_64 1.26-3.fc40                fedora      62.3 KiB
 ansible-srpm-macros              noarch 1-14.fc40                  fedora      35.7 KiB
 audit-libs                       x86_64 4.0.1-1.fc40               fedora     327.3 KiB
 authselect                       x86_64 1.5.0-5.fc40               fedora     153.6 KiB
 authselect-libs                  x86_64 1.5.0-5.fc40               fedora     818.3 KiB
 basesystem                       noarch 11-20.fc40                 fedora       0.0   B
 binutils                         x86_64 2.41-34.fc40               fedora      26.4 MiB
 binutils-gold                    x86_64 2.41-34.fc40               fedora       2.0 MiB
 bzip2-libs                       x86_64 1.0.8-18.fc40              fedora      80.7 KiB
 ca-certificates                  noarch 2023.2.62_v7.0.401-6.fc40  fedora       2.3 MiB
 coreutils-common                 x86_64 9.4-6.fc40                 fedora      11.4 MiB
 cracklib                         x86_64 2.9.11-5.fc40              fedora     238.9 KiB
 crypto-policies                  noarch 20240201-2.git9f501f3.fc40 fedora     149.3 KiB
 curl                             x86_64 8.6.0-8.fc40               updates    734.6 KiB
 cyrus-sasl-lib                   x86_64 2.1.28-19.fc40             fedora       2.3 MiB
 debugedit                        x86_64 5.0-14.fc40                fedora     199.0 KiB
 dwz                              x86_64 0.15-6.fc40                fedora     290.9 KiB
 ed                               x86_64 1.20.1-1.fc40              fedora     146.5 KiB
 efi-srpm-macros                  noarch 5-11.fc40                  fedora      40.1 KiB
 elfutils                         x86_64 0.191-4.fc40               fedora       2.5 MiB
 elfutils-debuginfod-client       x86_64 0.191-4.fc40               fedora      64.9 KiB
 elfutils-default-yama-scope      noarch 0.191-4.fc40               fedora       1.8 KiB
 elfutils-libelf                  x86_64 0.191-4.fc40               fedora       1.2 MiB
 elfutils-libs                    x86_64 0.191-4.fc40               fedora     646.1 KiB
 fedora-gpg-keys                  noarch 40-1                       fedora     125.0 KiB
 fedora-release                   noarch 40-39                      updates      0.0   B
 fedora-release-identity-basic    noarch 40-39                      updates    654.0   B
 fedora-repos                     noarch 40-1                       fedora       4.9 KiB
 file                             x86_64 5.45-4.fc40                fedora     103.5 KiB
 file-libs                        x86_64 5.45-4.fc40                fedora       9.9 MiB
 filesystem                       x86_64 3.18-8.fc40                fedora     106.0   B
 fonts-srpm-macros                noarch 1:2.0.5-14.fc40            fedora      55.3 KiB
 forge-srpm-macros                noarch 0.2.0-3.fc40               fedora      37.4 KiB
 fpc-srpm-macros                  noarch 1.3-12.fc40                fedora     144.0   B
 gdb-minimal                      x86_64 14.2-1.fc40                fedora      12.7 MiB
 gdbm                             x86_64 1:1.23-6.fc40              fedora     460.9 KiB
 gdbm-libs                        x86_64 1:1.23-6.fc40              fedora     121.9 KiB
 ghc-srpm-macros                  noarch 1.9-1.fc40                 fedora     716.0   B
 glibc                            x86_64 2.39-8.fc40                updates      6.7 MiB
 glibc-common                     x86_64 2.39-8.fc40                updates      1.0 MiB
 glibc-gconv-extra                x86_64 2.39-8.fc40                updates      7.8 MiB
 gmp                              x86_64 1:6.2.1-8.fc40             fedora     794.6 KiB
 gnat-srpm-macros                 noarch 6-5.fc40                   fedora       1.0 KiB
 go-srpm-macros                   noarch 3.5.0-1.fc40               fedora      60.6 KiB
 jansson                          x86_64 2.13.1-9.fc40              fedora      88.3 KiB
 kernel-srpm-macros               noarch 1.0-23.fc40                fedora       1.9 KiB
 keyutils-libs                    x86_64 1.6.3-3.fc40               fedora      54.4 KiB
 krb5-libs                        x86_64 1.21.2-5.fc40              fedora       2.3 MiB
 libacl                           x86_64 2.3.2-1.fc40               fedora      40.0 KiB
 libarchive                       x86_64 3.7.2-3.fc40               fedora     914.6 KiB
 libattr                          x86_64 2.5.2-3.fc40               fedora      28.5 KiB
 libblkid                         x86_64 2.40-13.fc40               updates    262.5 KiB
 libbrotli                        x86_64 1.1.0-3.fc40               fedora     829.5 KiB
 libcap                           x86_64 2.69-8.fc40                updates    219.8 KiB
 libcap-ng                        x86_64 0.8.4-4.fc40               fedora      73.1 KiB
 libcom_err                       x86_64 1.47.0-5.fc40              fedora      67.2 KiB
 libcurl                          x86_64 8.6.0-8.fc40               updates    772.8 KiB
 libeconf                         x86_64 0.6.2-1.fc40               fedora      58.0 KiB
 libevent                         x86_64 2.1.12-12.fc40             fedora     895.6 KiB
 libfdisk                         x86_64 2.40-13.fc40               updates    362.9 KiB
 libffi                           x86_64 3.4.4-7.fc40               fedora      81.6 KiB
 libgcc                           x86_64 14.0.1-0.15.fc40           fedora     270.6 KiB
 libgomp                          x86_64 14.0.1-0.15.fc40           fedora     519.4 KiB
 libidn2                          x86_64 2.3.7-1.fc40               fedora     329.1 KiB
 libmount                         x86_64 2.40-13.fc40               updates    351.8 KiB
 libnghttp2                       x86_64 1.59.0-3.fc40              updates    166.1 KiB
 libnsl2                          x86_64 2.0.1-1.fc40               fedora      57.9 KiB
 libpkgconf                       x86_64 2.1.0-1.fc40               fedora      74.2 KiB
 libpsl                           x86_64 0.21.5-3.fc40              fedora      80.5 KiB
 libpwquality                     x86_64 1.4.5-9.fc40               fedora     417.8 KiB
 libselinux                       x86_64 3.6-4.fc40                 fedora     173.0 KiB
 libsemanage                      x86_64 3.6-3.fc40                 fedora     293.5 KiB
 libsepol                         x86_64 3.6-3.fc40                 fedora     802.0 KiB
 libsmartcols                     x86_64 2.40-13.fc40               updates    180.4 KiB
 libssh                           x86_64 0.10.6-5.fc40              fedora     509.3 KiB
 libssh-config                    noarch 0.10.6-5.fc40              fedora     277.0   B
 libstdc++                        x86_64 14.0.1-0.15.fc40           fedora       2.8 MiB
 libtasn1                         x86_64 4.19.0-6.fc40              fedora     175.7 KiB
 libtirpc                         x86_64 1.3.4-1.rc3.fc40           fedora     202.8 KiB
 libtool-ltdl                     x86_64 2.4.7-10.fc40              fedora      66.2 KiB
 libunistring                     x86_64 1.1-7.fc40                 fedora       1.7 MiB
 libutempter                      x86_64 1.2.1-13.fc40              fedora      57.7 KiB
 libuuid                          x86_64 2.40-13.fc40               updates     37.4 KiB
 libverto                         x86_64 0.3.2-8.fc40               fedora      29.5 KiB
 libxcrypt                        x86_64 4.4.36-5.fc40              fedora     262.8 KiB
 libxml2                          x86_64 2.12.6-1.fc40              updates      1.7 MiB
 libzstd                          x86_64 1.5.6-1.fc40               updates    787.9 KiB
 lua-libs                         x86_64 5.4.6-5.fc40               fedora     281.1 KiB
 lua-srpm-macros                  noarch 1-13.fc40                  fedora       1.3 KiB
 lz4-libs                         x86_64 1.9.4-6.fc40               fedora     129.4 KiB
 mpfr                             x86_64 4.2.1-3.fc40               fedora     832.0 KiB
 ncurses-base                     noarch 6.4-12.20240127.fc40       fedora     326.2 KiB
 ncurses-libs                     x86_64 6.4-12.20240127.fc40       fedora     963.2 KiB
 ocaml-srpm-macros                noarch 9-3.fc40                   fedora       1.9 KiB
 openblas-srpm-macros             noarch 2-16.fc40                  fedora     104.0   B
 openldap                         x86_64 2.6.7-1.fc40               fedora     635.1 KiB
 openssl-libs                     x86_64 1:3.2.1-2.fc40             fedora       7.8 MiB
 p11-kit                          x86_64 0.25.3-4.fc40              fedora       2.2 MiB
 p11-kit-trust                    x86_64 0.25.3-4.fc40              fedora     391.4 KiB
 package-notes-srpm-macros        noarch 0.5-11.fc40                fedora       1.6 KiB
 pam                              x86_64 1.6.0-2.fc40               fedora       1.8 MiB
 pam-libs                         x86_64 1.6.0-2.fc40               fedora     135.0 KiB
 pcre2                            x86_64 10.42-2.fc40.2             fedora     637.6 KiB
 pcre2-syntax                     noarch 10.42-2.fc40.2             fedora     235.1 KiB
 perl-srpm-macros                 noarch 1-53.fc40                  fedora     861.0   B
 pkgconf                          x86_64 2.1.0-1.fc40               fedora      82.4 KiB
 pkgconf-m4                       noarch 2.1.0-1.fc40               fedora      13.9 KiB
 pkgconf-pkg-config               x86_64 2.1.0-1.fc40               fedora     989.0   B
 popt                             x86_64 1.19-6.fc40                fedora     136.9 KiB
 publicsuffix-list-dafsa          noarch 20240107-3.fc40            fedora      67.5 KiB
 pyproject-srpm-macros            noarch 1.12.0-1.fc40              fedora       1.5 KiB
 python-srpm-macros               noarch 3.12-7.fc40                fedora      50.1 KiB
 qt5-srpm-macros                  noarch 5.15.13-1.fc40             fedora     492.0   B
 qt6-srpm-macros                  noarch 6.7.0-1.fc40               updates    456.0   B
 readline                         x86_64 8.2-8.fc40                 fedora     489.2 KiB
 rpm                              x86_64 4.19.1.1-1.fc40            fedora       3.0 MiB
 rpm-build-libs                   x86_64 4.19.1.1-1.fc40            fedora     198.4 KiB
 rpm-libs                         x86_64 4.19.1.1-1.fc40            fedora     709.9 KiB
 rpm-sequoia                      x86_64 1.6.0-2.fc40               fedora       2.2 MiB
 rust-srpm-macros                 noarch 26.2-1.fc40                fedora       4.8 KiB
 setup                            noarch 2.14.5-2.fc40              fedora     720.4 KiB
 sqlite-libs                      x86_64 3.45.1-2.fc40              fedora       1.4 MiB
 systemd-libs                     x86_64 255.4-1.fc40               fedora       1.9 MiB
 util-linux-core                  x86_64 2.40-13.fc40               updates      1.5 MiB
 xxhash-libs                      x86_64 0.8.2-2.fc40               fedora      88.5 KiB
 xz-libs                          x86_64 1:5.4.6-3.fc40             fedora     209.8 KiB
 zig-srpm-macros                  noarch 1-2.fc40                   fedora       1.1 KiB
 zip                              x86_64 3.0-40.fc40                fedora     703.2 KiB
 zlib-ng-compat                   x86_64 2.1.6-2.fc40               fedora     134.0 KiB
 zstd                             x86_64 1.5.6-1.fc40               updates      1.7 MiB
Installing groups:                                                                      
 Buildsystem building group                                                             

Transaction Summary:
 Installing:      152 packages

Total size of inbound packages is 53 MiB. Need to download 0 B.
After this operation 178 MiB will be used (install 178 MiB, remove 0 B).
[  1/152] tar-2:1.35-3.fc40.x86_64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  2/152] bzip2-0:1.0.8-18.fc40.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  3/152] redhat-rpm-config-0:286-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  4/152] rpm-build-0:4.19.1.1-1.fc40.x 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  5/152] unzip-0:6.0-63.fc40.x86_64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  6/152] cpio-0:2.15-1.fc40.x86_64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  7/152] which-0:2.21-41.fc40.x86_64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[  8/152] bash-0:5.2.26-3.fc40.x86_64   100% |   0.0   B/s |   0.0   B |  00m00s
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[  9/152] coreutils-0:9.4-6.fc40.x86_64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 10/152] grep-0:3.11-7.fc40.x86_64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 11/152] patch-0:2.7.6-24.fc40.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 12/152] sed-0:4.9-1.fc40.x86_64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 13/152] diffutils-0:3.10-5.fc40.x86_6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 14/152] findutils-1:4.9.0-8.fc40.x86_ 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 15/152] gzip-0:1.13-1.fc40.x86_64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 16/152] info-0:7.1-2.fc40.x86_64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 17/152] xz-1:5.4.6-3.fc40.x86_64      100% |   0.0   B/s |   0.0   B |  00m00s
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[ 18/152] shadow-utils-2:4.15.1-2.fc40. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 19/152] util-linux-0:2.40-13.fc40.x86 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 20/152] fedora-release-common-0:40-39 100% |   0.0   B/s |   0.0   B |  00m00s
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--------------------------------------------------------------------------------
[152/152] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
Importing PGP key 0xA15B79CC:
 Userid     : "Fedora (40) <fedora-40-primary@fedoraproject.org>"
 Fingerprint: 115DF9AEF857853EE8445D0A0727707EA15B79CC
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary
The key was successfully imported.
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>>> Running pre-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64
>>> Stop pre-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64
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[  3/154] Installing libgcc-0:14.0.1-0. 100% | 133.0 MiB/s | 272.3 KiB |  00m00s
>>> Running post-install scriptlet: libgcc-0:14.0.1-0.15.fc40.x86_64
>>> Stop post-install scriptlet: libgcc-0:14.0.1-0.15.fc40.x86_64
[  4/154] Installing crypto-policies-0: 100% |  44.4 MiB/s | 181.7 KiB |  00m00s
>>> Running post-install scriptlet: crypto-policies-0:20240201-2.git9f501f3.fc40
>>> Stop post-install scriptlet: crypto-policies-0:20240201-2.git9f501f3.fc40.no
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>>> Running post-install scriptlet: setup-0:2.14.5-2.fc40.noarch
>>> Stop post-install scriptlet: setup-0:2.14.5-2.fc40.noarch
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[ 13/154] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[ 14/154] Installing publicsuffix-list- 100% |   0.0   B/s |  68.3 KiB |  00m00s
[ 15/154] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[ 16/154] Installing pkgconf-m4-0:2.1.0 100% |   0.0   B/s |  14.3 KiB |  00m00s
[ 17/154] Installing pcre2-syntax-0:10. 100% | 232.0 MiB/s | 237.6 KiB |  00m00s
[ 18/154] Installing ncurses-base-0:6.4 100% |  85.8 MiB/s | 351.6 KiB |  00m00s
[ 19/154] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 20/154] Installing ncurses-libs-0:6.4 100% | 236.7 MiB/s | 969.7 KiB |  00m00s
>>> Running pre-install scriptlet: glibc-0:2.39-8.fc40.x86_64
>>> Stop pre-install scriptlet: glibc-0:2.39-8.fc40.x86_64
[ 21/154] Installing glibc-0:2.39-8.fc4 100% | 232.8 MiB/s |   6.8 MiB |  00m00s
>>> Running post-install scriptlet: glibc-0:2.39-8.fc40.x86_64
>>> Stop post-install scriptlet: glibc-0:2.39-8.fc40.x86_64
[ 22/154] Installing bash-0:5.2.26-3.fc 100% | 408.1 MiB/s |   8.2 MiB |  00m00s
>>> Running post-install scriptlet: bash-0:5.2.26-3.fc40.x86_64
>>> Stop post-install scriptlet: bash-0:5.2.26-3.fc40.x86_64
[ 23/154] Installing glibc-common-0:2.3 100% | 204.1 MiB/s |   1.0 MiB |  00m00s
[ 24/154] Installing glibc-gconv-extra- 100% | 231.2 MiB/s |   7.9 MiB |  00m00s
>>> Running post-install scriptlet: glibc-gconv-extra-0:2.39-8.fc40.x86_64
>>> Stop post-install scriptlet: glibc-gconv-extra-0:2.39-8.fc40.x86_64
[ 25/154] Installing zlib-ng-compat-0:2 100% | 131.7 MiB/s | 134.8 KiB |  00m00s
[ 26/154] Installing xz-libs-1:5.4.6-3. 100% | 103.0 MiB/s | 210.9 KiB |  00m00s
[ 27/154] Installing bzip2-libs-0:1.0.8 100% |  79.9 MiB/s |  81.8 KiB |  00m00s
[ 28/154] Installing popt-0:1.19-6.fc40 100% |  70.1 MiB/s | 143.5 KiB |  00m00s
[ 29/154] Installing readline-0:8.2-8.f 100% | 239.9 MiB/s | 491.4 KiB |  00m00s
[ 30/154] Installing libstdc++-0:14.0.1 100% | 345.3 MiB/s |   2.8 MiB |  00m00s
[ 31/154] Installing libzstd-0:1.5.6-1. 100% | 385.3 MiB/s | 789.2 KiB |  00m00s
[ 32/154] Installing elfutils-libelf-0: 100% | 389.8 MiB/s |   1.2 MiB |  00m00s
[ 33/154] Installing libuuid-0:2.40-13. 100% |  37.6 MiB/s |  38.5 KiB |  00m00s
[ 34/154] Installing libblkid-0:2.40-13 100% | 257.5 MiB/s | 263.7 KiB |  00m00s
[ 35/154] Installing gmp-1:6.2.1-8.fc40 100% | 389.1 MiB/s | 796.8 KiB |  00m00s
[ 36/154] Installing libattr-0:2.5.2-3. 100% |   0.0   B/s |  29.5 KiB |  00m00s
[ 37/154] Installing libacl-0:2.3.2-1.f 100% |   0.0   B/s |  40.8 KiB |  00m00s
[ 38/154] Installing libxcrypt-0:4.4.36 100% | 259.3 MiB/s | 265.5 KiB |  00m00s
[ 39/154] Installing libeconf-0:0.6.2-1 100% |  58.2 MiB/s |  59.6 KiB |  00m00s
[ 40/154] Installing lz4-libs-0:1.9.4-6 100% | 127.4 MiB/s | 130.5 KiB |  00m00s
[ 41/154] Installing gdbm-libs-1:1.23-6 100% | 120.7 MiB/s | 123.6 KiB |  00m00s
[ 42/154] Installing mpfr-0:4.2.1-3.fc4 100% | 271.3 MiB/s | 833.5 KiB |  00m00s
[ 43/154] Installing gawk-0:5.3.0-3.fc4 100% | 288.0 MiB/s |   1.7 MiB |  00m00s
[ 44/154] Installing dwz-0:0.15-6.fc40. 100% | 285.5 MiB/s | 292.3 KiB |  00m00s
[ 45/154] Installing unzip-0:6.0-63.fc4 100% | 188.6 MiB/s | 386.3 KiB |  00m00s
[ 46/154] Installing file-libs-0:5.45-4 100% | 662.0 MiB/s |   9.9 MiB |  00m00s
[ 47/154] Installing file-0:5.45-4.fc40 100% | 102.6 MiB/s | 105.0 KiB |  00m00s
[ 48/154] Installing pcre2-0:10.42-2.fc 100% | 312.0 MiB/s | 639.1 KiB |  00m00s
[ 49/154] Installing grep-0:3.11-7.fc40 100% | 200.7 MiB/s |   1.0 MiB |  00m00s
[ 50/154] Installing xz-1:5.4.6-3.fc40. 100% | 286.1 MiB/s |   2.0 MiB |  00m00s
[ 51/154] Installing libcap-ng-0:0.8.4- 100% |  73.2 MiB/s |  75.0 KiB |  00m00s
[ 52/154] Installing audit-libs-0:4.0.1 100% | 321.7 MiB/s | 329.4 KiB |  00m00s
[ 53/154] Installing pam-libs-0:1.6.0-2 100% | 134.2 MiB/s | 137.4 KiB |  00m00s
[ 54/154] Installing libcap-0:2.69-8.fc 100% | 109.8 MiB/s | 224.8 KiB |  00m00s
[ 55/154] Installing systemd-libs-0:255 100% | 386.0 MiB/s |   1.9 MiB |  00m00s
[ 56/154] Installing libsepol-0:3.6-3.f 100% | 392.1 MiB/s | 803.0 KiB |  00m00s
[ 57/154] Installing libselinux-0:3.6-4 100% | 170.2 MiB/s | 174.3 KiB |  00m00s
[ 58/154] Installing sed-0:4.9-1.fc40.x 100% | 212.3 MiB/s | 869.7 KiB |  00m00s
[ 59/154] Installing findutils-1:4.9.0- 100% | 293.2 MiB/s |   1.5 MiB |  00m00s
[ 60/154] Installing libmount-0:2.40-13 100% | 344.6 MiB/s | 352.9 KiB |  00m00s
[ 61/154] Installing lua-libs-0:5.4.6-5 100% | 275.7 MiB/s | 282.3 KiB |  00m00s
[ 62/154] Installing alternatives-0:1.2 100% |  62.5 MiB/s |  64.0 KiB |  00m00s
[ 63/154] Installing jansson-0:2.13.1-9 100% |  87.6 MiB/s |  89.7 KiB |  00m00s
[ 64/154] Installing libtasn1-0:4.19.0- 100% | 173.3 MiB/s | 177.5 KiB |  00m00s
[ 65/154] Installing libsmartcols-0:2.4 100% | 177.1 MiB/s | 181.4 KiB |  00m00s
[ 66/154] Installing libcom_err-0:1.47. 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 67/154] Installing libunistring-0:1.1 100% | 346.1 MiB/s |   1.7 MiB |  00m00s
[ 68/154] Installing libidn2-0:2.3.7-1. 100% | 163.6 MiB/s | 335.0 KiB |  00m00s
[ 69/154] Installing libpsl-0:0.21.5-3. 100% |  79.7 MiB/s |  81.6 KiB |  00m00s
[ 70/154] Installing util-linux-core-0: 100% | 247.5 MiB/s |   1.5 MiB |  00m00s
[ 71/154] Installing tar-2:1.35-3.fc40. 100% | 368.8 MiB/s |   3.0 MiB |  00m00s
[ 72/154] Installing libsemanage-0:3.6- 100% | 144.2 MiB/s | 295.3 KiB |  00m00s
[ 73/154] Installing shadow-utils-2:4.1 100% | 149.0 MiB/s |   4.2 MiB |  00m00s
>>> Running pre-install scriptlet: libutempter-0:1.2.1-13.fc40.x86_64
>>> Stop pre-install scriptlet: libutempter-0:1.2.1-13.fc40.x86_64
[ 74/154] Installing libutempter-0:1.2. 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[ 75/154] Installing zip-0:3.0-40.fc40. 100% | 230.2 MiB/s | 707.1 KiB |  00m00s
[ 76/154] Installing gdbm-1:1.23-6.fc40 100% | 151.6 MiB/s | 465.8 KiB |  00m00s
[ 77/154] Installing cyrus-sasl-lib-0:2 100% | 380.5 MiB/s |   2.3 MiB |  00m00s
[ 78/154] Installing zstd-0:1.5.6-1.fc4 100% | 419.0 MiB/s |   1.7 MiB |  00m00s
[ 79/154] Installing libfdisk-0:2.40-13 100% | 177.7 MiB/s | 364.0 KiB |  00m00s
[ 80/154] Installing bzip2-0:1.0.8-18.f 100% |  93.9 MiB/s |  96.2 KiB |  00m00s
[ 81/154] Installing libxml2-0:2.12.6-1 100% | 340.0 MiB/s |   1.7 MiB |  00m00s
[ 82/154] Installing sqlite-libs-0:3.45 100% | 350.3 MiB/s |   1.4 MiB |  00m00s
[ 83/154] Installing ed-0:1.20.1-1.fc40 100% | 145.3 MiB/s | 148.8 KiB |  00m00s
[ 84/154] Installing patch-0:2.7.6-24.f 100% | 258.1 MiB/s | 264.3 KiB |  00m00s
[ 85/154] Installing elfutils-default-y 100% | 340.5 KiB/s |   2.0 KiB |  00m00s
>>> Running post-install scriptlet: elfutils-default-yama-scope-0:0.191-4.fc40.n
>>> Stop post-install scriptlet: elfutils-default-yama-scope-0:0.191-4.fc40.noar
[ 86/154] Installing cpio-0:2.15-1.fc40 100% | 274.9 MiB/s |   1.1 MiB |  00m00s
[ 87/154] Installing diffutils-0:3.10-5 100% | 317.2 MiB/s |   1.6 MiB |  00m00s
[ 88/154] Installing libgomp-0:14.0.1-0 100% | 254.3 MiB/s | 520.8 KiB |  00m00s
[ 89/154] Installing libpkgconf-0:2.1.0 100% |  73.6 MiB/s |  75.3 KiB |  00m00s
[ 90/154] Installing pkgconf-0:2.1.0-1. 100% |  82.9 MiB/s |  84.9 KiB |  00m00s
[ 91/154] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[ 92/154] Installing libffi-0:3.4.4-7.f 100% |  81.0 MiB/s |  83.0 KiB |  00m00s
[ 93/154] Installing p11-kit-0:0.25.3-4 100% | 243.8 MiB/s |   2.2 MiB |  00m00s
[ 94/154] Installing p11-kit-trust-0:0. 100% |  42.7 MiB/s | 393.1 KiB |  00m00s
>>> Running post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.x86_64
>>> Stop post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.x86_64
[ 95/154] Installing keyutils-libs-0:1. 100% |  54.5 MiB/s |  55.8 KiB |  00m00s
[ 96/154] Installing libverto-0:0.3.2-8 100% |  30.5 MiB/s |  31.3 KiB |  00m00s
[ 97/154] Installing xxhash-libs-0:0.8. 100% |  87.8 MiB/s |  89.9 KiB |  00m00s
[ 98/154] Installing libbrotli-0:1.1.0- 100% | 270.8 MiB/s | 831.8 KiB |  00m00s
[ 99/154] Installing libtool-ltdl-0:2.4 100% |  65.7 MiB/s |  67.3 KiB |  00m00s
[100/154] Installing libnghttp2-0:1.59. 100% | 163.3 MiB/s | 167.2 KiB |  00m00s
[101/154] Installing coreutils-common-0 100% | 395.3 MiB/s |  11.5 MiB |  00m00s
[102/154] Installing openssl-libs-1:3.2 100% | 409.9 MiB/s |   7.8 MiB |  00m00s
[103/154] Installing coreutils-0:9.4-6. 100% | 264.3 MiB/s |   5.8 MiB |  00m00s
>>> Running pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.n
>>> Stop pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noar
[104/154] Installing ca-certificates-0: 100% |   4.0 MiB/s |   2.3 MiB |  00m01s
>>> Running post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.
>>> Stop post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noa
[105/154] Installing krb5-libs-0:1.21.2 100% | 286.8 MiB/s |   2.3 MiB |  00m00s
[106/154] Installing libtirpc-0:1.3.4-1 100% | 199.8 MiB/s | 204.6 KiB |  00m00s
[107/154] Installing gzip-0:1.13-1.fc40 100% | 190.7 MiB/s | 390.6 KiB |  00m00s
[108/154] Installing authselect-libs-0: 100% | 162.7 MiB/s | 833.2 KiB |  00m00s
[109/154] Installing libarchive-0:3.7.2 100% | 298.4 MiB/s | 916.6 KiB |  00m00s
[110/154] Installing authselect-0:1.5.0 100% |  77.1 MiB/s | 157.9 KiB |  00m00s
[111/154] Installing cracklib-0:2.9.11- 100% |  61.1 MiB/s | 250.3 KiB |  00m00s
[112/154] Installing libpwquality-0:1.4 100% | 105.0 MiB/s | 430.1 KiB |  00m00s
[113/154] Installing libnsl2-0:2.0.1-1. 100% |  57.7 MiB/s |  59.0 KiB |  00m00s
[114/154] Installing pam-0:1.6.0-2.fc40 100% | 150.9 MiB/s |   1.8 MiB |  00m00s
[115/154] Installing libssh-0:0.10.6-5. 100% | 249.7 MiB/s | 511.4 KiB |  00m00s
[116/154] Installing rpm-sequoia-0:1.6. 100% | 371.5 MiB/s |   2.2 MiB |  00m00s
[117/154] Installing rpm-libs-0:4.19.1. 100% | 347.4 MiB/s | 711.4 KiB |  00m00s
[118/154] Installing libevent-0:2.1.12- 100% | 292.8 MiB/s | 899.4 KiB |  00m00s
[119/154] Installing openldap-0:2.6.7-1 100% | 208.0 MiB/s | 638.9 KiB |  00m00s
[120/154] Installing libcurl-0:8.6.0-8. 100% | 251.9 MiB/s | 773.9 KiB |  00m00s
[121/154] Installing elfutils-libs-0:0. 100% | 316.4 MiB/s | 648.0 KiB |  00m00s
[122/154] Installing elfutils-debuginfo 100% |  65.3 MiB/s |  66.9 KiB |  00m00s
[123/154] Installing binutils-gold-0:2. 100% | 168.9 MiB/s |   2.0 MiB |  00m00s
>>> Running post-install scriptlet: binutils-gold-0:2.41-34.fc40.x86_64
>>> Stop post-install scriptlet: binutils-gold-0:2.41-34.fc40.x86_64
[124/154] Installing binutils-0:2.41-34 100% | 382.6 MiB/s |  26.4 MiB |  00m00s
>>> Running post-install scriptlet: binutils-0:2.41-34.fc40.x86_64
>>> Stop post-install scriptlet: binutils-0:2.41-34.fc40.x86_64
[125/154] Installing elfutils-0:0.191-4 100% | 319.6 MiB/s |   2.6 MiB |  00m00s
[126/154] Installing gdb-minimal-0:14.2 100% | 408.5 MiB/s |  12.7 MiB |  00m00s
[127/154] Installing debugedit-0:5.0-14 100% | 197.0 MiB/s | 201.7 KiB |  00m00s
[128/154] Installing rpm-build-libs-0:4 100% | 194.5 MiB/s | 199.2 KiB |  00m00s
[129/154] Installing curl-0:8.6.0-8.fc4 100% |  65.4 MiB/s | 736.9 KiB |  00m00s
>>> Running pre-install scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64
>>> Stop pre-install scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64
[130/154] Installing rpm-0:4.19.1.1-1.f 100% | 159.8 MiB/s |   2.4 MiB |  00m00s
[131/154] Installing efi-srpm-macros-0: 100% |   0.0   B/s |  41.2 KiB |  00m00s
[132/154] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[133/154] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[134/154] Installing rust-srpm-macros-0 100% |   5.4 MiB/s |   5.6 KiB |  00m00s
[135/154] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 768.0   B |  00m00s
[136/154] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[137/154] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[138/154] Installing openblas-srpm-macr 100% |   0.0   B/s | 384.0   B |  00m00s
[139/154] Installing ocaml-srpm-macros- 100% |   2.1 MiB/s |   2.2 KiB |  00m00s
[140/154] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[141/154] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[142/154] Installing ghc-srpm-macros-0: 100% |   0.0   B/s | 992.0   B |  00m00s
[143/154] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[144/154] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[145/154] Installing fonts-srpm-macros- 100% |   0.0   B/s |  56.5 KiB |  00m00s
[146/154] Installing forge-srpm-macros- 100% |   0.0   B/s |  38.6 KiB |  00m00s
[147/154] Installing go-srpm-macros-0:3 100% |  60.2 MiB/s |  61.6 KiB |  00m00s
[148/154] Installing python-srpm-macros 100% |  50.1 MiB/s |  51.3 KiB |  00m00s
[149/154] Installing redhat-rpm-config- 100% |  93.6 MiB/s | 191.7 KiB |  00m00s
[150/154] Installing rpm-build-0:4.19.1 100% |  88.8 MiB/s | 182.0 KiB |  00m00s
[151/154] Installing pyproject-srpm-mac 100% |   2.0 MiB/s |   2.1 KiB |  00m00s
[152/154] Installing util-linux-0:2.40- 100% | 162.6 MiB/s |   3.7 MiB |  00m00s
>>> Running post-install scriptlet: util-linux-0:2.40-13.fc40.x86_64
>>> Stop post-install scriptlet: util-linux-0:2.40-13.fc40.x86_64
[153/154] Installing which-0:2.21-41.fc 100% |  80.5 MiB/s |  82.4 KiB |  00m00s
[154/154] Installing info-0:7.1-2.fc40. 100% | 423.4 KiB/s | 358.2 KiB |  00m01s
>>> Running post-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64
>>> Stop post-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64
>>> Running post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.f
>>> Stop post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40
>>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc40.x86_64
>>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc40.x86_64
>>> Running post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64
>>> Stop post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64
>>> Running trigger-install scriptlet: glibc-common-0:2.39-8.fc40.x86_64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39-8.fc40.x86_64
>>> Running trigger-install scriptlet: info-0:7.1-2.fc40.x86_64
>>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.x86_64
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.26-3.fc40.x86_64
ansible-srpm-macros-1-14.fc40.noarch
audit-libs-4.0.1-1.fc40.x86_64
authselect-1.5.0-5.fc40.x86_64
authselect-libs-1.5.0-5.fc40.x86_64
basesystem-11-20.fc40.noarch
bash-5.2.26-3.fc40.x86_64
binutils-2.41-34.fc40.x86_64
binutils-gold-2.41-34.fc40.x86_64
bzip2-1.0.8-18.fc40.x86_64
bzip2-libs-1.0.8-18.fc40.x86_64
ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch
coreutils-9.4-6.fc40.x86_64
coreutils-common-9.4-6.fc40.x86_64
cpio-2.15-1.fc40.x86_64
cracklib-2.9.11-5.fc40.x86_64
crypto-policies-20240201-2.git9f501f3.fc40.noarch
curl-8.6.0-8.fc40.x86_64
cyrus-sasl-lib-2.1.28-19.fc40.x86_64
debugedit-5.0-14.fc40.x86_64
diffutils-3.10-5.fc40.x86_64
dwz-0.15-6.fc40.x86_64
ed-1.20.1-1.fc40.x86_64
efi-srpm-macros-5-11.fc40.noarch
elfutils-0.191-4.fc40.x86_64
elfutils-debuginfod-client-0.191-4.fc40.x86_64
elfutils-default-yama-scope-0.191-4.fc40.noarch
elfutils-libelf-0.191-4.fc40.x86_64
elfutils-libs-0.191-4.fc40.x86_64
fedora-gpg-keys-40-1.noarch
fedora-release-40-39.noarch
fedora-release-common-40-39.noarch
fedora-release-identity-basic-40-39.noarch
fedora-repos-40-1.noarch
file-5.45-4.fc40.x86_64
file-libs-5.45-4.fc40.x86_64
filesystem-3.18-8.fc40.x86_64
findutils-4.9.0-8.fc40.x86_64
fonts-srpm-macros-2.0.5-14.fc40.noarch
forge-srpm-macros-0.2.0-3.fc40.noarch
fpc-srpm-macros-1.3-12.fc40.noarch
gawk-5.3.0-3.fc40.x86_64
gdb-minimal-14.2-1.fc40.x86_64
gdbm-1.23-6.fc40.x86_64
gdbm-libs-1.23-6.fc40.x86_64
ghc-srpm-macros-1.9-1.fc40.noarch
glibc-2.39-8.fc40.x86_64
glibc-common-2.39-8.fc40.x86_64
glibc-gconv-extra-2.39-8.fc40.x86_64
glibc-minimal-langpack-2.39-8.fc40.x86_64
gmp-6.2.1-8.fc40.x86_64
gnat-srpm-macros-6-5.fc40.noarch
go-srpm-macros-3.5.0-1.fc40.noarch
gpg-pubkey-a15b79cc-63d04c2c
grep-3.11-7.fc40.x86_64
gzip-1.13-1.fc40.x86_64
info-7.1-2.fc40.x86_64
jansson-2.13.1-9.fc40.x86_64
kernel-srpm-macros-1.0-23.fc40.noarch
keyutils-libs-1.6.3-3.fc40.x86_64
krb5-libs-1.21.2-5.fc40.x86_64
libacl-2.3.2-1.fc40.x86_64
libarchive-3.7.2-3.fc40.x86_64
libattr-2.5.2-3.fc40.x86_64
libblkid-2.40-13.fc40.x86_64
libbrotli-1.1.0-3.fc40.x86_64
libcap-2.69-8.fc40.x86_64
libcap-ng-0.8.4-4.fc40.x86_64
libcom_err-1.47.0-5.fc40.x86_64
libcurl-8.6.0-8.fc40.x86_64
libeconf-0.6.2-1.fc40.x86_64
libevent-2.1.12-12.fc40.x86_64
libfdisk-2.40-13.fc40.x86_64
libffi-3.4.4-7.fc40.x86_64
libgcc-14.0.1-0.15.fc40.x86_64
libgomp-14.0.1-0.15.fc40.x86_64
libidn2-2.3.7-1.fc40.x86_64
libmount-2.40-13.fc40.x86_64
libnghttp2-1.59.0-3.fc40.x86_64
libnsl2-2.0.1-1.fc40.x86_64
libpkgconf-2.1.0-1.fc40.x86_64
libpsl-0.21.5-3.fc40.x86_64
libpwquality-1.4.5-9.fc40.x86_64
libselinux-3.6-4.fc40.x86_64
libsemanage-3.6-3.fc40.x86_64
libsepol-3.6-3.fc40.x86_64
libsmartcols-2.40-13.fc40.x86_64
libssh-0.10.6-5.fc40.x86_64
libssh-config-0.10.6-5.fc40.noarch
libstdc++-14.0.1-0.15.fc40.x86_64
libtasn1-4.19.0-6.fc40.x86_64
libtirpc-1.3.4-1.rc3.fc40.x86_64
libtool-ltdl-2.4.7-10.fc40.x86_64
libunistring-1.1-7.fc40.x86_64
libutempter-1.2.1-13.fc40.x86_64
libuuid-2.40-13.fc40.x86_64
libverto-0.3.2-8.fc40.x86_64
libxcrypt-4.4.36-5.fc40.x86_64
libxml2-2.12.6-1.fc40.x86_64
libzstd-1.5.6-1.fc40.x86_64
lua-libs-5.4.6-5.fc40.x86_64
lua-srpm-macros-1-13.fc40.noarch
lz4-libs-1.9.4-6.fc40.x86_64
mpfr-4.2.1-3.fc40.x86_64
ncurses-base-6.4-12.20240127.fc40.noarch
ncurses-libs-6.4-12.20240127.fc40.x86_64
ocaml-srpm-macros-9-3.fc40.noarch
openblas-srpm-macros-2-16.fc40.noarch
openldap-2.6.7-1.fc40.x86_64
openssl-libs-3.2.1-2.fc40.x86_64
p11-kit-0.25.3-4.fc40.x86_64
p11-kit-trust-0.25.3-4.fc40.x86_64
package-notes-srpm-macros-0.5-11.fc40.noarch
pam-1.6.0-2.fc40.x86_64
pam-libs-1.6.0-2.fc40.x86_64
patch-2.7.6-24.fc40.x86_64
pcre2-10.42-2.fc40.2.x86_64
pcre2-syntax-10.42-2.fc40.2.noarch
perl-srpm-macros-1-53.fc40.noarch
pkgconf-2.1.0-1.fc40.x86_64
pkgconf-m4-2.1.0-1.fc40.noarch
pkgconf-pkg-config-2.1.0-1.fc40.x86_64
popt-1.19-6.fc40.x86_64
publicsuffix-list-dafsa-20240107-3.fc40.noarch
pyproject-srpm-macros-1.12.0-1.fc40.noarch
python-srpm-macros-3.12-7.fc40.noarch
qt5-srpm-macros-5.15.13-1.fc40.noarch
qt6-srpm-macros-6.7.0-1.fc40.noarch
readline-8.2-8.fc40.x86_64
redhat-rpm-config-286-1.fc40.noarch
rpm-4.19.1.1-1.fc40.x86_64
rpm-build-4.19.1.1-1.fc40.x86_64
rpm-build-libs-4.19.1.1-1.fc40.x86_64
rpm-libs-4.19.1.1-1.fc40.x86_64
rpm-sequoia-1.6.0-2.fc40.x86_64
rust-srpm-macros-26.2-1.fc40.noarch
sed-4.9-1.fc40.x86_64
setup-2.14.5-2.fc40.noarch
shadow-utils-4.15.1-2.fc40.x86_64
sqlite-libs-3.45.1-2.fc40.x86_64
systemd-libs-255.4-1.fc40.x86_64
tar-1.35-3.fc40.x86_64
unzip-6.0-63.fc40.x86_64
util-linux-2.40-13.fc40.x86_64
util-linux-core-2.40-13.fc40.x86_64
which-2.21-41.fc40.x86_64
xxhash-libs-0.8.2-2.fc40.x86_64
xz-5.4.6-3.fc40.x86_64
xz-libs-5.4.6-3.fc40.x86_64
zig-srpm-macros-1-2.fc40.noarch
zip-3.0-40.fc40.x86_64
zlib-ng-compat-2.1.6-2.fc40.x86_64
zstd-1.5.6-1.fc40.x86_64
Start: buildsrpm
Start: rpmbuild -bs
warning: source_date_epoch_from_changelog set but %changelog is missing
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm

RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-40-x86_64-1714166301.082308/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-40-x86_64-1714166301.082308/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-56a7s7da/R-CRAN-castor/R-CRAN-castor.spec) Config(child) 0 minutes 9 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/R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm)  Config(fedora-40-x86_64)
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-1714166301.082308/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 from host and used with --installroot:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.19.2-1.fc39.noarch
  python3-dnf-plugins-core-4.6.0-1.fc39.noarch
  yum-4.19.2-1.fc39.noarch
  dnf5-5.1.17-1.fc39.x86_64
  dnf5-plugins-5.1.17-1.fc39.x86_64
Finish: chroot init
Start: build phase for R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
Start: build setup for R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
warning: source_date_epoch_from_changelog set but %changelog is missing
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm

RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
Updating and loading repositories:
 updates                                100% | 191.8 KiB/s |  21.5 KiB |  00m00s
 fedora                                 100% | 252.0 KiB/s |  22.7 KiB |  00m00s
 Copr repository                        100% |  96.2 KiB/s |   1.5 KiB |  00m00s
 Copr repository                        100% | 174.4 MiB/s |  12.9 MiB |  00m00s
Repositories loaded.
Package                      Arch   Version                          Repository      Size
Installing:                                                                              
 R-CRAN-Matrix               x86_64 1.6.5-1.fc40.copr7355271         copr_base    7.2 MiB
 R-CRAN-RSpectra             x86_64 0.16.1-1.fc40.copr7356093        copr_base    1.2 MiB
 R-CRAN-Rcpp                 x86_64 1.0.12-1.fc40.copr7349917        copr_base    8.3 MiB
 R-CRAN-jsonlite             x86_64 1.8.8-1.fc40.copr7349934         copr_base    2.3 MiB
 R-CRAN-naturalsort          noarch 0.1.3-1.fc40.copr7350570         copr_base   23.2 KiB
 R-core                      x86_64 4.4.0-1.fc40~bootstrap           copr_base  100.7 MiB
 R-devel                     x86_64 4.4.0-1.fc40~bootstrap           copr_base    0.0   B
Installing dependencies:                                                                 
 R-CRAN-lattice              x86_64 0.22.6-1.fc40.copr7352639        copr_base    2.0 MiB
 R-core-devel                x86_64 4.4.0-1.fc40~bootstrap           copr_base  394.1 KiB
 R-java                      x86_64 4.4.0-1.fc40~bootstrap           copr_base    0.0   B
 R-java-devel                x86_64 4.4.0-1.fc40~bootstrap           copr_base    0.0   B
 R-littler                   x86_64 0.3.19-3.fc40                    fedora     189.7 KiB
 R-rpm-macros                noarch 1.2.1-9.fc40                     fedora       5.6 KiB
 abattis-cantarell-vf-fonts  noarch 0.301-12.fc40                    fedora     192.7 KiB
 alsa-lib                    x86_64 1.2.11-2.fc40                    fedora       1.4 MiB
 annobin-docs                noarch 12.46-1.fc40                     updates     95.7 KiB
 annobin-plugin-gcc          x86_64 12.46-1.fc40                     updates    969.9 KiB
 avahi-libs                  x86_64 0.8-26.fc40                      fedora     166.3 KiB
 brotli                      x86_64 1.1.0-3.fc40                     fedora      31.8 KiB
 brotli-devel                x86_64 1.1.0-3.fc40                     fedora      65.6 KiB
 bzip2-devel                 x86_64 1.0.8-18.fc40                    fedora     309.8 KiB
 cairo                       x86_64 1.18.0-3.fc40                    fedora       1.7 MiB
 cmake-filesystem            x86_64 3.28.2-1.fc40                    fedora       0.0   B
 copy-jdk-configs            noarch 4.1-5.fc40                       fedora      20.3 KiB
 cpp                         x86_64 14.0.1-0.15.fc40                 fedora      34.9 MiB
 crypto-policies-scripts     noarch 20240201-2.git9f501f3.fc40       fedora     313.8 KiB
 cups-libs                   x86_64 1:2.4.7-13.fc40                  updates    618.9 KiB
 dbus-libs                   x86_64 1:1.14.10-3.fc40                 fedora     368.9 KiB
 default-fonts-core-sans     noarch 4.0-12.fc40                      fedora      11.9 KiB
 desktop-file-utils          x86_64 0.26-12.fc40                     fedora     226.0 KiB
 emacs-filesystem            noarch 1:29.3-5.fc40                    updates      0.0   B
 expat                       x86_64 2.6.2-1.fc40                     updates    280.8 KiB
 flexiblas                   x86_64 3.4.2-1.fc40                     fedora      46.9 KiB
 flexiblas-devel             x86_64 3.4.2-1.fc40                     fedora       4.7 MiB
 flexiblas-netlib            x86_64 3.4.2-1.fc40                     fedora      10.4 MiB
 flexiblas-netlib64          x86_64 3.4.2-1.fc40                     fedora      10.5 MiB
 flexiblas-openblas-openmp   x86_64 3.4.2-1.fc40                     fedora      39.3 KiB
 flexiblas-openblas-openmp64 x86_64 3.4.2-1.fc40                     fedora      39.3 KiB
 fontconfig                  x86_64 2.15.0-4.fc40                    fedora     767.3 KiB
 fontconfig-devel            x86_64 2.15.0-4.fc40                    fedora     117.2 KiB
 fonts-filesystem            noarch 1:2.0.5-14.fc40                  fedora       0.0   B
 freetype                    x86_64 2.13.2-5.fc40                    fedora     842.6 KiB
 freetype-devel              x86_64 2.13.2-5.fc40                    fedora       7.8 MiB
 fribidi                     x86_64 1.0.13-4.fc40                    fedora     365.3 KiB
 gc                          x86_64 8.2.2-6.fc40                     fedora     258.7 KiB
 gcc                         x86_64 14.0.1-0.15.fc40                 fedora     104.0 MiB
 gcc-c++                     x86_64 14.0.1-0.15.fc40                 fedora      38.1 MiB
 gcc-gfortran                x86_64 14.0.1-0.15.fc40                 fedora      37.2 MiB
 gcc-plugin-annobin          x86_64 14.0.1-0.15.fc40                 fedora      57.1 KiB
 gettext                     x86_64 0.22.5-2.fc40                    fedora       5.2 MiB
 gettext-envsubst            x86_64 0.22.5-2.fc40                    fedora      74.9 KiB
 gettext-libs                x86_64 0.22.5-2.fc40                    fedora       1.7 MiB
 gettext-runtime             x86_64 0.22.5-2.fc40                    fedora     481.3 KiB
 glib2                       x86_64 2.80.0-1.fc40                    fedora      14.4 MiB
 glib2-devel                 x86_64 2.80.0-1.fc40                    fedora      15.4 MiB
 glibc-devel                 x86_64 2.39-8.fc40                      updates     36.3 KiB
 glibc-headers-x86           noarch 2.39-8.fc40                      updates      2.2 MiB
 gnutls                      x86_64 3.8.5-1.fc40                     updates      3.2 MiB
 google-noto-fonts-common    noarch 20240301-2.fc40                  fedora      17.5 KiB
 google-noto-sans-vf-fonts   noarch 20240301-2.fc40                  fedora       1.2 MiB
 graphite2                   x86_64 1.3.14-15.fc40                   fedora     192.0 KiB
 graphite2-devel             x86_64 1.3.14-15.fc40                   fedora      49.1 KiB
 guile30                     x86_64 3.0.7-12.fc40                    fedora      51.5 MiB
 harfbuzz                    x86_64 8.3.0-5.fc40                     fedora       2.6 MiB
 harfbuzz-devel              x86_64 8.3.0-5.fc40                     fedora       5.1 MiB
 harfbuzz-icu                x86_64 8.3.0-5.fc40                     fedora      15.5 KiB
 java-21-openjdk             x86_64 1:21.0.2.0.13-3.fc40             fedora       1.1 MiB
 java-21-openjdk-devel       x86_64 1:21.0.2.0.13-3.fc40             fedora      11.2 MiB
 java-21-openjdk-headless    x86_64 1:21.0.2.0.13-3.fc40             fedora     204.9 MiB
 javapackages-filesystem     noarch 6.2.0-9.fc40                     fedora       1.9 KiB
 jbigkit-libs                x86_64 2.1-29.fc40                      fedora     117.6 KiB
 kernel-headers              x86_64 6.8.3-300.fc40                   fedora       6.2 MiB
 libICE                      x86_64 1.1.1-3.fc40                     fedora     181.2 KiB
 libRmath                    x86_64 4.4.0-1.fc40~bootstrap           copr_base  242.8 KiB
 libRmath-devel              x86_64 4.4.0-1.fc40~bootstrap           copr_base   17.4 KiB
 libSM                       x86_64 1.2.4-3.fc40                     fedora      97.3 KiB
 libX11                      x86_64 1.8.9-1.fc40                     updates      1.3 MiB
 libX11-common               noarch 1.8.9-1.fc40                     updates      1.1 MiB
 libX11-devel                x86_64 1.8.9-1.fc40                     updates      1.0 MiB
 libX11-xcb                  x86_64 1.8.9-1.fc40                     updates     15.0 KiB
 libXau                      x86_64 1.0.11-6.fc40                    fedora      66.9 KiB
 libXau-devel                x86_64 1.0.11-6.fc40                    fedora       6.4 KiB
 libXcomposite               x86_64 0.4.6-3.fc40                     fedora      44.5 KiB
 libXext                     x86_64 1.3.6-1.fc40                     fedora      90.1 KiB
 libXft                      x86_64 2.3.8-6.fc40                     fedora     164.5 KiB
 libXft-devel                x86_64 2.3.8-6.fc40                     fedora      31.7 KiB
 libXi                       x86_64 1.8.1-5.fc40                     fedora      80.7 KiB
 libXmu                      x86_64 1.2.0-1.fc40                     updates    186.4 KiB
 libXrender                  x86_64 0.9.11-6.fc40                    fedora      50.1 KiB
 libXrender-devel            x86_64 0.9.11-6.fc40                    fedora      50.1 KiB
 libXt                       x86_64 1.3.0-3.fc40                     fedora     425.9 KiB
 libXtst                     x86_64 1.2.4-6.fc40                     fedora      33.6 KiB
 libb2                       x86_64 0.98.1-11.fc40                   fedora      42.2 KiB
 libblkid-devel              x86_64 2.40-13.fc40                     updates     44.9 KiB
 libdatrie                   x86_64 0.2.13-9.fc40                    fedora      57.9 KiB
 libffi-devel                x86_64 3.4.4-7.fc40                     fedora      33.3 KiB
 libfontenc                  x86_64 1.1.7-3.fc40                     fedora      65.0 KiB
 libgfortran                 x86_64 14.0.1-0.15.fc40                 fedora       2.9 MiB
 libicu                      x86_64 74.2-1.fc40                      fedora      34.9 MiB
 libicu-devel                x86_64 74.2-1.fc40                      fedora       5.6 MiB
 libjpeg-turbo               x86_64 3.0.2-1.fc40                     fedora     776.9 KiB
 liblerc                     x86_64 4.0.0-6.fc40                     fedora     603.5 KiB
 libmount-devel              x86_64 2.40-13.fc40                     updates     63.5 KiB
 libmpc                      x86_64 1.3.1-5.fc40                     fedora     164.7 KiB
 libpng                      x86_64 2:1.6.40-3.fc40                  fedora     241.8 KiB
 libpng-devel                x86_64 2:1.6.40-3.fc40                  fedora     881.5 KiB
 libquadmath                 x86_64 14.0.1-0.15.fc40                 fedora     325.9 KiB
 libquadmath-devel           x86_64 14.0.1-0.15.fc40                 fedora      21.8 KiB
 libselinux-devel            x86_64 3.6-4.fc40                       fedora     126.1 KiB
 libsepol-devel              x86_64 3.6-3.fc40                       fedora     120.2 KiB
 libstdc++-devel             x86_64 14.0.1-0.15.fc40                 fedora      15.4 MiB
 libthai                     x86_64 0.1.29-8.fc40                    fedora     783.5 KiB
 libtiff                     x86_64 4.6.0-2.fc40                     fedora       1.1 MiB
 libtirpc-devel              x86_64 1.3.4-1.rc3.fc40                 fedora     251.6 KiB
 libwebp                     x86_64 1.3.2-5.fc40                     fedora     793.6 KiB
 libxcb                      x86_64 1.16-4.fc40                      fedora       1.1 MiB
 libxcb-devel                x86_64 1.16-4.fc40                      fedora       2.7 MiB
 libxcrypt-devel             x86_64 4.4.36-5.fc40                    fedora      30.3 KiB
 libxml2-devel               x86_64 2.12.6-1.fc40                    updates      3.4 MiB
 lksctp-tools                x86_64 1.0.19-6.fc40                    fedora     269.6 KiB
 lua                         x86_64 5.4.6-5.fc40                     fedora     597.8 KiB
 lua-posix                   x86_64 36.2.1-6.fc40                    fedora     599.7 KiB
 make                        x86_64 1:4.4.1-6.fc40                   fedora       1.8 MiB
 mkfontscale                 x86_64 1.2.2-6.fc40                     fedora      49.2 KiB
 mpdecimal                   x86_64 2.5.1-9.fc40                     fedora     200.9 KiB
 nettle                      x86_64 3.9.1-6.fc40                     fedora     790.1 KiB
 nspr                        x86_64 4.35.0-22.fc40                   updates    312.6 KiB
 nss                         x86_64 3.99.0-1.fc40                    updates      1.9 MiB
 nss-softokn                 x86_64 3.99.0-1.fc40                    updates      1.9 MiB
 nss-softokn-freebl          x86_64 3.99.0-1.fc40                    updates    896.6 KiB
 nss-sysinit                 x86_64 3.99.0-1.fc40                    updates     18.2 KiB
 nss-util                    x86_64 3.99.0-1.fc40                    updates    226.1 KiB
 openblas                    x86_64 0.3.26-4.fc40                    fedora      96.0 KiB
 openblas-openmp             x86_64 0.3.26-4.fc40                    fedora      38.9 MiB
 openblas-openmp64           x86_64 0.3.26-4.fc40                    fedora      39.1 MiB
 pango                       x86_64 1.52.2-1.fc40                    updates    995.9 KiB
 pcre2-devel                 x86_64 10.42-2.fc40.2                   fedora       1.9 MiB
 pcre2-utf16                 x86_64 10.42-2.fc40.2                   fedora     570.2 KiB
 pcre2-utf32                 x86_64 10.42-2.fc40.2                   fedora     542.1 KiB
 pixman                      x86_64 0.43.0-3.fc40                    fedora     714.1 KiB
 python-pip-wheel            noarch 23.3.2-1.fc40                    fedora       1.5 MiB
 python3                     x86_64 3.12.2-2.fc40                    fedora      31.9 KiB
 python3-libs                x86_64 3.12.2-2.fc40                    fedora      41.0 MiB
 python3-packaging           noarch 23.2-4.fc40                      fedora     421.1 KiB
 sysprof-capture-devel       x86_64 46.0-1.fc40                      fedora     252.8 KiB
 tcl                         x86_64 1:8.6.13-2.fc40                  fedora       4.2 MiB
 tcl-devel                   x86_64 1:8.6.13-2.fc40                  fedora     809.0 KiB
 tk                          x86_64 1:8.6.13-3.fc40                  fedora       3.6 MiB
 tk-devel                    x86_64 1:8.6.13-3.fc40                  fedora     983.9 KiB
 tre                         x86_64 0.8.0-43.20140228gitc2f5d13.fc40 fedora      75.9 KiB
 tre-common                  noarch 0.8.0-43.20140228gitc2f5d13.fc40 fedora      81.0 KiB
 tre-devel                   x86_64 0.8.0-43.20140228gitc2f5d13.fc40 fedora      10.7 KiB
 ttmkfdir                    x86_64 3.0.9-70.fc40                    fedora     122.7 KiB
 tzdata                      noarch 2024a-5.fc40                     updates      1.6 MiB
 tzdata-java                 noarch 2024a-5.fc40                     updates    101.7 KiB
 xdg-utils                   noarch 1.2.1-1.fc40                     fedora     346.3 KiB
 xml-common                  noarch 0.6.3-63.fc40                    fedora      78.4 KiB
 xorg-x11-fonts-Type1        noarch 7.5-38.fc40                      fedora     863.3 KiB
 xorg-x11-proto-devel        noarch 2024.1-1.fc40                    updates      1.7 MiB
 xz-devel                    x86_64 1:5.4.6-3.fc40                   fedora     255.8 KiB
 zlib-ng-compat-devel        x86_64 2.1.6-2.fc40                     fedora     103.4 KiB

Transaction Summary:
 Installing:      161 packages

Total size of inbound packages is 287 MiB. Need to download 1 MiB.
After this operation 934 MiB will be used (install 934 MiB, remove 0 B).
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--------------------------------------------------------------------------------
[161/161] Total                         100% |   3.6 MiB/s |   1.1 MiB |  00m00s
Running transaction
[  1/163] Verify package files          100% | 157.0   B/s | 161.0   B |  00m01s
>>> Running pre-transaction scriptlet: copy-jdk-configs-0:4.1-5.fc40.noarch
>>> Stop pre-transaction scriptlet: copy-jdk-configs-0:4.1-5.fc40.noarch
>>> Running pre-transaction scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.
>>> Stop pre-transaction scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.fc4
[  2/163] Prepare transaction           100% |   1.2 KiB/s | 161.0   B |  00m00s
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[ 18/163] Installing xz-devel-1:5.4.6-3 100% | 253.8 MiB/s | 259.9 KiB |  00m00s
[ 19/163] Installing bzip2-devel-0:1.0. 100% | 303.5 MiB/s | 310.7 KiB |  00m00s
[ 20/163] Installing graphite2-0:1.3.14 100% | 189.6 MiB/s | 194.2 KiB |  00m00s
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[ 27/163] Installing libSM-0:1.2.4-3.fc 100% |  96.3 MiB/s |  98.6 KiB |  00m00s
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[ 31/163] Installing openblas-openmp-0: 100% | 607.8 MiB/s |  38.9 MiB |  00m00s
[ 32/163] Installing openblas-openmp64- 100% | 620.5 MiB/s |  39.1 MiB |  00m00s
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[ 41/163] Installing cpp-0:14.0.1-0.15. 100% | 384.1 MiB/s |  35.0 MiB |  00m00s
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[ 49/163] Installing expat-0:2.6.2-1.fc 100% |  69.1 MiB/s | 282.9 KiB |  00m00s
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[ 51/163] Installing libX11-xcb-0:1.8.9 100% |   0.0   B/s |  15.9 KiB |  00m00s
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[ 53/163] Installing python-pip-wheel-0 100% | 759.9 MiB/s |   1.5 MiB |  00m00s
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[ 60/163] Installing nss-0:3.99.0-1.fc4 100% | 146.1 MiB/s |   1.9 MiB |  00m00s
>>> Running post-install scriptlet: nss-0:3.99.0-1.fc40.x86_64
>>> Stop post-install scriptlet: nss-0:3.99.0-1.fc40.x86_64
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[ 93/163] Installing libXt-0:1.3.0-3.fc 100% | 208.6 MiB/s | 427.1 KiB |  00m00s
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[ 98/163] Installing pcre2-utf32-0:10.4 100% | 265.1 MiB/s | 543.0 KiB |  00m00s
[ 99/163] Installing pcre2-utf16-0:10.4 100% | 278.8 MiB/s | 571.0 KiB |  00m00s
[100/163] Installing pcre2-devel-0:10.4 100% | 275.3 MiB/s |   1.9 MiB |  00m00s
[101/163] Installing libselinux-devel-0 100% |  39.2 MiB/s | 160.6 KiB |  00m00s
[102/163] Installing libmount-devel-0:2 100% |  63.0 MiB/s |  64.5 KiB |  00m00s
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[104/163] Installing libtirpc-devel-0:1 100% | 128.4 MiB/s | 263.0 KiB |  00m00s
[105/163] Installing libfontenc-0:1.1.7 100% |  64.8 MiB/s |  66.4 KiB |  00m00s
[106/163] Installing google-noto-fonts- 100% |   0.0   B/s |  18.3 KiB |  00m00s
[107/163] Installing google-noto-sans-v 100% | 312.2 MiB/s |   1.2 MiB |  00m00s
[108/163] Installing default-fonts-core 100% |  17.8 MiB/s |  18.2 KiB |  00m00s
[109/163] Installing lua-posix-0:36.2.1 100% | 150.1 MiB/s | 614.7 KiB |  00m00s
[110/163] Installing copy-jdk-configs-0 100% |   0.0   B/s |  21.0 KiB |  00m00s
[111/163] Installing lksctp-tools-0:1.0 100% | 133.8 MiB/s | 274.0 KiB |  00m00s
[112/163] Installing javapackages-files 100% |   5.2 MiB/s |   5.3 KiB |  00m00s
[113/163] Installing alsa-lib-0:1.2.11- 100% | 231.2 MiB/s |   1.4 MiB |  00m00s
[114/163] Installing java-21-openjdk-he 100% | 441.7 MiB/s | 204.9 MiB |  00m00s
>>> Running post-install scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.fc4
>>> Stop post-install scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.fc40.x
[115/163] Installing gc-0:8.2.2-6.fc40. 100% |  63.8 MiB/s | 261.2 KiB |  00m00s
[116/163] Installing guile30-0:3.0.7-12 100% | 460.6 MiB/s |  51.6 MiB |  00m00s
[117/163] Installing make-1:4.4.1-6.fc4 100% | 225.0 MiB/s |   1.8 MiB |  00m00s
[118/163] Installing gcc-0:14.0.1-0.15. 100% | 419.4 MiB/s | 104.0 MiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
[119/163] Installing gcc-c++-0:14.0.1-0 100% | 392.9 MiB/s |  38.1 MiB |  00m00s
[120/163] Installing libquadmath-devel- 100% |  22.7 MiB/s |  23.2 KiB |  00m00s
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>>> Running pre-install scriptlet: xml-common-0:0.6.3-63.fc40.noarch
>>> Stop pre-install scriptlet: xml-common-0:0.6.3-63.fc40.noarch
[122/163] Installing xml-common-0:0.6.3 100% |  79.2 MiB/s |  81.1 KiB |  00m00s
[123/163] Installing tre-common-0:0.8.0 100% |  81.2 MiB/s |  83.1 KiB |  00m00s
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[126/163] Installing libwebp-0:1.3.2-5. 100% | 259.7 MiB/s | 797.7 KiB |  00m00s
[127/163] Installing liblerc-0:4.0.0-6. 100% | 295.4 MiB/s | 605.0 KiB |  00m00s
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[129/163] Installing libtiff-0:4.6.0-2. 100% | 279.9 MiB/s |   1.1 MiB |  00m00s
[130/163] Installing pixman-0:0.43.0-3. 100% | 349.2 MiB/s | 715.2 KiB |  00m00s
[131/163] Installing cairo-0:1.18.0-3.f 100% | 346.4 MiB/s |   1.7 MiB |  00m00s
[132/163] Installing harfbuzz-0:8.3.0-5 100% | 324.0 MiB/s |   2.6 MiB |  00m00s
[133/163] Installing freetype-0:2.13.2- 100% | 274.8 MiB/s | 844.3 KiB |  00m00s
[134/163] Installing fontconfig-0:2.15. 100% | 769.1 KiB/s | 786.0 KiB |  00m01s
>>> Running post-install scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
>>> Stop post-install scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
[135/163] Installing libXft-0:2.3.8-6.f 100% |  23.2 MiB/s | 166.0 KiB |  00m00s
>>> Running pre-install scriptlet: tk-1:8.6.13-3.fc40.x86_64
>>> Stop pre-install scriptlet: tk-1:8.6.13-3.fc40.x86_64
[136/163] Installing tk-1:8.6.13-3.fc40 100% | 191.6 MiB/s |   3.6 MiB |  00m00s
[137/163] Installing pango-0:1.52.2-1.f 100% |  48.9 MiB/s |   1.0 MiB |  00m00s
[138/163] Installing R-core-0:4.4.0-1.f 100% | 272.8 MiB/s | 102.9 MiB |  00m00s
[139/163] Installing R-littler-0:0.3.19 100% |  63.8 MiB/s | 196.0 KiB |  00m00s
[140/163] Installing R-CRAN-Rcpp-0:1.0. 100% | 282.5 MiB/s |   8.5 MiB |  00m00s
[141/163] Installing R-rpm-macros-0:1.2 100% |   0.0   B/s |   6.6 KiB |  00m00s
[142/163] Installing R-java-0:4.4.0-1.f 100% |   0.0   B/s | 124.0   B |  00m00s
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[146/163] Installing ttmkfdir-0:3.0.9-7 100% | 120.9 MiB/s | 123.8 KiB |  00m00s
[147/163] Installing xorg-x11-fonts-Typ 100% |  23.5 MiB/s | 865.6 KiB |  00m00s
>>> Running post-install scriptlet: xorg-x11-fonts-Type1-0:7.5-38.fc40.noarch
>>> Stop post-install scriptlet: xorg-x11-fonts-Type1-0:7.5-38.fc40.noarch
[148/163] Installing java-21-openjdk-1: 100% | 100.2 MiB/s |   1.1 MiB |  00m00s
>>> Running post-install scriptlet: java-21-openjdk-1:21.0.2.0.13-3.fc40.x86_64
>>> Stop post-install scriptlet: java-21-openjdk-1:21.0.2.0.13-3.fc40.x86_64
[149/163] Installing java-21-openjdk-de 100% | 401.4 MiB/s |  11.2 MiB |  00m00s
>>> Running post-install scriptlet: java-21-openjdk-devel-1:21.0.2.0.13-3.fc40.x
>>> Stop post-install scriptlet: java-21-openjdk-devel-1:21.0.2.0.13-3.fc40.x86_
[150/163] Installing harfbuzz-icu-0:8.3 100% |  15.9 MiB/s |  16.2 KiB |  00m00s
[151/163] Installing freetype-devel-0:2 100% | 413.5 MiB/s |   7.9 MiB |  00m00s
[152/163] Installing harfbuzz-devel-0:8 100% | 426.4 MiB/s |   5.1 MiB |  00m00s
[153/163] Installing fontconfig-devel-0 100% |  37.1 MiB/s | 151.9 KiB |  00m00s
[154/163] Installing libXft-devel-0:2.3 100% |  21.6 MiB/s |  44.3 KiB |  00m00s
[155/163] Installing tk-devel-1:8.6.13- 100% | 168.3 MiB/s |   1.0 MiB |  00m00s
[156/163] Installing R-core-devel-0:4.4 100% | 195.7 MiB/s | 400.7 KiB |  00m00s
[157/163] Installing R-java-devel-0:4.4 100% |   0.0   B/s | 124.0   B |  00m00s
[158/163] Installing R-devel-0:4.4.0-1. 100% |   0.0   B/s | 124.0   B |  00m00s
[159/163] Installing R-CRAN-RSpectra-0: 100% | 210.7 MiB/s |   1.3 MiB |  00m00s
[160/163] Installing R-CRAN-jsonlite-0: 100% | 392.7 MiB/s |   2.4 MiB |  00m00s
[161/163] Installing R-CRAN-naturalsort 100% |  28.0 MiB/s |  28.7 KiB |  00m00s
[162/163] Installing gcc-plugin-annobin 100% |   4.1 MiB/s |  58.6 KiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
[163/163] Installing annobin-plugin-gcc 100% |   1.8 MiB/s | 971.4 KiB |  00m01s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:286-1.fc40.noarch
>>> Running post-transaction scriptlet: crypto-policies-scripts-0:20240201-2.git
>>> Stop post-transaction scriptlet: crypto-policies-scripts-0:20240201-2.git9f5
>>> Running post-transaction scriptlet: nss-0:3.99.0-1.fc40.x86_64
>>> Stop post-transaction scriptlet: nss-0:3.99.0-1.fc40.x86_64
>>> Running post-transaction scriptlet: copy-jdk-configs-0:4.1-5.fc40.noarch
>>> Stop post-transaction scriptlet: copy-jdk-configs-0:4.1-5.fc40.noarch
>>> Running post-transaction scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3
>>> Stop post-transaction scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.fc
>>> Running post-transaction scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
>>> Stop post-transaction scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
>>> Running post-transaction scriptlet: java-21-openjdk-1:21.0.2.0.13-3.fc40.x86
>>> Stop post-transaction scriptlet: java-21-openjdk-1:21.0.2.0.13-3.fc40.x86_64
>>> Running post-transaction scriptlet: java-21-openjdk-devel-1:21.0.2.0.13-3.fc
>>> Stop post-transaction scriptlet: java-21-openjdk-devel-1:21.0.2.0.13-3.fc40.
>>> Running trigger-install scriptlet: glibc-common-0:2.39-8.fc40.x86_64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39-8.fc40.x86_64
>>> Running trigger-install scriptlet: info-0:7.1-2.fc40.x86_64
>>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.x86_64
>>> Running trigger-install scriptlet: glib2-0:2.80.0-1.fc40.x86_64
>>> Stop trigger-install scriptlet: glib2-0:2.80.0-1.fc40.x86_64
>>> Running trigger-install scriptlet: glib2-0:2.80.0-1.fc40.x86_64
>>> Stop trigger-install scriptlet: glib2-0:2.80.0-1.fc40.x86_64
>>> Running trigger-install scriptlet: desktop-file-utils-0:0.26-12.fc40.x86_64
>>> Stop trigger-install scriptlet: desktop-file-utils-0:0.26-12.fc40.x86_64
>>> Running trigger-install scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
>>> Stop trigger-install scriptlet: fontconfig-0:2.15.0-4.fc40.x86_64
Warning: skipped PGP checks for 13 package(s).
Finish: build setup for R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
Start: rpmbuild R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
warning: source_date_epoch_from_changelog set but %changelog is missing
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jk6XB7
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf castor
+ /usr/bin/mkdir -p castor
+ cd castor
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/castor_1.8.0.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ rm -rf /builddir/build/BUILD/castor-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/castor-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ find -type f -executable -exec grep -Iq . '{}' ';' -exec sed -i -e '$a\' '{}' ';'
+ '[' -d castor/src ']'
+ find castor/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';'
+ '[' -d castor/src ']'
+ find 'castor/src/Make*' -type f -exec sed -i s@-g0@@g '{}' ';'
find: ‘castor/src/Make*’: No such file or directory
+ true
+ find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' '{}' ';'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.QNpl80
+ umask 022
+ cd /builddir/build/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 -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 -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 -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 -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-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 castor
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.6ImV50
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
++ dirname /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
+ 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 -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 -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 -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 -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-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 castor
+ mkdir -p /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64/usr/local/lib/R/library
+ /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64/usr/local/lib/R/library castor
* installing *source* package ‘castor’ ...
** package ‘castor’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’
using C++ compiler: ‘g++ (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c STMathExpression.cpp -o STMathExpression.o
STMathExpression.cpp:10: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   10 | #pragma mark -
STMathExpression.cpp:11: warning: ignoring ‘#pragma mark String’ [-Wunknown-pragmas]
   11 | #pragma mark String manipulations
STMathExpression.cpp:12: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   12 | #pragma mark
STMathExpression.cpp:65: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   65 | #pragma mark -
STMathExpression.cpp:66: warning: ignoring ‘#pragma mark MathExpression’ [-Wunknown-pragmas]
   66 | #pragma mark MathExpression
STMathExpression.cpp:67: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   67 | #pragma mark
STMathExpression.cpp: In static member function ‘static long int MathExpression::splitBinaryOperatorInverseOrder(const std::string&, long int, long int, const std::vector<long int>&)’:
STMathExpression.cpp:256:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  256 |                                 else if(j==string::npos){ if(!STMath_isReal(expression.substr(0,i-1))) return getLeftMostOfPlusMinusOperatorChain(expression,start,i); }
      |                                         ~^~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘std::string MathExpression::parseBlock(const std::string&, long int, long int, const std::vector<long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, long int, bool)’:
STMathExpression.cpp:313:105: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  313 |         if(isWhiteSpace(expression,start,end)) return "Missing "+(start==0 ? "leading expression" : (end==expression.size()-1 ? "trailing expression" : "expression between '"+expression.substr(0,start)+"' and '"+expression.substr(end+1)+"'"));
      |                                                                                                      ~~~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:359:37: warning: comparison of integer expressions of different signedness: ‘const long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  359 |                 if((rightMostBracket==string::npos) || (rightMostBracket<start)){
      |                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:463:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  463 |         for(long i=0; i<expression.length(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findRoundBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:500:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  500 |         for(long i=0; i<expression.length(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘void MathExpression::printDebug(std::ostream&) const’:
STMathExpression.cpp:953:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  953 |         for(long i=0; i<variableValues.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:957:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  957 |         for(long i=0; i<stackValues.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&) const’:
STMathExpression.cpp:981:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  981 |                 if(variableIDs[i]>=x.size()){ variableValues[i]=0; }
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&, long int, ...) const’:
STMathExpression.cpp:1044:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘long unsigned int’ [-Wsign-compare]
 1044 |                 if(variableIDs[i]>=x.size()+numberOfAdditionalVariables){ variableValues[i]=0; }
STMathExpression.cpp:1045:39: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1045 |                 else if(variableIDs[i]<x.size()){ variableValues[i]=x[variableIDs[i]]; }
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariable(const std::string&) const’:
STMathExpression.cpp:1195:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1195 |         for(long i=0; i<variableNames.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariableWithPrefix(const std::string&) const’:
STMathExpression.cpp:1202:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1202 |         for(long i=0; i<variableNames.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::isValidName(const std::string&, std::string&)’:
STMathExpression.cpp:1258:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1258 |         for(long i=0; i<s.size(); ++i){
      |                       ~^~~~~~~~~
STMathExpression.cpp: In static member function ‘static std::string MathExpression::lowercase(std::string)’:
STMathExpression.cpp:1269:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1269 |         for(long n=0; n<s.length(); ++n){ s[n] = tolower(s[n]); }
      |                       ~^~~~~~~~~~~
STMathExpression.cpp: In function ‘Rcpp::List evaluate_univariate_expression_CPP(const std::string&, const std::string&, const std::vector<double>&)’:
STMathExpression.cpp:1378:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1378 |         for(long i=0; i<X.size(); ++i){
      |                       ~^~~~~~~~~
STMathExpression.cpp: In instantiation of ‘void MathExpression::printTuple(std::ostream&, const std::vector<T>&) const [with TYPE = long int; std::ostream = std::basic_ostream<char>]’:
STMathExpression.cpp:961:14:   required from here
STMathExpression.cpp:1378:24: warning:   961 |                         printTuple(stream, stackArguments[i]);
STMathExpression.cpp:1378:24: warning:       |                         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:1227:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1227 |         for(long i=0; i<components.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c phylogenetics_cpp_routines.cpp -o phylogenetics_cpp_routines.o
phylogenetics_cpp_routines.cpp:153: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  153 | #pragma mark -
phylogenetics_cpp_routines.cpp:154: warning: ignoring ‘#pragma mark Declarations’ [-Wunknown-pragmas]
  154 | #pragma mark Declarations
phylogenetics_cpp_routines.cpp:155: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  155 | #pragma mark
phylogenetics_cpp_routines.cpp:167: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  167 | #pragma mark -
phylogenetics_cpp_routines.cpp:168: warning: ignoring ‘#pragma mark Functions’ [-Wunknown-pragmas]
  168 | #pragma mark Functions for debugging
phylogenetics_cpp_routines.cpp:169: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  169 | #pragma mark
phylogenetics_cpp_routines.cpp:242: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  242 | #pragma mark -
phylogenetics_cpp_routines.cpp:243: warning: ignoring ‘#pragma mark Auxiliary’ [-Wunknown-pragmas]
  243 | #pragma mark Auxiliary functions
phylogenetics_cpp_routines.cpp:244: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  244 | #pragma mark
phylogenetics_cpp_routines.cpp:1416: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1416 | #pragma mark -
phylogenetics_cpp_routines.cpp:1417: warning: ignoring ‘#pragma mark Graphs’ [-Wunknown-pragmas]
 1417 | #pragma mark Graphs
phylogenetics_cpp_routines.cpp:1418: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1418 | #pragma mark
phylogenetics_cpp_routines.cpp:1563: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1563 | #pragma mark -
phylogenetics_cpp_routines.cpp:1564: warning: ignoring ‘#pragma mark Polynomials’ [-Wunknown-pragmas]
 1564 | #pragma mark Polynomials
phylogenetics_cpp_routines.cpp:1565: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1565 | #pragma mark
phylogenetics_cpp_routines.cpp:2902: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 2902 | #pragma mark -
phylogenetics_cpp_routines.cpp:2903: warning: ignoring ‘#pragma mark Integration’ [-Wunknown-pragmas]
 2903 | #pragma mark Integration, antiderivatives, derivatives
phylogenetics_cpp_routines.cpp:2904: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 2904 | #pragma mark
phylogenetics_cpp_routines.cpp:3407: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3407 | #pragma mark -
phylogenetics_cpp_routines.cpp:3408: warning: ignoring ‘#pragma mark Vectorized’ [-Wunknown-pragmas]
 3408 | #pragma mark Vectorized basic arithmetics
phylogenetics_cpp_routines.cpp:3409: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3409 | #pragma mark
phylogenetics_cpp_routines.cpp:3558: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3558 | #pragma mark -
phylogenetics_cpp_routines.cpp:3559: warning: ignoring ‘#pragma mark Random’ [-Wunknown-pragmas]
 3559 | #pragma mark Random numbers
phylogenetics_cpp_routines.cpp:3560: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3560 | #pragma mark
phylogenetics_cpp_routines.cpp:3954: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3954 | #pragma mark -
phylogenetics_cpp_routines.cpp:3955: warning: ignoring ‘#pragma mark Matrix’ [-Wunknown-pragmas]
 3955 | #pragma mark Matrix algebra
phylogenetics_cpp_routines.cpp:3956: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3956 | #pragma mark
phylogenetics_cpp_routines.cpp:7164: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 7164 | #pragma mark -
phylogenetics_cpp_routines.cpp:7165: warning: ignoring ‘#pragma mark Numerical’ [-Wunknown-pragmas]
 7165 | #pragma mark Numerical solvers
phylogenetics_cpp_routines.cpp:7166: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 7166 | #pragma mark
phylogenetics_cpp_routines.cpp:8577: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 8577 | #pragma mark -
phylogenetics_cpp_routines.cpp:8578: warning: ignoring ‘#pragma mark Time’ [-Wunknown-pragmas]
 8578 | #pragma mark Time series analysis
phylogenetics_cpp_routines.cpp:8579: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 8579 | #pragma mark
phylogenetics_cpp_routines.cpp:9984: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 9984 | #pragma mark -
phylogenetics_cpp_routines.cpp:9985: warning: ignoring ‘#pragma mark Class’ [-Wunknown-pragmas]
 9985 | #pragma mark Class: LinearInterpolationFunctor
phylogenetics_cpp_routines.cpp:9986: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 9986 | #pragma mark -
phylogenetics_cpp_routines.cpp:10464: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10464 | #pragma mark -
phylogenetics_cpp_routines.cpp:10465: warning: ignoring ‘#pragma mark Stochastic’ [-Wunknown-pragmas]
10465 | #pragma mark Stochastic processes
phylogenetics_cpp_routines.cpp:10466: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10466 | #pragma mark
phylogenetics_cpp_routines.cpp:10659: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10659 | #pragma mark -
phylogenetics_cpp_routines.cpp:10660: warning: ignoring ‘#pragma mark Deterministic’ [-Wunknown-pragmas]
10660 | #pragma mark Deterministic diversity dynamics
phylogenetics_cpp_routines.cpp:10661: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10661 | #pragma mark
phylogenetics_cpp_routines.cpp:11760: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11760 | #pragma mark -
phylogenetics_cpp_routines.cpp:11761: warning: ignoring ‘#pragma mark Building’ [-Wunknown-pragmas]
11761 | #pragma mark Building auxiliary data structures
phylogenetics_cpp_routines.cpp:11762: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11762 | #pragma mark
phylogenetics_cpp_routines.cpp:12445: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12445 | #pragma mark -
phylogenetics_cpp_routines.cpp:12446: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
12446 | #pragma mark Tree statistics
phylogenetics_cpp_routines.cpp:12447: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12447 | #pragma mark
phylogenetics_cpp_routines.cpp:14631: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14631 | #pragma mark -
phylogenetics_cpp_routines.cpp:14632: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
14632 | #pragma mark Generating & manipulating trees
phylogenetics_cpp_routines.cpp:14633: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14633 | #pragma mark
phylogenetics_cpp_routines.cpp:18025: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18025 | #pragma mark -
phylogenetics_cpp_routines.cpp:18026: warning: ignoring ‘#pragma mark Comparing’ [-Wunknown-pragmas]
18026 | #pragma mark Comparing trees
phylogenetics_cpp_routines.cpp:18027: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18027 | #pragma mark
phylogenetics_cpp_routines.cpp:18445: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18445 | #pragma mark -
phylogenetics_cpp_routines.cpp:18446: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
18446 | #pragma mark Tree dating
phylogenetics_cpp_routines.cpp:18447: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18447 | #pragma mark
phylogenetics_cpp_routines.cpp:18546: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18546 | #pragma mark -
phylogenetics_cpp_routines.cpp:18547: warning: ignoring ‘#pragma mark Plotting’ [-Wunknown-pragmas]
18547 | #pragma mark Plotting trees
phylogenetics_cpp_routines.cpp:18548: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18548 | #pragma mark
phylogenetics_cpp_routines.cpp:18643: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18643 | #pragma mark -
phylogenetics_cpp_routines.cpp:18644: warning: ignoring ‘#pragma mark Writing’ [-Wunknown-pragmas]
18644 | #pragma mark Writing/reading trees
phylogenetics_cpp_routines.cpp:18645: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18645 | #pragma mark
phylogenetics_cpp_routines.cpp:19134: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19134 | #pragma mark -
phylogenetics_cpp_routines.cpp:19135: warning: ignoring ‘#pragma mark Statistics’ [-Wunknown-pragmas]
19135 | #pragma mark Statistics of trait distribution
phylogenetics_cpp_routines.cpp:19136: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19136 | #pragma mark
phylogenetics_cpp_routines.cpp:20512: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20512 | #pragma mark -
phylogenetics_cpp_routines.cpp:20513: warning: ignoring ‘#pragma mark Most’ [-Wunknown-pragmas]
20513 | #pragma mark Most recent common ancestors
phylogenetics_cpp_routines.cpp:20514: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20514 | #pragma mark
phylogenetics_cpp_routines.cpp:20951: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20951 | #pragma mark -
phylogenetics_cpp_routines.cpp:20952: warning: ignoring ‘#pragma mark Ancestral’ [-Wunknown-pragmas]
20952 | #pragma mark Ancestral state reconstruction
phylogenetics_cpp_routines.cpp:20953: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20953 | #pragma mark
phylogenetics_cpp_routines.cpp:22664: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22664 | #pragma mark -
phylogenetics_cpp_routines.cpp:22665: warning: ignoring ‘#pragma mark MuSSE’ [-Wunknown-pragmas]
22665 | #pragma mark MuSSE model fitting
phylogenetics_cpp_routines.cpp:22666: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22666 | #pragma mark
phylogenetics_cpp_routines.cpp:23930: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
23930 | #pragma mark -
phylogenetics_cpp_routines.cpp:23931: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
23931 | #pragma mark Homogenous Birth-Death models
phylogenetics_cpp_routines.cpp:23932: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
23932 | #pragma mark
phylogenetics_cpp_routines.cpp:25388: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25388 | #pragma mark -
phylogenetics_cpp_routines.cpp:25389: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
25389 | #pragma mark Homogenous Birth-Death-Sampling model
phylogenetics_cpp_routines.cpp:25390: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25390 | #pragma mark
phylogenetics_cpp_routines.cpp:26499: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26499 | #pragma mark -
phylogenetics_cpp_routines.cpp:26500: warning: ignoring ‘#pragma mark Simulate’ [-Wunknown-pragmas]
26500 | #pragma mark Simulate models of trait evolution
phylogenetics_cpp_routines.cpp:26501: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26501 | #pragma mark
phylogenetics_cpp_routines.cpp:27013: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27013 | #pragma mark -
phylogenetics_cpp_routines.cpp:27014: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
27014 | #pragma mark Generating random trees via cladogenic models
phylogenetics_cpp_routines.cpp:27015: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27015 | #pragma mark
phylogenetics_cpp_routines.cpp:29679: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29679 | #pragma mark -
phylogenetics_cpp_routines.cpp:29680: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
29680 | #pragma mark Generating gene trees
phylogenetics_cpp_routines.cpp:29681: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29681 | #pragma mark
phylogenetics_cpp_routines.cpp:30928: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
30928 | #pragma mark -
phylogenetics_cpp_routines.cpp:30929: warning: ignoring ‘#pragma mark Spherical’ [-Wunknown-pragmas]
30929 | #pragma mark Spherical Brownian motion
phylogenetics_cpp_routines.cpp:30930: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
30930 | #pragma mark
phylogenetics_cpp_routines.cpp:32472: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32472 | #pragma mark -
phylogenetics_cpp_routines.cpp:32473: warning: ignoring ‘#pragma mark Loading’ [-Wunknown-pragmas]
32473 | #pragma mark Loading files
phylogenetics_cpp_routines.cpp:32474: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32474 | #pragma mark
phylogenetics_cpp_routines.cpp: In function ‘long int count_occurrences(const std::string&, char, bool)’:
phylogenetics_cpp_routines.cpp:334:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  334 |         for(long i=0; i<haystack.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void split_string(const std::string&, const std::string&, long int, std::vector<std::__cxx11::basic_string<char> >&)’:
phylogenetics_cpp_routines.cpp:357:46: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
  357 |         while((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                                  ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:359:23: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  359 |                 if(pos==string::npos) break;
      |                    ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:363:43: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
  363 |         if((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                               ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int find_first_non_nan(const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:460:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  460 |         for(long n=start; n<haystack.size(); ++n){
      |                           ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int vector_sum(const std::vector<char>&)’:
phylogenetics_cpp_routines.cpp:707:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  707 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double smallest_nonzero_step(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:722:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  722 |         for(long i=0; i<times.size(); ++i){
      |                       ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_mean(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:740:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  740 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_abs_mean(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:747:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  747 |         for(long i=0; i<values.size(); ++i) S += abs(values[i]);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_max_abs(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:776:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  776 |         for(long i=0; i<values.size(); ++i) A = max(A, abs(values[i]));
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void make_vector_positive(std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:807:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  807 |         for(long i=0; i<values.size(); ++i) values[i] = max(0.0, values[i]);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void replace_negatives(std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:812:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  812 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void replace_non_positives(std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:819:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  819 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void cap_values(double, double, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:829:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  829 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int vector_count_zeros(const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:882:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  882 |         for(long i=0; i<values.size(); ++i) S += (values[i]==0 ? 1 : 0);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘int taxon_descends(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&)’:
phylogenetics_cpp_routines.cpp:902:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
  902 |         for(long level=0; level<min(parent_taxonomy.size(),     child_taxonomy.size()); ++level){
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void remove_item_from_mapped_list(lvector&, lvector&, long int)’:
phylogenetics_cpp_routines.cpp:948:33: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘long int’} and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  948 |         if(pool2list[pool_index]==list2pool.size()-1){
phylogenetics_cpp_routines.cpp: In function ‘long int get_nearest_index(const std::vector<long int>&, long int)’:
phylogenetics_cpp_routines.cpp:976:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  976 |         for(long i=0; i<(haystack.size()-1); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List dense_binary_matrix_row2column_major_CPP(long int, long int, const Rcpp::List&, bool)’:
phylogenetics_cpp_routines.cpp:997:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  997 |                 for(long i=0; i<dense_row.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double sum_piecewise_polynomials(const std::vector<std::vector<double> >&, const lvector&, const dvector&, double, long int)’:
phylogenetics_cpp_routines.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1599 |         for(long i=0; i<Ydegrees.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector evaluate_spline_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::string&, long int)’:
phylogenetics_cpp_routines.cpp:2820:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2820 |         for(long t=0, g=-1; t<Xtarget.size(); ++t){
      |                             ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_antiderivative_CPP(const std::vector<double>&, double, const std::vector<double>&, long int, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:3260:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3260 |         for(long t=0, g=0; t<Xtarget.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_derivative_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:3287:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3287 |         for(long t=0, g=0, p; t<Xtarget.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void QR_linear_least_squares(double*, long int, long int, long int, long int, const double*, long int*, double*, double*, double*)’:
phylogenetics_cpp_routines.cpp:4484:17: warning: variable ‘info’ set but not used [-Wunused-but-set-variable]
 4484 |         long i, info, j, k;
      |                 ^~~~
phylogenetics_cpp_routines.cpp: In member function ‘void matrix_exponentiator::initialize(long int, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, double)’:
phylogenetics_cpp_routines.cpp:5835:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5835 |                         for(long r=0; r<eigenvalues.size(); ++r) eigenvalues[r] *= rescaling;
      |                                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void apply_approximate_RosenbrockEuler_exponential(long int, long int, const std::vector<double>&, const double&, const std::vector<double>&, const long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:5915:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5915 |         for(k=0; k<Y.size(); ++k) Y[k] = scaling*X[k];
      |                  ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double dot_product(const dvector&, const dvector&)’:
phylogenetics_cpp_routines.cpp:5947:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5947 |         for(long i=0; i<X.size(); ++i) S += X[i]*Y[i];
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void refine_piecewise_polynomial(long int, long int, const double*, const double*, bool, const dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:8860:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 8860 |         for(long ng=0, og=0; ng<newTimes.size(); ++ng){
      |                              ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void refine_piecewise_polynomial(long int, const dvector&, const dvector&, bool, const dvector&, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:8897:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 8897 |         for(long ng=0, og=0; ng<newTimes.size(); ++ng){
      |                              ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List monotonize_series_via_interpolation_CPP(const std::vector<double>&, std::vector<double>, bool, bool)’:
phylogenetics_cpp_routines.cpp:9941:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 9941 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9967:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 9967 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()’:
phylogenetics_cpp_routines.cpp:10929:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
10929 |                 for(long t=0; t<times.size(); ++t){
      |                               ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_cumulative_edge_lengths_per_node(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:12662:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12662 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_clade_ages(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const tree_traversal&, dvector&)’:
phylogenetics_cpp_routines.cpp:12791:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12791 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_closest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:12897:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12897 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12928:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12928 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_farthest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13016:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13016 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13047:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13047 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13075:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13075 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_farthest_tips_per_edge_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:13144:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13144 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13174:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13174 |         for(long q=0; q<traversal.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13266:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13266 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13286:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13286 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_distances_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13397:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13397 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13417:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13417 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List count_clades_at_regular_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int, double, double, bool, long int, bool)’:
phylogenetics_cpp_routines.cpp:13624:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13624 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector count_clades_at_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:13732:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13732 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_speciation_extinction_events_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:13889:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13889 |         for(long q=0; q<queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13913:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13913 |         for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13914:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13914 |         for(long c=0; c<omit_clades.size(); ++c) include_clade[omit_clades[c]] = false;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_relative_evolutionary_divergences(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:14066:45: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14066 |         for(long q=1, clade, pnode, cnode; q<traversal.queue.size(); ++q){
      |                                            ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double get_gamma_statistic_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:14324:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14324 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector extract_tip_neighborhood_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int)’:
phylogenetics_cpp_routines.cpp:14493:16: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14493 |         while(k<clade_queue.size()){
      |               ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector extract_deep_frame_CPP(long int, long int, long int, const std::vector<long int>&, long int)’:
phylogenetics_cpp_routines.cpp:14550:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14550 |         while(queue_pointer<clades.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14567:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14567 |         for(long c=0, clade; c<clades.size(); ++c){
      |                              ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_all_distances_to_tip_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:14615:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14615 |         for(long q=0; q<traversal.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_subtree_with_specific_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:15174:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15174 |         for(long c=0; c<clades_to_keep.size(); ++c){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15191:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15191 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int find_root_for_monophyletic_clade_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:16015:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16015 |         for(long t=0; t<target_tips.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16038:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16038 |         for(long q=1, cnode, pnode; q<traversal_queue_root2tips.size(); ++q){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:16145:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16145 |         for(long t=0, tip; t<target_tips.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16159:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16159 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16194:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16194 |                 for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List trim_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:16461:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16461 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List split_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double)’:
phylogenetics_cpp_routines.cpp:16571:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16571 |                 for(long q=0; q<traversal.queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List merge_nodes_to_multifurcations_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool)’:
phylogenetics_cpp_routines.cpp:16911:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16911 |                 for(long n=0, node; n<nodes_to_merge.size(); ++n){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16921:49: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16921 |                 for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
      |                                                ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16985:89: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16985 |         for(long q=0, clade, node, absorbing_ancestor, parent, child, e, edge, inedge; q<traversal.queue.size(); ++q){
      |                                                                                        ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List shift_clade_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:17082:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17082 |         for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17105:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17105 |                 for(long q=1, clade, node, inedge, e; q<traversal.queue.size(); ++q){
      |                                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17139:47: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17139 |                 for(long q=1, clade, inedge; q<traversal.queue.size(); ++q){
      |                                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void assign_clades_to_taxa(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:17475:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17475 |         for(long q=0, clade; q<traversal_queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List place_tips_taxonomically_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, bool)’:
phylogenetics_cpp_routines.cpp:17954:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17954 |                 for(long f=0; f<fits.size(); ++f){
      |                               ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17955:66: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
17955 |                         if(clade_taxonomies_split[fits[f]].size()==max_precision) precise_fits.push_back(fits[f]);
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List tree_from_placements_CPP(long int, long int, long int, std::vector<long int>, std::vector<double>, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:17991:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17991 |         for(long i=0; i<tree_edge.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List congruify_trees_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18189:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18189 |         for(long m=0, Tnode, Rnode; m<mapped_Tnodes.size(); ++m){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_Robinson_Foulds_distance_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18419:60: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18419 |                                 for(long fb=0, fa=-1, f; fb<membershipsB[nodeB].size(); ++fb){
      |                                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> relative_to_absolute_node_ages_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:18475:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18475 |         for(long q=1, clade, node, pnode; q<traversal_queue.size(); ++q){
      |                                           ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> propagate_min_ages_upstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18499:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18499 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> propagate_max_ages_downstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18528:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18528 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18533:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18533 |         for(long q=0, clade, node, pnode; q<traversal_queue.size(); ++q){
      |                                           ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_phylogram_geometry_CPP(long int, long int, long int, std::vector<long int>, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:18595:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18595 |         for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18612:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18612 |         for(long q=0, clade, node; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_get_trait_depth_consenTRAIT(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, bool, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, double&, double&, double&, double&, long int&, std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:19209:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19209 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_get_discrete_trait_depths(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, std::vector<long int>&, double&, double&, double&, double&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:19522:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19522 |         for(long q=0, dominant_state; q<traversal_queue.size(); ++q){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_mrca_defining_tips_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:20571:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20571 |         for(long q=0, parent; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector get_pairwise_ancestries_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:20642:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20642 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20648:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20648 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector get_most_recent_common_ancestors_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:20776:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20776 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20795:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20795 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool is_monophyletic_tip_set_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:20931:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20931 |         for(long t=0; t<focal_tips.size(); ++t) tip_is_focal[focal_tips[t]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List WMPR_ASR_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, double, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:21161:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21161 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_with_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const std::vector<double>&, const std::string&, const std::vector<double>&, bool, bool, double, double, long int, bool)’:
phylogenetics_cpp_routines.cpp:21523:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21523 |                 for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21564:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21564 |         for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
      |                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_fixed_rate_Markov_model_to_missing_clades_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, long int, Rcpp::LogicalVector, std::vector<double>, bool)’:
phylogenetics_cpp_routines.cpp:21968:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21968 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_attributes_to_descendants_CPP(long int, long int, long int, long int, const std::vector<long int>&, std::vector<long int>, std::vector<double>)’:
phylogenetics_cpp_routines.cpp:22024:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22024 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_via_squared_change_parsimony_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)’:
phylogenetics_cpp_routines.cpp:22198:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22198 |                 for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
      |                                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_via_independent_contrasts_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)’:
phylogenetics_cpp_routines.cpp:22459:30: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22459 |         if(node_states.size()>Nnodes) node_states.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22460:39: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22460 |         if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22461:29: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22461 |         if(node_CI95s.size()>Nnodes) node_CI95s.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_BM_parsimony_to_missing_clades_CPP(long int, long int, long int, const std::vector<long int>&, Rcpp::LogicalVector, std::vector<double>)’:
phylogenetics_cpp_routines.cpp:22502:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22502 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::operator()(double) const’:
phylogenetics_cpp_routines.cpp:22537:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22537 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::gradient(double) const’:
phylogenetics_cpp_routines.cpp:22556:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22556 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::Hessian(double) const’:
phylogenetics_cpp_routines.cpp:22576:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22576 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void MuSSEmodelD::registerState(double, const MuSSEstateD&)’:
phylogenetics_cpp_routines.cpp:22781:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22781 |                 for(long s=0; s<trajectory[i].size(); ++s) trajectory[i][s] = max(0.0, min(1.0, trajectory[i][s]));
      |                               ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void MuSSEmodelD::registerScaledState(double, const MuSSEstateD&, double)’:
phylogenetics_cpp_routines.cpp:22795:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22795 |                 for(long s=0; s<trajectory_shape[i].size(); ++s) trajectory_shape[i][s] = max(0.0, trajectory_shape[i][s]);
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, const MuSSEstateD&) const’:
phylogenetics_cpp_routines.cpp:22887:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22887 |                         for(long i=0; i<candidate_state.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, double, const MuSSEstateD&, double) const’:
phylogenetics_cpp_routines.cpp:22900:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22900 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22905:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22905 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double&, MuSSEstateD&, bool) const’:
phylogenetics_cpp_routines.cpp:22925:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22925 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22947:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22947 |                         for(long s=0; s<candidate_state.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double, double&, MuSSEstateD&, double&, bool) const’:
phylogenetics_cpp_routines.cpp:22970:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22970 |                 for(long s=0; s<candidateY.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22994:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22994 |                         for(long s=0; s<candidateY.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelE::checkShouldRefineTimeStep(double, const MuSSEstateE&, double, const MuSSEstateE&) const’:
phylogenetics_cpp_routines.cpp:23177:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23177 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double MuSSEmodelE::getRelativeChange(const MuSSEstateE&, const MuSSEstateE&) const’:
phylogenetics_cpp_routines.cpp:23190:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23190 |                 for(long s=0; s<stateA.size(); ++s){
      |                               ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelE::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateE&, double&, MuSSEstateE&, bool) const’:
phylogenetics_cpp_routines.cpp:23207:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23207 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23229:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23229 |                         for(long s=0; s<candidate_state.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool get_MuSSE_flow(long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, double, double, double, double, bool, std::vector<std::__cxx11::basic_string<char> >&, std::string&, double&, long int&, MuSSEmodelE&, MuSSEmodelD&, std::vector<LinearInterpolationFunctor<std::vector<double> > >&, std::vector<LinearInterpolationFunctor<double> >&)’:
phylogenetics_cpp_routines.cpp:23478:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23478 |         for(long a=0; a<ages.size(); ++a){
      |                       ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_deterministic_HBD_model_CPP(double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, std::vector<double>, const std::vector<double>&, double, double, double, double, long int, double, bool)’:
phylogenetics_cpp_routines.cpp:24303:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
24303 |                         for(long i=0; i<lambdas.size(); ++i) coarse_mus[i] = lambdas[i] * mu_over_lambda[i];
      |                                       ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26559:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26559 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26639:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26639 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_reflected_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26721:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26721 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_scalar_Brownian_motion_model_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26792:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26792 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_multivariate_Brownian_motion_model_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26872:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26872 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_neutral_gene_evolution_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26964:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26964 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_finalize_generated_random_tree(double, bool, bool, bool, const dvector&, const dvector&, const dvector&, long int&, long int&, long int&, long int&, double&, lvector&, dvector&, lvector&, lvector&, lvector&, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:27076:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27076 |         for(long i=0; i<sampled_tips.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27079:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27079 |         for(long i=0; i<sampled_node_clades.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27085:53: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
27085 |         if(only_sampled_tips && (sampled_tips.size()<Ntips)){
      |                                  ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:27122:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27122 |                 for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
      |                                       ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27128:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27128 |                 for(long i=0; i<sampled_tips.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27131:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27131 |                 for(long i=0; i<sampled_node_clades.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_CPP(long int, long int, double, double, double, double, double, double, double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:27217:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
27217 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp:27217:133: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27217 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                                                                                                   ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_HBDS_CPP(long int, long int, long int, long int, long int, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, double, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:27432:100: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27432 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                 ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27432:167: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27432 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                                                                                     ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27432:235: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27432 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                                                                                                                                                        ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27618:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27618 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27625:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27625 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27632:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27632 |         for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_BM_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:28286:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28286 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_OU_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:28480:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28480 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_Mk_rates_CPP(long int, long int, long int, double, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:28941:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28941 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28947:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28947 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28952:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28952 |         for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_tdSSE_CPP(long int, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, bool, long int, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:29620:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29620 |                 for(long stip=0; stip<extant_tips[state].size(); ++stip){
      |                                  ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_coalesce_genes(const std::vector<double>&, double, EdgeLengthUnit, double, double, long int, std::vector<long int>&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:29864:44: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29864 |                 if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29866:42: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29866 |                 if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29875:41: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29875 |         for(long orphan=0, clade; orphan<orphan_clades.size(); ++orphan){
      |                                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void add_edges_from_branching_heights(const std::vector<double>&, std::vector<long int>&, long int&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:29928:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29928 |                 if(clade_heights.size()<=next_clade) clade_heights.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool generate_gene_tree_in_species_tree_MSC(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, long int&, long int&, long int&, long int&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, std::string&)’:
phylogenetics_cpp_routines.cpp:29978:64: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
29978 |         const bool got_allele_counts    = (allele_counts.size()==NStips);
      |                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:29979:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
29979 |         const bool got_population_sizes = (population_sizes.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29980:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
29980 |         const bool got_generation_times = (generation_times.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29981:65: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
29981 |         const bool got_mutation_rates   = (mutation_rates.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30007:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30007 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30024:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30024 |                 for(allele=0; allele<gene_orphans[stip].size(); ++allele){
      |                               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30109:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30109 |                         for(long orphan=0; orphan<gene_orphans[root].size()-1; ++orphan){
      |                                            ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_gene_tree_in_species_tree_MSC_HGT_DL_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, bool, bool, double, double, bool)’:
phylogenetics_cpp_routines.cpp:30263:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30263 |         const bool got_population_sizes                 = (population_sizes.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30264:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30264 |         const bool got_generation_times                 = (generation_times.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30265:81: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30265 |         const bool got_mutation_rates                   = (mutation_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30266:80: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30266 |         const bool got_allele_counts                    = (allele_counts.size()==NStips);
      |                                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30267:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30267 |         const bool got_HGT_rates                                = (HGT_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30268:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30268 |         const bool got_duplication_rates                = (duplication_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30269:85: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30269 |         const bool got_loss_rates                               = (loss_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30290:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30290 |         for(long q=0; q<traversal.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30297:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30297 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30400:66: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30400 |                                 for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
      |                                                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30426:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30426 |                 for(long l=0, locus; l<clade_current_loci[mclade].size(); ++l){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, double, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:31245:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31245 |         for(long q=0, parent, child, e, edge; q<traversal.queue.size(); ++q){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_SBM_trajectory_CPP(const std::vector<double>&, double, double, double, double)’:
phylogenetics_cpp_routines.cpp:31361:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31361 |         for(long t=1; t<times.size(); ++t){
      |                       ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double Spherical_Brownian_Motion_LL::operator()(double) const’:
phylogenetics_cpp_routines.cpp:31834:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31834 |                 for(long p=0; p<time_steps.size(); ++p){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List SBM_LLs_of_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, long int)’:
phylogenetics_cpp_routines.cpp:31876:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31876 |         for(long d=0; d<diffusivities.size(); ++d){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List SBM_LLs_of_sampled_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, long int, const std::vector<double>&, double, long int)’:
phylogenetics_cpp_routines.cpp:31914:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31914 |         for(long d=0; d<diffusivities.size(); ++d){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double SBM_planar_diffusivity_estimate(const dvector&, const dvector&, const std::vector<char>&)’:
phylogenetics_cpp_routines.cpp:32076:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32076 |         for(long p=0; p<time_steps.size(); ++p){
      |                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List read_distances_list_CPP(const std::string&, const std::string&, const std::string&, long int, double, double, long int, long int, const std::string&)’:
phylogenetics_cpp_routines.cpp:32557:32: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32557 |                 if(parts.size()<=distances_column){
      |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32585:56: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32585 |                 if((max_Nedges>=0) && (distances.size()>=max_Nedges)) break;
      |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void multiply_array_with_scalar(ARRAY_TYPE&, double) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5326:29:   required from here
phylogenetics_cpp_routines.cpp:32585:56: warning:  5326 |                 multiply_array_with_scalar(A,factor);
phylogenetics_cpp_routines.cpp:32585:56: warning:       |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:580:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  580 |         for(long i=0; i<X.size(); ++i) X[i] *= scalar;
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘double get_norm_L2_of_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5521:34:   required from here
phylogenetics_cpp_routines.cpp:580:24: warning:  5521 |         epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
phylogenetics_cpp_routines.cpp:580:24: warning:       |                    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4927:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 4927 |         for(long i=0; i<X.size(); ++i) S += SQR(X[i]);
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘double get_norm_L2_of_inverted_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5521:77:   required from here
phylogenetics_cpp_routines.cpp:4927:24: warning:  5521 |         epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
phylogenetics_cpp_routines.cpp:4927:24: warning:       |                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4935:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 4935 |         for(long i=0; i<X.size(); ++i) S += SQR(1.0/X[i]);
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_sum(const std::vector<T>&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:8734:48:   required from here
phylogenetics_cpp_routines.cpp:4935:24: warning:  8734 |         const long NR = (end_c-start_c+1) + vector_sum(dN);
phylogenetics_cpp_routines.cpp:4935:24: warning:       |                                             ~~~~~~~~~~^~~~
phylogenetics_cpp_routines.cpp:692:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  692 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:8956:25:   required from here
phylogenetics_cpp_routines.cpp:692:24: warning:  8956 |         if(!LUsolveLinearSystem(        &matrix[0],
phylogenetics_cpp_routines.cpp:692:24: warning:       |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
    8957 |                                                         &scratchSpace[0],
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~~~~~~~~~~~~~~~~
    8958 |                                                         3,
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~
    8959 |                                                         &b[0],
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~~~~~
    8960 |                                                         epsilon*3,
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~~~~~~~~~
    8961 |                                                         5,
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~
    8962 |                                                         &sol[0])){
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4777:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4777 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4778:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4778 |                 for(j=0; j<N; ++j){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4793:87: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 4793 |                 while((errorInLinearSolution(matrix, N, b, x) > maxError) && (impCount<maxImprovements)){
      |                                                                              ~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool fitLeastSquares_affine_real_scalar(const std::vector<T>&, const std::vector<T>&, long int, long int, double, bool, bool, REAL_TYPE&, REAL_TYPE&, REAL_TYPE&, long int&) [with REAL_TYPE = double]’:
phylogenetics_cpp_routines.cpp:9326:40:   required from here
phylogenetics_cpp_routines.cpp:4793:87: warning:  9326 |                 if(fitLeastSquares_affine_real_scalar(X, logY, start, end, Xshift[n], false, false, A[n], rate[n], RSS, count[n])){
phylogenetics_cpp_routines.cpp:4793:87: warning:       |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9188:21: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
 9188 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |            ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9188:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
 9188 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |                               ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator*=(std::vector<T>&, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:9760:24:   required from here
phylogenetics_cpp_routines.cpp:9188:40: warning:  9760 |         Acoeff *= (Ngrid-1.0)/Aend;
phylogenetics_cpp_routines.cpp:9188:40: warning:       |                               ^~~~
phylogenetics_cpp_routines.cpp:3450:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3450 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_tree_traversal_root_to_tips(long int, long int, long int, long int, const ARRAY_TYPE&, bool, bool, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, bool, const std::string&) [with ARRAY_TYPE = std::vector<long int>; std::string = std::__cxx11::basic_string<char>]’:
phylogenetics_cpp_routines.cpp:12143:33:   required from here
phylogenetics_cpp_routines.cpp:3450:24: warning: 12143 |         get_tree_traversal_root_to_tips(Ntips,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
   12144 |                                                                         Nnodes,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~
   12145 |                                                                         Nedges,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~
   12146 |                                                                         -1,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~
   12147 |                                                                         tree_edge,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~~~~
   12148 |                                                                         include_tips,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~~~~~~~
   12149 |                                                                         false,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~
   12150 |                                                                         queue,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~
   12151 |                                                                         node2first_edge,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~~~~~~~~~~
   12152 |                                                                         node2last_edge,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~~~~~~~~~~
   12153 |                                                                         edges,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~
   12154 |                                                                         false,
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~~~~
   12155 |                                                                         "");
phylogenetics_cpp_routines.cpp:3450:24: warning:       |                                                                         ~~~
phylogenetics_cpp_routines.cpp:12116:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12116 |         while(queue_pointer<queue.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_max(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:12801:36:   required from here
phylogenetics_cpp_routines.cpp:12116:28: warning: 12801 |         const double root_age = vector_max(ages);
phylogenetics_cpp_routines.cpp:12116:28: warning:       |                                 ~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:770:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  770 |         for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void qsortIndices(const std::vector<T>&, std::vector<long int>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:13898:14:   required from here
phylogenetics_cpp_routines.cpp:770:24: warning: 13898 |         qsortIndices(distances_from_root, chronological_clade_order);
phylogenetics_cpp_routines.cpp:770:24: warning:       |         ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:1071:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1071 |         for(long n=0; n<sortedIndices.size(); ++n) sortedIndices[n] = n;
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_max(const std::vector<T>&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:14197:33:   required from here
phylogenetics_cpp_routines.cpp:1071:24: warning: 14197 |         const long Nsplits = vector_max(node2child_count);
phylogenetics_cpp_routines.cpp:1071:24: warning:       |                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:770:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  770 |         for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void sort_tree_edges_root_to_tips(long int, long int, long int, bool, bool, const ARRAY_TYPE&, std::vector<long int>&) [with ARRAY_TYPE = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:14866:30:   required from here
phylogenetics_cpp_routines.cpp:770:24: warning: 14866 |         sort_tree_edges_root_to_tips(   Ntips,
phylogenetics_cpp_routines.cpp:770:24: warning:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
   14867 |                                                                         Nnodes,
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~
   14868 |                                                                         Nedges,
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~
   14869 |                                                                         depth_first_search,
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~~~~~~~~~~~~~
   14870 |                                                                         root_to_tips,
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~~~~~~~
   14871 |                                                                         tree_edge,
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~~~~
   14872 |                                                                         new2old_edge);
phylogenetics_cpp_routines.cpp:770:24: warning:       |                                                                         ~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14838:36: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14838 |                 while(queue_pointer<scratch_queue.size()){
      |                       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_tree_with_collapsed_monofurcations(long int, long int, long int, long int, bool, const lvector&, const ARRAY_INT&, const ARRAY_DOUBLE&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:15102:40:   required from here
phylogenetics_cpp_routines.cpp:14838:36: warning: 15102 |         get_tree_with_collapsed_monofurcations( Ntips,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
   15103 |                                                                                         Nnodes,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~
   15104 |                                                                                         Nedges,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~
   15105 |                                                                                         root,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~
   15106 |                                                                                         force_keep_root,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~~~~~
   15107 |                                                                                         force_keep_nodes,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~~~~~~
   15108 |                                                                                         tree_edge,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~
   15109 |                                                                                         edge_length,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~
   15110 |                                                                                         new_tree_edge,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~~~
   15111 |                                                                                         new_edge_length,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~~~~~
   15112 |                                                                                         new2old_node,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~~~
   15113 |                                                                                         new_root,
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~
   15114 |                                                                                         root_shift);
phylogenetics_cpp_routines.cpp:14838:36: warning:       |                                                                                         ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14998:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14998 |         for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
      |                              ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15012:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15012 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15035:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15035 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_subtree_with_specific_tips(long int, long int, long int, const ARRAY_INT&, const ARRAY_DOUBLE&, const ARRAY_INT&, bool, bool, const lvector&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, long int&, long int&, long int&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:15714:32:   required from here
phylogenetics_cpp_routines.cpp:15035:24: warning: 15714 |         get_subtree_with_specific_tips( Ntips,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
   15715 |                                                                         Nnodes,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~
   15716 |                                                                         Nedges,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~
   15717 |                                                                         tree_edge,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~
   15718 |                                                                         edge_length,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~
   15719 |                                                                         tips_to_keep,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~
   15720 |                                                                         collapse_monofurcations,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~~~~~~~~~~~
   15721 |                                                                         force_keep_root,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~~~
   15722 |                                                                         lvector(),
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~
   15723 |                                                                         new_tree_edge,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~
   15724 |                                                                         new_edge_length,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~~~
   15725 |                                                                         new2old_clade,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~
   15726 |                                                                         new_root,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~
   15727 |                                                                         old_stem_edge,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~~~
   15728 |                                                                         Ntips_kept,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~
   15729 |                                                                         Nnodes_kept,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~
   15730 |                                                                         Nedges_kept,
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~~
   15731 |                                                                         root_shift);
phylogenetics_cpp_routines.cpp:15035:24: warning:       |                                                                         ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15572:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15572 |         for(long t=0; t<tips_to_keep.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15575:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15575 |         for(long fn=0; fn<force_keep_nodes.size(); ++fn){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15648:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15648 |         for(long fn=0, new_clade; fn<force_keep_nodes.size(); ++fn){
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_distances_from_root(long int, long int, long int, const ARRAY_TYPE_INT&, const ARRAY_TYPE_D&, const tree_traversal&, dvector&) [with ARRAY_TYPE_INT = std::vector<long int>; ARRAY_TYPE_D = std::vector<double>; dvector = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:16941:26:   required from here
phylogenetics_cpp_routines.cpp:15648:37: warning: 16941 |                 get_distances_from_root(Ntips, Nnodes, Nedges, tree_edge, edge_length, traversal, clade_times);
phylogenetics_cpp_routines.cpp:15648:37: warning:       |                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12742:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12742 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘long int find_in_ascending_list(const std::vector<T>&, TYPE2, long int) [with TYPE1 = long int; TYPE2 = long int]’:
phylogenetics_cpp_routines.cpp:18421:33:   required from here
phylogenetics_cpp_routines.cpp:12742:31: warning: 18421 |                                         fa = find_in_ascending_list(membershipsA[nodeA],f,fa+1);
phylogenetics_cpp_routines.cpp:12742:31: warning:       |                                              ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:486:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  486 |         for(long n=start; n<haystack.size(); ++n){
      |                           ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator/(std::vector<T>, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22770:19:   required from here
phylogenetics_cpp_routines.cpp:486:28: warning: 22770 |                 shape = initial/initial_mean;
phylogenetics_cpp_routines.cpp:486:28: warning:       |                                 ^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3532:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3532 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(std::vector<T>, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22833:27:   required from here
phylogenetics_cpp_routines.cpp:3532:24: warning: 22833 |                                 rateY = YA - currentY*rateS;
phylogenetics_cpp_routines.cpp:3532:24: warning:       |                                                       ^~~~~
phylogenetics_cpp_routines.cpp:3432:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3432 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator-(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22833:27:   required from here
phylogenetics_cpp_routines.cpp:3432:24: warning: 22833 |                                 rateY = YA - currentY*rateS;
phylogenetics_cpp_routines.cpp:3432:24: warning:       |                                                       ^~~~~
phylogenetics_cpp_routines.cpp:3486:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3486 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator+(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22942:66:   required from here
phylogenetics_cpp_routines.cpp:3486:24: warning: 22942 |                         candidate_state = previous_state*(1-lambda) + candidate_state*lambda;
phylogenetics_cpp_routines.cpp:3486:24: warning:       |                                                                                       ^~~~~~
phylogenetics_cpp_routines.cpp:3459:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3459 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool contains_nan(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23006:22:   required from here
phylogenetics_cpp_routines.cpp:3459:24: warning: 23006 |                 return contains_nan(state);
phylogenetics_cpp_routines.cpp:3459:24: warning:       |                        ~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:865:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  865 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator*=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23366:32:   required from here
phylogenetics_cpp_routines.cpp:865:24: warning: 23366 |                                 posteriors[node] *= modelD.initial;
phylogenetics_cpp_routines.cpp:865:24: warning:       |                                                            ^~~~~~~
phylogenetics_cpp_routines.cpp:3423:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3423 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_sum(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23387:30:   required from here
phylogenetics_cpp_routines.cpp:3423:24: warning: 23387 |                 const double S = vector_sum(posteriors[node]);
phylogenetics_cpp_routines.cpp:3423:24: warning:       |                                  ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:692:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  692 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator/=(std::vector<T>&, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23388:23:   required from here
phylogenetics_cpp_routines.cpp:692:24: warning: 23388 |                 posteriors[node] /= S;
phylogenetics_cpp_routines.cpp:692:24: warning:       |                                     ^
phylogenetics_cpp_routines.cpp:3541:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3541 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23396:56:   required from here
phylogenetics_cpp_routines.cpp:3541:24: warning: 23396 |         loglikelihood += log(vector_sum(posteriors[root_node]*root_prior));
phylogenetics_cpp_routines.cpp:3541:24: warning:       |                                                               ^~~~~~~~~~
phylogenetics_cpp_routines.cpp:3414:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3414 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE scalar_product(const std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23906:38:   required from here
phylogenetics_cpp_routines.cpp:3414:24: warning: 23906 |                 loglikelihood += log(scalar_product(substem_D,substem_prior));
phylogenetics_cpp_routines.cpp:3414:24: warning:       |                                      ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:715:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
  715 |         for(long i=0; i<min(A.size(),B.size()); ++i) S += A[i] * B[i];
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator-=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:24305:83:   required from here
phylogenetics_cpp_routines.cpp:715:24: warning: 24305 |                 dvector coarse_diversification_rates = lambdas; coarse_diversification_rates -= mus;
phylogenetics_cpp_routines.cpp:715:24: warning:       |                                                                                                 ^~~
phylogenetics_cpp_routines.cpp:3504:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3504 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> abs(std::vector<T>) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:24925:48:   required from here
phylogenetics_cpp_routines.cpp:3504:24: warning: 24925 |         dvector coarse_abs_diversification_rates = abs(coarse_diversification_rates);
phylogenetics_cpp_routines.cpp:3504:24: warning:       |                                                    ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3550:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3550 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs() const [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:25417:26:   required from here
phylogenetics_cpp_routines.cpp:3550:24: warning: 25417 |                 return lambda.getMaxAbs() + mu.getMaxAbs() + psi.getMaxAbs();
phylogenetics_cpp_routines.cpp:3550:24: warning:       |                        ~~~~~~~~~~~~~~~~^~
phylogenetics_cpp_routines.cpp:2646:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2646 |                 for(long i=0; i<X.size()-1; ++i){
      |                               ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs(double, double) const [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:25422:26:   required from here
phylogenetics_cpp_routines.cpp:2646:32: warning: 25422 |                 return lambda.getMaxAbs(start_time,end_time) + mu.getMaxAbs(start_time,end_time) + psi.getMaxAbs(start_time,end_time);
phylogenetics_cpp_routines.cpp:2646:32: warning:       |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:2657:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2657 |                 for(long i=0; i<X.size()-1; ++i){
      |                               ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator+=(std::vector<T>&, const TYPE&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:25845:20:   required from here
phylogenetics_cpp_routines.cpp:2657:32: warning: 25845 |                 NCSAcrossings += 1l;
phylogenetics_cpp_routines.cpp:2657:32: warning:       |                                  ^~
phylogenetics_cpp_routines.cpp:3477:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3477 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator-(std::vector<T>, const TYPE&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:27088:52:   required from here
phylogenetics_cpp_routines.cpp:3477:24: warning: 27088 |                 lvector force_keep_nodes = sampled_node_clades - Ntips;
phylogenetics_cpp_routines.cpp:3477:24: warning:       |                                                                  ^~~~~
phylogenetics_cpp_routines.cpp:3495:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3495 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void remove_item_from_vector(std::vector<T>&, long int) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:27554:27:   required from here
phylogenetics_cpp_routines.cpp:3495:24: warning: 27554 |                         remove_item_from_vector(extant_tips, tip);
phylogenetics_cpp_routines.cpp:3495:24: warning:       |                         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:918:17: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  918 |         if(index==list.size()-1){
      |            ~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, const DFUNCTOR&, double, double, dvector&, dvector&) [with DFUNCTOR = PiecewisePolynomial<double>; dvector = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:31394:22:   required from here
phylogenetics_cpp_routines.cpp:918:17: warning: 31394 |         simulate_SBM_on_tree(   Ntips,
phylogenetics_cpp_routines.cpp:918:17: warning:       |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
   31395 |                                                         Nnodes,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~
   31396 |                                                         Nedges,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~
   31397 |                                                         tree_edge,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~
   31398 |                                                         edge_length,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~~~
   31399 |                                                         radius,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~
   31400 |                                                         diffusivity_integral,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~~~~~~~~~~~~
   31401 |                                                         root_theta,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~~
   31402 |                                                         root_phi,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~
   31403 |                                                         clade_theta,
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~~~
   31404 |                                                         clade_phi);
phylogenetics_cpp_routines.cpp:918:17: warning:       |                                                         ~~~~~~~~~~
phylogenetics_cpp_routines.cpp:31296:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31296 |         for(long q=0, parent, child, e, edge; q<traversal.queue.size(); ++q){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4784:21:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
phylogenetics_cpp_routines.cpp:31296:48: warning:  4784 |         if(!LUDecomposition(scratchSpace, N, pivoting_indices, Psign)){
phylogenetics_cpp_routines.cpp:31296:48: warning:       |             ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8956:25:   required from here
phylogenetics_cpp_routines.cpp:31296:48: warning:  8956 |         if(!LUsolveLinearSystem(        &matrix[0],
phylogenetics_cpp_routines.cpp:31296:48: warning:       |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
    8957 |                                                         &scratchSpace[0],
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~~~~~~~~~~~~~~~~
    8958 |                                                         3,
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~
    8959 |                                                         &b[0],
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~~~~~
    8960 |                                                         epsilon*3,
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~~~~~~~~~
    8961 |                                                         5,
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~
    8962 |                                                         &sol[0])){
phylogenetics_cpp_routines.cpp:31296:48: warning:       |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4632:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4632 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4633:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4633 |                 for(j=0, big=0; j<N; ++j){
      |                                 ~^~
phylogenetics_cpp_routines.cpp:4642:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4642 |         for(j=0; j<N; ++j){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4649:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4649 |                 for(i=j; i<N; ++i){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4659:35: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4659 |                         for(k=0; k<N; ++k){
      |                                  ~^~
phylogenetics_cpp_routines.cpp:4671:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4671 |                 if(j < N-1){
      |                    ~~^~~~~
phylogenetics_cpp_routines.cpp:4673:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4673 |                         for(i=j+1; i<N; ++i){ matrix[i*N+j] *= dummyT; }
      |                                    ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void LUSolveLinearSystem(const TYPE*, long unsigned int, const long unsigned int*, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4789:21:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
phylogenetics_cpp_routines.cpp:4673:37: warning:  4789 |         LUSolveLinearSystem(scratchSpace, N, pivoting_indices, x);
phylogenetics_cpp_routines.cpp:4673:37: warning:       |         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8956:25:   required from here
phylogenetics_cpp_routines.cpp:4673:37: warning:  8956 |         if(!LUsolveLinearSystem(        &matrix[0],
phylogenetics_cpp_routines.cpp:4673:37: warning:       |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
    8957 |                                                         &scratchSpace[0],
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~~~~~~~~~~~~~~~~
    8958 |                                                         3,
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~
    8959 |                                                         &b[0],
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~~~~~
    8960 |                                                         epsilon*3,
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~~~~~~~~~
    8961 |                                                         5,
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~
    8962 |                                                         &sol[0])){
phylogenetics_cpp_routines.cpp:4673:37: warning:       |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4694:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4694 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4707:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4707 |                 for(j=i+1; j<N; ++j){ sum -= LUmatrix[i*N+j]*b[j]; }
      |                            ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void LUImproveSolutionToLinearSystem(const TYPE*, const TYPE*, long unsigned int, const long unsigned int*, const TYPE*, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4794:35:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
phylogenetics_cpp_routines.cpp:4707:29: warning:  4794 |                         LUImproveSolutionToLinearSystem(matrix, scratchSpace, N, pivoting_indices, b, x);
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8956:25:   required from here
phylogenetics_cpp_routines.cpp:4707:29: warning:  8956 |         if(!LUsolveLinearSystem(        &matrix[0],
phylogenetics_cpp_routines.cpp:4707:29: warning:       |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
    8957 |                                                         &scratchSpace[0],
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~~~~~~~~~~~~~~~~
    8958 |                                                         3,
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~
    8959 |                                                         &b[0],
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~~~~~
    8960 |                                                         epsilon*3,
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~~~~~~~~~
    8961 |                                                         5,
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~
    8962 |                                                         &sol[0])){
phylogenetics_cpp_routines.cpp:4707:29: warning:       |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4745:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4745 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4747:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4747 |                 for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
      |                          ~^~
phylogenetics_cpp_routines.cpp:4751:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4751 |         for(i=0; i<N; ++i){ x[i] -= r[i]; }
      |                  ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘long int find_first_occurrence(const std::vector<T>&, TYPE2) [with TYPE1 = double; TYPE2 = double]’:
phylogenetics_cpp_routines.cpp:5400:27:   required from ‘long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’
phylogenetics_cpp_routines.cpp:4751:19: warning:  5400 |                 if(find_first_occurrence(sum_of_powers, 0.0)<0) return (p+1);
phylogenetics_cpp_routines.cpp:4751:19: warning:       |                    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21465:94:   required from here
phylogenetics_cpp_routines.cpp:4751:19: warning: 21465 |                 const long min_polynomials = min_polynomials_for_positive_exponential_of_irreducible_matrix(Nstates, transition_matrix);
phylogenetics_cpp_routines.cpp:4751:19: warning:       |                                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:468:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  468 |         for(long n=0; n<haystack.size(); ++n){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(double, std::vector<T>) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:10194:64:   required from ‘LinearInterpolationFunctor<VALUE_TYPE>::LinearInterpolationFunctor(const std::vector<double>&, const std::vector<T>&, bool, const VALUE_TYPE&, const VALUE_TYPE&, bool, double) [with VALUE_TYPE = std::vector<double>]’
phylogenetics_cpp_routines.cpp:468:24: warning: 10194 |                         referenceValues[0] = referenceValues[referenceCount-1] = 0.5*(referenceValues[0] + referenceValues[referenceCount-1]);
phylogenetics_cpp_routines.cpp:468:24: warning:       |                                                                                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23339:141:   required from here
phylogenetics_cpp_routines.cpp:468:24: warning: 23339 |         modelD.E = LinearInterpolationFunctor<MuSSEstateE>(modelE.ages,modelE.trajectory,false,modelE.trajectory[0],modelE.trajectory.back(),true,0);
phylogenetics_cpp_routines.cpp:468:24: warning:       |                                                                                                                                                    ^
phylogenetics_cpp_routines.cpp:3441:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3441 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void linear_combination(double, const std::vector<T>&, double, const std::vector<T>&, std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:7458:21:   required from ‘bool RungeKutta2(double, double, double, MODEL&, double, double, double, double, long int, double, const PROGRESS_REPORTER&, double, std::string&) [with COORDINATE = std::vector<double>; MODEL = MuSSEmodelE; PROGRESS_REPORTER = ProgressReporter; std::string = std::__cxx11::basic_string<char>]’
phylogenetics_cpp_routines.cpp:3441:24: warning:  7458 |                 linear_combination(1.0,currentPoint,current_dt1,k1,point2); // point2 = currentPoint + k1*current_dt1;
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23441:9:   required from here
phylogenetics_cpp_routines.cpp:3441:24: warning: 23440 |         bool success = RungeKutta2<MuSSEstateE,MuSSEmodelE,ProgressReporter>
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23441 |                                                                 (0, // start_time
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ^~~~~~~~~~~~~~~~~
   23442 |                                                                 oldest_age, // end_time
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~
   23443 |                                                                 max(0.000001*oldest_age,min(0.2*oldest_age,relative_ODE_step/maxErate)), // default integration time step
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23444 |                                                                 modelE,
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~
   23445 |                                                                 minRecordingTimeStep,
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~
   23446 |                                                                 maxRecordingTimeStep,
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~
   23447 |                                                                 guessNrecordings,
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~
   23448 |                                                                 E_value_step,   // recordingRelValueStep
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23449 |                                                                 5,                              // maxTimeStepRefinements
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23450 |                                                                 4,                              // refinement_factor
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23451 |                                                                 ProgressReporter(true),
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~
   23452 |                                                                 (runtime_out_seconds>0 ? max(runtime_out_seconds*0.01, runtime_out_seconds+start_runtime-get_thread_monotonic_walltime_seconds()) : 0.0),
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   23453 |                                                                 warningMessage);
phylogenetics_cpp_routines.cpp:3441:24: warning:       |                                                                 ~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:431:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |         for(long i=0; i<X.size(); ++i) result[i] = a*X[i] + b*Y[i];
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘first_Wasserstein_distance_CPP(std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&)’:
phylogenetics_cpp_routines.cpp:1322:25: warning: ‘t1’ may be used uninitialized [-Wmaybe-uninitialized]
 1322 |                 W += (t2-t1) * abs(CDFY-CDFX);
      |                      ~~~^~~~
phylogenetics_cpp_routines.cpp:1306:32: note: ‘t1’ was declared here
 1306 |         double CDFX=0, CDFY=0, t1, t2;
      |                                ^~
phylogenetics_cpp_routines.cpp: In function ‘legendre_polynomial(long, double)’:
phylogenetics_cpp_routines.cpp:30948:16: warning: ‘Pn’ may be used uninitialized [-Wmaybe-uninitialized]
30948 |         return Pn;
      |                ^~
phylogenetics_cpp_routines.cpp:30942:16: note: ‘Pn’ was declared here
30942 |         double Pn;
      |                ^~
phylogenetics_cpp_routines.cpp: In function ‘solve_polynomial_via_bisection(double const*, long, double, double, double, double, double, double, long)’:
phylogenetics_cpp_routines.cpp:2260:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2260 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2206:36: note: ‘c’ was declared here
 2206 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘solve_piecewise_polynomial_bisection(std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, long, bool, double, double, double, bool, double, double, long, long&, long&)’:
phylogenetics_cpp_routines.cpp:2343:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2343 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2281:36: note: ‘c’ was declared here
 2281 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘solve_piecewise_polynomial_sum_bisection(std::vector<double, std::allocator<double> > const&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > const&, std::vector<long, std::allocator<long> > const&, bool, std::vector<double, std::allocator<double> > const&, double, double, double, bool, double, double, long, long&, long&)’:
phylogenetics_cpp_routines.cpp:2440:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2440 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2373:36: note: ‘c’ was declared here
 2373 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘get_dominant_eigenvalue(long, std::vector<double, std::allocator<double> > const&, long, double, std::vector<double, std::allocator<double> >&, double&)’:
phylogenetics_cpp_routines.cpp:6031:37: warning: ‘error’ may be used uninitialized [-Wmaybe-uninitialized]
 6031 |         return (best_error<tolerance);
      |                                     ^
phylogenetics_cpp_routines.cpp:5961:21: note: ‘error’ was declared here
 5961 |         double XAX, error, best_lambda=0, best_error=INFTY_D;
      |                     ^~~~~
In file included from /usr/include/c++/14/cmath:49,
                 from phylogenetics_cpp_routines.cpp:31:
In function ‘std::abs(double)’,
    inlined from ‘polynomial_bound_abs<double>(long, double const*, double, double)double’ at phylogenetics_cpp_routines.cpp:1738:17:
/usr/include/c++/14/bits/std_abs.h:72:30: warning: ‘Yvertex’ may be used uninitialized [-Wmaybe-uninitialized]
   72 |   { return __builtin_fabs(__x); }
      |                              ^
phylogenetics_cpp_routines.cpp: In function ‘polynomial_bound_abs<double>(long, double const*, double, double)double’:
phylogenetics_cpp_routines.cpp:1736:28: note: ‘Yvertex’ was declared here
 1736 |                 VALUE_TYPE Yvertex;
      |                            ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘LUDecomposition<double>(double*, unsigned long, unsigned long*, int&)bool’:
phylogenetics_cpp_routines.cpp:4658:17: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized]
 4658 |                 if(j != imax){
      |                 ^~
phylogenetics_cpp_routines.cpp:4626:16: note: ‘imax’ was declared here
 4626 |         long i,imax,j,k;
      |                ^~~~
phylogenetics_cpp_routines.cpp: In member function ‘TreeSpeciationExtinctionModel::get_coalescent_trajectory(double, double, std::vector<TreeStateHistory, std::allocator<TreeStateHistory> >&) const’:
phylogenetics_cpp_routines.cpp:10918:96: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
10918 |                                 coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
      |                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10895:59: note: ‘coalescent_diversity_at_resolution_age’ was declared here
10895 |                 double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘get_distance_matrix_between_clades_CPP(long, long, long, std::vector<long, std::allocator<long> > const&, std::vector<double, std::allocator<double> > const&, std::vector<long, std::allocator<long> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)’:
phylogenetics_cpp_routines.cpp:13326:155: warning: ‘mrca’ may be used uninitialized [-Wmaybe-uninitialized]
13326 |                         distances(i,j) = distance_from_root_per_clade[cladeA] + distance_from_root_per_clade[cladeB] - 2*distance_from_root_per_clade[mrca];
      |                                                                                                                                                           ^
phylogenetics_cpp_routines.cpp:13299:30: note: ‘mrca’ was declared here
13299 |         long cladeA, cladeB, mrca;
      |                              ^~~~
phylogenetics_cpp_routines.cpp: In function ‘get_trait_richness_collectors_curve_CPP(long, long, long, long, long, std::vector<long, std::allocator<long> > const&, std::vector<double, std::allocator<double> > const&, std::vector<long, std::allocator<long> > const&, std::vector<long, std::allocator<long> > const&, std::vector<long, std::allocator<long> > const&, std::vector<long, std::allocator<long> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)’:
phylogenetics_cpp_routines.cpp:20142:49: warning: ‘tip’ may be used uninitialized [-Wmaybe-uninitialized]
20142 |                                 tip_included[tip] = true;
      |                                                 ^
phylogenetics_cpp_routines.cpp:20005:14: note: ‘tip’ was declared here
20005 |         long tip, clade, count_tips_remaining;
      |              ^~~
phylogenetics_cpp_routines.cpp:20102:76: warning: ‘count_tips_remaining’ may be used uninitialized [-Wmaybe-uninitialized]
20102 |                                         long tip_counter = uniformIntWithin(0,count_tips_remaining-1);
      |                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20005:26: note: ‘count_tips_remaining’ was declared here
20005 |         long tip, clade, count_tips_remaining;
      |                          ^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘HBD_PDR_loglikelihood_CPP(std::vector<double, std::allocator<double> > const&, double, double, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double, double, std::vector<double, std::allocator<double> >, long)’:
phylogenetics_cpp_routines.cpp:25186:102: warning: ‘Zdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25186 |                                 branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
      |                                                                                              ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25152:14: note: ‘Zdegree’ was declared here
25152 |         long Zdegree, EZdegree, Wdegree;
      |              ^~~~~~~
phylogenetics_cpp_routines.cpp:25187:102: warning: ‘Wdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25187 |                                 branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
      |                                                                                              ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25152:33: note: ‘Wdegree’ was declared here
25152 |         long Zdegree, EZdegree, Wdegree;
      |                                 ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘HBD_PSR_loglikelihood_CPP(std::vector<double, std::allocator<double> > const&, double, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double, double)’:
phylogenetics_cpp_routines.cpp:25359:51: warning: ‘W_degree’ may be used uninitialized [-Wmaybe-uninitialized]
25359 |         const double origin_W   = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
      |                                   ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25287:24: note: ‘W_degree’ was declared here
25287 |         long I_degree, W_degree, NRG;
      |                        ^~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘simulate_deterministic_diversity_growth_CPP(double, double, double, double, double, double, double, double, long, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, bool, std::vector<double, std::allocator<double> > const&, double, double, double, double, bool, bool, bool, bool, bool, bool, double)’:
phylogenetics_cpp_routines.cpp:11139:86: warning: ‘Pmissing_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11139 |                                 const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
      |                                                                                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11114:24: note: ‘Pmissing_at_resolution_age’ was declared here
11114 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11147:88: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11147 |                                 Pmissing = 1.0 - coalescent_diversity_at_resolution_age/total_diversities[t]; // effective Pmissing, based on coalescent and total diversity after collapsing and rarefaction
phylogenetics_cpp_routines.cpp:11114:87: note: ‘coalescent_diversity_at_resolution_age’ was declared here
11114 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘get_HBDS_model_loglikelihood_CPP(std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, double, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double, double, double)’:
phylogenetics_cpp_routines.cpp:25908:110: warning: ‘logPhi_degree’ may be used uninitialized [-Wmaybe-uninitialized]
25908 |                         CSA_logPhi       = polynomial_value(logPhi_degree, &logPhi_coeff[k][sg*(logPhi_degree+1)], age-(splines_slideX ? Phi_ages[k][sg] : 0.0));
      |                                                                                                ~~~~~~~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25794:42: note: ‘logPhi_degree’ was declared here
25794 |         long dummyL1, dummyL2, I_degree, logPhi_degree, E_degree;
      |                                          ^~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o castor.so RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64/usr/local/lib/R/library/00LOCK-castor/00new/castor/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘castor’
    finding HTML links ... done
    asr_empirical_probabilities             html  
    asr_independent_contrasts               html  
    asr_max_parsimony                       html  
    asr_mk_model                            html  
    asr_squared_change_parsimony            html  
    asr_subtree_averaging                   html  
    castor                                  html  
    clade_densities                         html  
    collapse_monofurcations                 html  
    collapse_tree_at_resolution             html  
    congruent_divergence_times              html  
    congruent_hbds_model                    html  
    consensus_taxonomies                    html  
    consentrait_depth                       html  
    correlate_phylo_geodistances            html  
    count_lineages_through_time             html  
    count_tips_per_node                     html  
    count_transitions_between_clades        html  
    date_tree_red                           html  
    discrete_trait_depth                    html  
    evaluate_spline                         html  
    expanded_tree_from_jplace               html  
    expected_distances_sbm                  html  
    exponentiate_matrix                     html  
    extend_tree_to_height                   html  
    extract_deep_frame                      html  
    extract_fasttree_constraints            html  
    extract_tip_neighborhood                html  
    extract_tip_radius                      html  
    find_farthest_tip_pair                  html  
    find_farthest_tips                      html  
    find_nearest_tips                       html  
    find_root                               html  
    find_root_of_monophyletic_tips          html  
    fit_and_compare_bm_models               html  
    fit_and_compare_sbm_const               html  
    fit_bm_model                            html  
    fit_hbd_model_on_grid                   html  
    fit_hbd_model_parametric                html  
    fit_hbd_pdr_on_best_grid_size           html  
    fit_hbd_pdr_on_grid                     html  
    fit_hbd_pdr_parametric                  html  
    fit_hbd_psr_on_best_grid_size           html  
    fit_hbd_psr_on_grid                     html  
    fit_hbd_psr_parametric                  html  
    fit_hbds_model_on_grid                  html  
    fit_hbds_model_parametric               html  
    fit_mk                                  html  
    fit_musse                               html  
    fit_sbm_const                           html  
    fit_sbm_geobiased_const                 html  
    fit_sbm_linear                          html  
    fit_sbm_on_grid                         html  
    fit_sbm_parametric                      html  
    fit_tree_model                          html  
    gamma_statistic                         html  
    generate_gene_tree_msc                  html  
    generate_gene_tree_msc_hgt_dl           html  
    generate_random_tree                    html  
    generate_tree_hbd_reverse               html  
    generate_tree_hbds                      html  
    generate_tree_with_evolving_rates       html  
    geographic_acf                          html  
    get_all_distances_to_root               html  
    get_all_distances_to_tip                html  
    get_all_node_depths                     html  
    get_all_pairwise_distances              html  
    get_ancestral_nodes                     html  
    get_clade_list                          html  
    get_independent_contrasts               html  
    get_independent_sister_tips             html  
    get_mrca_of_set                         html  
    get_pairwise_distances                  html  
    get_pairwise_mrcas                      html  
    get_random_diffusivity_matrix           html  
    get_random_mk_transition_matrix         html  
    get_reds                                html  
    get_stationary_distribution             html  
    get_subtree_at_node                     html  
    get_subtree_with_tips                   html  
    get_subtrees_at_nodes                   html  
    get_tips_for_mrcas                      html  
    get_trait_acf                           html  
    get_trait_stats_over_time               html  
    get_transition_index_matrix             html  
    get_tree_span                           html  
    get_tree_traversal_root_to_tips         html  
    hsp_binomial                            html  
    hsp_empirical_probabilities             html  
    hsp_independent_contrasts               html  
    hsp_max_parsimony                       html  
    hsp_mk_model                            html  
    hsp_nearest_neighbor                    html  
    hsp_squared_change_parsimony            html  
    hsp_subtree_averaging                   html  
    is_bifurcating                          html  
    is_monophyletic                         html  
    join_rooted_trees                       html  
    loglikelihood_hbd                       html  
    map_to_state_space                      html  
    mean_abs_change_scalar_ou               html  
    merge_nodes_to_multifurcations          html  
    merge_short_edges                       html  
    model_adequacy_hbd                      html  
    model_adequacy_hbds                     html  
    multifurcations_to_bifurcations         html  
    pick_random_tips                        html  
    place_tips_taxonomically                html  
    read_tree                               html  
    reconstruct_past_diversification        html  
    reorder_tree_edges                      html  
    root_at_midpoint                        html  
    root_at_node                            html  
    root_in_edge                            html  
    root_via_outgroup                       html  
    root_via_rtt                            html  
    shift_clade_times                       html  
    simulate_bm_model                       html  
    simulate_deterministic_hbd              html  
    simulate_deterministic_hbds             html  
    simulate_diversification_model          html  
    simulate_dsse                           html  
    simulate_mk_model                       html  
    simulate_ou_model                       html  
    simulate_rou_model                      html  
    simulate_sbm                            html  
    simulate_tdsse                          html  
    spline_coefficients                     html  
    split_tree_at_height                    html  
    tree_distance                           html  
    tree_from_branching_ages                html  
    tree_from_sampling_branching_ages       html  
    tree_imbalance                          html  
    trim_tree_at_height                     html  
    write_tree                              html  
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (castor)
+ test -d castor/src
+ cd castor/src
+ rm -f RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o castor.so
+ rm -f /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64/usr/local/lib/R/library/R.css
+ find /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64@@g '{}' ';'
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.8.0-1.fc40.copr7358077 --unique-debug-suffix -1.8.0-1.fc40.copr7358077.x86_64 --unique-debug-src-base R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/castor
find-debuginfo: starting
Extracting debug info from 1 files
DWARF-compressing 1 files
sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
3899 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
Provides: R-CRAN-castor = 1.8.0-1.fc40.copr7358077 R-CRAN-castor(x86-64) = 1.8.0-1.fc40.copr7358077
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.38)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: R-CRAN-castor-debugsource-1.8.0-1.fc40.copr7358077.x86_64
Provides: R-CRAN-castor-debugsource = 1.8.0-1.fc40.copr7358077 R-CRAN-castor-debugsource(x86-64) = 1.8.0-1.fc40.copr7358077
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-CRAN-castor-debuginfo-1.8.0-1.fc40.copr7358077.x86_64
Provides: R-CRAN-castor-debuginfo = 1.8.0-1.fc40.copr7358077 R-CRAN-castor-debuginfo(x86-64) = 1.8.0-1.fc40.copr7358077 debuginfo(build-id) = 463c789e941a6b3885f9a4b98e085fa3dfdd11c2
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-CRAN-castor-debugsource(x86-64) = 1.8.0-1.fc40.copr7358077
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
Wrote: /builddir/build/RPMS/R-CRAN-castor-debugsource-1.8.0-1.fc40.copr7358077.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-castor-debuginfo-1.8.0-1.fc40.copr7358077.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.kYNWzM
+ umask 022
+ cd /builddir/build/BUILD
+ cd castor
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-castor-1.8.0-1.fc40.copr7358077.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.y2UolW
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/castor-SPECPARTS
+ rm -rf castor castor.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0

RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
Finish: rpmbuild R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
Finish: build phase for R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-40-x86_64-1714166301.082308/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/R-CRAN-castor-1.8.0-1.fc40.copr7358077.src.rpm) Config(child) 1 minutes 40 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
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "R-CRAN-castor-debugsource",
            "epoch": null,
            "version": "1.8.0",
            "release": "1.fc40.copr7358077",
            "arch": "x86_64"
        },
        {
            "name": "R-CRAN-castor",
            "epoch": null,
            "version": "1.8.0",
            "release": "1.fc40.copr7358077",
            "arch": "src"
        },
        {
            "name": "R-CRAN-castor-debuginfo",
            "epoch": null,
            "version": "1.8.0",
            "release": "1.fc40.copr7358077",
            "arch": "x86_64"
        },
        {
            "name": "R-CRAN-castor",
            "epoch": null,
            "version": "1.8.0",
            "release": "1.fc40.copr7358077",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished