Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c14f' (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/7692640-fedora-39-x86_64 --chroot fedora-39-x86_64


Version: 0.73
PID: 7193
Logging PID: 7194
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'bootstrap': 'off',
 'build_id': 7692640,
 'buildroot_pkgs': [],
 'chroot': 'fedora-39-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '7e7ef52150f2e3aa8c22d20fbe2fba93d4ec16f0',
 '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': '1.8.2-1.copr7692640',
 'project_dirname': 'cran',
 'project_name': 'cran',
 'project_owner': 'iucar',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/iucar/cran/fedora-39-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': '7692640-fedora-39-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-nycz4ntb/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-nycz4ntb/R-CRAN-castor', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor'...

Running: git checkout 7e7ef52150f2e3aa8c22d20fbe2fba93d4ec16f0 --

cmd: ['git', 'checkout', '7e7ef52150f2e3aa8c22d20fbe2fba93d4ec16f0', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor
rc: 0
stdout: 
stderr: Note: switching to '7e7ef52150f2e3aa8c22d20fbe2fba93d4ec16f0'.

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 7e7ef52 automatic import of R-CRAN-castor

Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/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_1.8.2.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o castor_1.8.2.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_1.8.2.tar.gz/md5/dcef37e53ef44e5e796ac957828176c2/castor_1.8.2.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  892k  100  892k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 10.2M
INFO: Reading stdout from command: md5sum castor_1.8.2.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor/R-CRAN-castor.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1719710865.390544 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor/R-CRAN-castor.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1719710865.390544 -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-nycz4ntb/R-CRAN-castor/R-CRAN-castor.spec)  Config(fedora-39-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1719710865.390544/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 dnf 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 dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered with an entitlement server. You can use subscription-manager to register.

Copr repository                                  46 MB/s |  26 MB     00:00    
fedora                                          907 kB/s |  89 MB     01:40    
updates                                          31 MB/s |  39 MB     00:01    
Last metadata expiration check: 0:00:05 ago on Sun Jun 30 01:29:52 2024.
Dependencies resolved.
================================================================================
 Package                       Arch   Version                     Repo     Size
================================================================================
Installing group/module packages:
 bash                          x86_64 5.2.26-1.fc39               updates 1.8 M
 bzip2                         x86_64 1.0.8-16.fc39               fedora   52 k
 coreutils                     x86_64 9.3-5.fc39                  updates 1.1 M
 cpio                          x86_64 2.14-4.fc39                 fedora  279 k
 diffutils                     x86_64 3.10-3.fc39                 fedora  398 k
 fedora-release-common         noarch 39-36                       updates  19 k
 findutils                     x86_64 1:4.9.0-5.fc39              fedora  492 k
 gawk                          x86_64 5.2.2-2.fc39                fedora  1.1 M
 glibc-minimal-langpack        x86_64 2.38-18.fc39                updates  73 k
 grep                          x86_64 3.11-3.fc39                 fedora  298 k
 gzip                          x86_64 1.12-6.fc39                 fedora  166 k
 info                          x86_64 7.0.3-3.fc39                fedora  182 k
 patch                         x86_64 2.7.6-22.fc39               fedora  125 k
 redhat-rpm-config             noarch 266-1.fc39                  updates  78 k
 rpm-build                     x86_64 4.19.1.1-1.fc39             updates  78 k
 sed                           x86_64 4.8-14.fc39                 fedora  306 k
 shadow-utils                  x86_64 2:4.14.0-2.fc39             updates 1.3 M
 tar                           x86_64 2:1.35-2.fc39               fedora  864 k
 unzip                         x86_64 6.0-62.fc39                 fedora  184 k
 util-linux                    x86_64 2.39.4-1.fc39               updates 1.2 M
 which                         x86_64 2.21-40.fc39                fedora   42 k
 xz                            x86_64 5.4.4-1.fc39                fedora  556 k
Installing dependencies:
 alternatives                  x86_64 1.26-1.fc39                 updates  39 k
 ansible-srpm-macros           noarch 1-12.fc39                   updates  21 k
 audit-libs                    x86_64 3.1.3-1.fc39                updates 124 k
 authselect                    x86_64 1.4.3-1.fc39                fedora  149 k
 authselect-libs               x86_64 1.4.3-1.fc39                fedora  249 k
 basesystem                    noarch 11-18.fc39                  fedora  7.2 k
 binutils                      x86_64 2.40-14.fc39                updates 5.6 M
 binutils-gold                 x86_64 2.40-14.fc39                updates 795 k
 bzip2-libs                    x86_64 1.0.8-16.fc39               fedora   41 k
 ca-certificates               noarch 2023.2.60_v7.0.306-2.fc39   fedora  837 k
 coreutils-common              x86_64 9.3-5.fc39                  updates 2.1 M
 cracklib                      x86_64 2.9.11-2.fc39               fedora   94 k
 crypto-policies               noarch 20231204-1.git1e3a2e4.fc39  updates 100 k
 curl                          x86_64 8.2.1-5.fc39                updates 344 k
 cyrus-sasl-lib                x86_64 2.1.28-11.fc39              fedora  793 k
 debugedit                     x86_64 5.0-12.fc39                 updates  79 k
 dwz                           x86_64 0.15-3.fc39                 fedora  134 k
 ed                            x86_64 1.19-4.fc39                 fedora   79 k
 efi-srpm-macros               noarch 5-9.fc39                    fedora   22 k
 elfutils                      x86_64 0.191-2.fc39                updates 559 k
 elfutils-debuginfod-client    x86_64 0.191-2.fc39                updates  38 k
 elfutils-default-yama-scope   noarch 0.191-2.fc39                updates  13 k
 elfutils-libelf               x86_64 0.191-2.fc39                updates 209 k
 elfutils-libs                 x86_64 0.191-2.fc39                updates 263 k
 fedora-gpg-keys               noarch 39-2                        updates 130 k
 fedora-release                noarch 39-36                       updates 8.6 k
 fedora-release-identity-basic noarch 39-36                       updates 9.4 k
 fedora-repos                  noarch 39-2                        updates 9.3 k
 file                          x86_64 5.44-5.fc39                 fedora   49 k
 file-libs                     x86_64 5.44-5.fc39                 fedora  729 k
 filesystem                    x86_64 3.18-6.fc39                 fedora  1.1 M
 fonts-srpm-macros             noarch 1:2.0.5-12.fc39             fedora   26 k
 forge-srpm-macros             noarch 0.3.1-1.fc39                updates  19 k
 fpc-srpm-macros               noarch 1.3-8.fc39                  fedora  7.4 k
 gdb-minimal                   x86_64 14.2-1.fc39                 updates 4.3 M
 gdbm-libs                     x86_64 1:1.23-4.fc39               fedora   56 k
 ghc-srpm-macros               noarch 1.6.1-2.fc39                fedora  7.8 k
 glibc                         x86_64 2.38-18.fc39                updates 2.2 M
 glibc-common                  x86_64 2.38-18.fc39                updates 353 k
 glibc-gconv-extra             x86_64 2.38-18.fc39                updates 1.6 M
 gmp                           x86_64 1:6.2.1-5.fc39              fedora  313 k
 gnat-srpm-macros              noarch 6-3.fc39                    fedora  8.8 k
 go-srpm-macros                noarch 3.5.0-1.fc39                updates  28 k
 jansson                       x86_64 2.13.1-7.fc39               fedora   44 k
 kernel-srpm-macros            noarch 1.0-20.fc39                 fedora   10 k
 keyutils-libs                 x86_64 1.6.3-1.fc39                updates  31 k
 krb5-libs                     x86_64 1.21.2-3.fc39               updates 765 k
 libacl                        x86_64 2.3.1-9.fc39                updates  23 k
 libarchive                    x86_64 3.7.1-2.fc39                updates 407 k
 libattr                       x86_64 2.5.1-8.fc39                fedora   18 k
 libblkid                      x86_64 2.39.4-1.fc39               updates 116 k
 libbrotli                     x86_64 1.1.0-1.fc39                fedora  336 k
 libcap                        x86_64 2.48-9.fc39                 updates  68 k
 libcap-ng                     x86_64 0.8.3-8.fc39                fedora   32 k
 libcom_err                    x86_64 1.47.0-2.fc39               fedora   26 k
 libcurl                       x86_64 8.2.1-5.fc39                updates 322 k
 libdb                         x86_64 5.3.28-56.fc39              fedora  760 k
 libeconf                      x86_64 0.5.2-2.fc39                updates  30 k
 libevent                      x86_64 2.1.12-9.fc39               fedora  258 k
 libfdisk                      x86_64 2.39.4-1.fc39               updates 161 k
 libffi                        x86_64 3.4.4-4.fc39                fedora   40 k
 libgcc                        x86_64 13.3.1-1.fc39               updates 118 k
 libgomp                       x86_64 13.3.1-1.fc39               updates 328 k
 libidn2                       x86_64 2.3.7-1.fc39                updates 119 k
 libmount                      x86_64 2.39.4-1.fc39               updates 154 k
 libnghttp2                    x86_64 1.55.1-5.fc39               updates  75 k
 libnsl2                       x86_64 2.0.0-6.fc39                fedora   30 k
 libpkgconf                    x86_64 1.9.5-2.fc39                fedora   38 k
 libpsl                        x86_64 0.21.2-4.fc39               fedora   63 k
 libpwquality                  x86_64 1.4.5-6.fc39                fedora  120 k
 libselinux                    x86_64 3.5-5.fc39                  fedora   87 k
 libsemanage                   x86_64 3.5-4.fc39                  fedora  120 k
 libsepol                      x86_64 3.5-2.fc39                  fedora  324 k
 libsigsegv                    x86_64 2.14-5.fc39                 fedora   27 k
 libsmartcols                  x86_64 2.39.4-1.fc39               updates  67 k
 libssh                        x86_64 0.10.6-2.fc39               updates 212 k
 libssh-config                 noarch 0.10.6-2.fc39               updates 9.0 k
 libstdc++                     x86_64 13.3.1-1.fc39               updates 869 k
 libtasn1                      x86_64 4.19.0-3.fc39               fedora   74 k
 libtirpc                      x86_64 1.3.4-1.rc3.fc39            updates  93 k
 libtool-ltdl                  x86_64 2.4.7-7.fc39                fedora   36 k
 libunistring                  x86_64 1.1-5.fc39                  fedora  543 k
 libutempter                   x86_64 1.2.1-10.fc39               fedora   26 k
 libuuid                       x86_64 2.39.4-1.fc39               updates  28 k
 libverto                      x86_64 0.3.2-6.fc39                fedora   20 k
 libxcrypt                     x86_64 4.4.36-2.fc39               fedora  119 k
 libxml2                       x86_64 2.10.4-3.fc39               fedora  701 k
 libzstd                       x86_64 1.5.6-1.fc39                updates 312 k
 lua-libs                      x86_64 5.4.6-3.fc39                fedora  133 k
 lua-srpm-macros               noarch 1-13.fc39                   updates 8.7 k
 lz4-libs                      x86_64 1.9.4-4.fc39                fedora   67 k
 mpfr                          x86_64 4.2.0-3.fc39                fedora  344 k
 ncurses-base                  noarch 6.4-7.20230520.fc39.1       updates  88 k
 ncurses-libs                  x86_64 6.4-7.20230520.fc39.1       updates 336 k
 ocaml-srpm-macros             noarch 8-2.fc39                    fedora   14 k
 openblas-srpm-macros          noarch 2-14.fc39                   fedora  7.5 k
 openldap                      x86_64 2.6.7-1.fc39                updates 254 k
 openssl-libs                  x86_64 1:3.1.1-4.fc39              fedora  2.2 M
 p11-kit                       x86_64 0.25.3-1.fc39               updates 520 k
 p11-kit-trust                 x86_64 0.25.3-1.fc39               updates 140 k
 package-notes-srpm-macros     noarch 0.5-9.fc39                  fedora   11 k
 pam                           x86_64 1.5.3-3.fc39                updates 542 k
 pam-libs                      x86_64 1.5.3-3.fc39                updates  56 k
 pcre2                         x86_64 10.42-1.fc39.2              fedora  233 k
 pcre2-syntax                  noarch 10.42-1.fc39.2              fedora  143 k
 perl-srpm-macros              noarch 1-51.fc39                   fedora  8.0 k
 pkgconf                       x86_64 1.9.5-2.fc39                fedora   42 k
 pkgconf-m4                    noarch 1.9.5-2.fc39                fedora   14 k
 pkgconf-pkg-config            x86_64 1.9.5-2.fc39                fedora  9.6 k
 popt                          x86_64 1.19-3.fc39                 fedora   66 k
 publicsuffix-list-dafsa       noarch 20240107-1.fc39             updates  58 k
 pyproject-srpm-macros         noarch 1.12.0-1.fc39               updates  14 k
 python-srpm-macros            noarch 3.12-4.fc39                 fedora   25 k
 qt5-srpm-macros               noarch 5.15.13-1.fc39              updates 8.5 k
 qt6-srpm-macros               noarch 6.6.2-1.fc39                updates 8.9 k
 readline                      x86_64 8.2-6.fc39                  updates 212 k
 rpm                           x86_64 4.19.1.1-1.fc39             updates 538 k
 rpm-build-libs                x86_64 4.19.1.1-1.fc39             updates  95 k
 rpm-libs                      x86_64 4.19.1.1-1.fc39             updates 312 k
 rpm-sequoia                   x86_64 1.6.0-3.fc39                updates 847 k
 rpmautospec-rpm-macros        noarch 0.6.3-1.fc39                updates  10 k
 rust-srpm-macros              noarch 26.3-1.fc39                 updates  13 k
 setup                         noarch 2.14.4-1.fc39               fedora  154 k
 sqlite-libs                   x86_64 3.42.0-7.fc39               fedora  678 k
 systemd-libs                  x86_64 254.13-1.fc39               updates 684 k
 util-linux-core               x86_64 2.39.4-1.fc39               updates 507 k
 xxhash-libs                   x86_64 0.8.2-1.fc39                fedora   37 k
 xz-libs                       x86_64 5.4.4-1.fc39                fedora  108 k
 zip                           x86_64 3.0-39.fc39                 fedora  266 k
 zlib                          x86_64 1.2.13-4.fc39               fedora   94 k
 zstd                          x86_64 1.5.6-1.fc39                updates 479 k
Installing Groups:
 Buildsystem building group                                                    

Transaction Summary
================================================================================
Install  153 Packages

Total download size: 52 M
Installed size: 179 M
Downloading Packages:
(1/153): basesystem-11-18.fc39.noarch.rpm        65 kB/s | 7.2 kB     00:00    
(2/153): bzip2-1.0.8-16.fc39.x86_64.rpm         659 kB/s |  52 kB     00:00    
(3/153): authselect-1.4.3-1.fc39.x86_64.rpm     671 kB/s | 149 kB     00:00    
(4/153): authselect-libs-1.4.3-1.fc39.x86_64.rp 1.1 MB/s | 249 kB     00:00    
(5/153): bzip2-libs-1.0.8-16.fc39.x86_64.rpm    916 kB/s |  41 kB     00:00    
(6/153): cpio-2.14-4.fc39.x86_64.rpm            4.6 MB/s | 279 kB     00:00    
(7/153): cracklib-2.9.11-2.fc39.x86_64.rpm      1.4 MB/s |  94 kB     00:00    
(8/153): ca-certificates-2023.2.60_v7.0.306-2.f 6.9 MB/s | 837 kB     00:00    
(9/153): cyrus-sasl-lib-2.1.28-11.fc39.x86_64.r  11 MB/s | 793 kB     00:00    
(10/153): dwz-0.15-3.fc39.x86_64.rpm            4.1 MB/s | 134 kB     00:00    
(11/153): ed-1.19-4.fc39.x86_64.rpm             2.5 MB/s |  79 kB     00:00    
(12/153): diffutils-3.10-3.fc39.x86_64.rpm      4.3 MB/s | 398 kB     00:00    
(13/153): efi-srpm-macros-5-9.fc39.noarch.rpm   749 kB/s |  22 kB     00:00    
(14/153): file-5.44-5.fc39.x86_64.rpm           1.6 MB/s |  49 kB     00:00    
(15/153): findutils-4.9.0-5.fc39.x86_64.rpm      12 MB/s | 492 kB     00:00    
(16/153): filesystem-3.18-6.fc39.x86_64.rpm      20 MB/s | 1.1 MB     00:00    
(17/153): file-libs-5.44-5.fc39.x86_64.rpm      9.9 MB/s | 729 kB     00:00    
(18/153): fonts-srpm-macros-2.0.5-12.fc39.noarc 873 kB/s |  26 kB     00:00    
(19/153): fpc-srpm-macros-1.3-8.fc39.noarch.rpm 250 kB/s | 7.4 kB     00:00    
(20/153): gawk-5.2.2-2.fc39.x86_64.rpm           20 MB/s | 1.1 MB     00:00    
(21/153): gdbm-libs-1.23-4.fc39.x86_64.rpm      1.8 MB/s |  56 kB     00:00    
(22/153): ghc-srpm-macros-1.6.1-2.fc39.noarch.r 260 kB/s | 7.8 kB     00:00    
(23/153): gnat-srpm-macros-6-3.fc39.noarch.rpm  299 kB/s | 8.8 kB     00:00    
(24/153): gmp-6.2.1-5.fc39.x86_64.rpm           8.9 MB/s | 313 kB     00:00    
(25/153): grep-3.11-3.fc39.x86_64.rpm           8.5 MB/s | 298 kB     00:00    
(26/153): gzip-1.12-6.fc39.x86_64.rpm           4.9 MB/s | 166 kB     00:00    
(27/153): info-7.0.3-3.fc39.x86_64.rpm          5.5 MB/s | 182 kB     00:00    
(28/153): jansson-2.13.1-7.fc39.x86_64.rpm      1.4 MB/s |  44 kB     00:00    
(29/153): kernel-srpm-macros-1.0-20.fc39.noarch 354 kB/s |  10 kB     00:00    
(30/153): libattr-2.5.1-8.fc39.x86_64.rpm       583 kB/s |  18 kB     00:00    
(31/153): libbrotli-1.1.0-1.fc39.x86_64.rpm     9.3 MB/s | 336 kB     00:00    
(32/153): libcap-ng-0.8.3-8.fc39.x86_64.rpm     1.0 MB/s |  32 kB     00:00    
(33/153): libcom_err-1.47.0-2.fc39.x86_64.rpm   878 kB/s |  26 kB     00:00    
(34/153): libdb-5.3.28-56.fc39.x86_64.rpm        17 MB/s | 760 kB     00:00    
(35/153): libffi-3.4.4-4.fc39.x86_64.rpm        1.3 MB/s |  40 kB     00:00    
(36/153): libevent-2.1.12-9.fc39.x86_64.rpm     7.2 MB/s | 258 kB     00:00    
(37/153): libnsl2-2.0.0-6.fc39.x86_64.rpm       999 kB/s |  30 kB     00:00    
(38/153): libpkgconf-1.9.5-2.fc39.x86_64.rpm    1.2 MB/s |  38 kB     00:00    
(39/153): libpsl-0.21.2-4.fc39.x86_64.rpm       2.0 MB/s |  63 kB     00:00    
(40/153): libpwquality-1.4.5-6.fc39.x86_64.rpm  3.8 MB/s | 120 kB     00:00    
(41/153): libselinux-3.5-5.fc39.x86_64.rpm      2.7 MB/s |  87 kB     00:00    
(42/153): libsemanage-3.5-4.fc39.x86_64.rpm     3.7 MB/s | 120 kB     00:00    
(43/153): libsepol-3.5-2.fc39.x86_64.rpm        8.2 MB/s | 324 kB     00:00    
(44/153): libsigsegv-2.14-5.fc39.x86_64.rpm     826 kB/s |  27 kB     00:00    
(45/153): libtasn1-4.19.0-3.fc39.x86_64.rpm     2.4 MB/s |  74 kB     00:00    
(46/153): libtool-ltdl-2.4.7-7.fc39.x86_64.rpm  1.2 MB/s |  36 kB     00:00    
(47/153): libutempter-1.2.1-10.fc39.x86_64.rpm  868 kB/s |  26 kB     00:00    
(48/153): libunistring-1.1-5.fc39.x86_64.rpm     14 MB/s | 543 kB     00:00    
(49/153): libverto-0.3.2-6.fc39.x86_64.rpm      689 kB/s |  20 kB     00:00    
(50/153): libxcrypt-4.4.36-2.fc39.x86_64.rpm    3.7 MB/s | 119 kB     00:00    
(51/153): libxml2-2.10.4-3.fc39.x86_64.rpm       16 MB/s | 701 kB     00:00    
(52/153): lua-libs-5.4.6-3.fc39.x86_64.rpm      4.2 MB/s | 133 kB     00:00    
(53/153): lz4-libs-1.9.4-4.fc39.x86_64.rpm      2.1 MB/s |  67 kB     00:00    
(54/153): ocaml-srpm-macros-8-2.fc39.noarch.rpm 458 kB/s |  14 kB     00:00    
(55/153): openblas-srpm-macros-2-14.fc39.noarch 253 kB/s | 7.5 kB     00:00    
(56/153): mpfr-4.2.0-3.fc39.x86_64.rpm          5.4 MB/s | 344 kB     00:00    
(57/153): package-notes-srpm-macros-0.5-9.fc39. 369 kB/s |  11 kB     00:00    
(58/153): patch-2.7.6-22.fc39.x86_64.rpm        3.8 MB/s | 125 kB     00:00    
(59/153): openssl-libs-3.1.1-4.fc39.x86_64.rpm   32 MB/s | 2.2 MB     00:00    
(60/153): pcre2-10.42-1.fc39.2.x86_64.rpm       6.6 MB/s | 233 kB     00:00    
(61/153): pcre2-syntax-10.42-1.fc39.2.noarch.rp 4.4 MB/s | 143 kB     00:00    
(62/153): perl-srpm-macros-1-51.fc39.noarch.rpm 271 kB/s | 8.0 kB     00:00    
(63/153): pkgconf-1.9.5-2.fc39.x86_64.rpm       1.4 MB/s |  42 kB     00:00    
(64/153): pkgconf-m4-1.9.5-2.fc39.noarch.rpm    470 kB/s |  14 kB     00:00    
(65/153): pkgconf-pkg-config-1.9.5-2.fc39.x86_6 323 kB/s | 9.6 kB     00:00    
(66/153): popt-1.19-3.fc39.x86_64.rpm           2.1 MB/s |  66 kB     00:00    
(67/153): python-srpm-macros-3.12-4.fc39.noarch 843 kB/s |  25 kB     00:00    
(68/153): sed-4.8-14.fc39.x86_64.rpm            9.0 MB/s | 306 kB     00:00    
(69/153): setup-2.14.4-1.fc39.noarch.rpm        4.4 MB/s | 154 kB     00:00    
(70/153): sqlite-libs-3.42.0-7.fc39.x86_64.rpm   16 MB/s | 678 kB     00:00    
(71/153): unzip-6.0-62.fc39.x86_64.rpm          4.8 MB/s | 184 kB     00:00    
(72/153): tar-1.35-2.fc39.x86_64.rpm             21 MB/s | 864 kB     00:00    
(73/153): which-2.21-40.fc39.x86_64.rpm         1.4 MB/s |  42 kB     00:00    
(74/153): xxhash-libs-0.8.2-1.fc39.x86_64.rpm   1.2 MB/s |  37 kB     00:00    
(75/153): xz-5.4.4-1.fc39.x86_64.rpm             15 MB/s | 556 kB     00:00    
(76/153): xz-libs-5.4.4-1.fc39.x86_64.rpm       3.4 MB/s | 108 kB     00:00    
(77/153): zip-3.0-39.fc39.x86_64.rpm            7.4 MB/s | 266 kB     00:00    
(78/153): zlib-1.2.13-4.fc39.x86_64.rpm         3.0 MB/s |  94 kB     00:00    
(79/153): alternatives-1.26-1.fc39.x86_64.rpm   315 kB/s |  39 kB     00:00    
(80/153): ansible-srpm-macros-1-12.fc39.noarch. 199 kB/s |  21 kB     00:00    
(81/153): audit-libs-3.1.3-1.fc39.x86_64.rpm    641 kB/s | 124 kB     00:00    
(82/153): binutils-gold-2.40-14.fc39.x86_64.rpm 381 kB/s | 795 kB     00:02    
(83/153): bash-5.2.26-1.fc39.x86_64.rpm         519 kB/s | 1.8 MB     00:03    
(84/153): coreutils-9.3-5.fc39.x86_64.rpm       667 kB/s | 1.1 MB     00:01    
(85/153): crypto-policies-20231204-1.git1e3a2e4 190 kB/s | 100 kB     00:00    
(86/153): curl-8.2.1-5.fc39.x86_64.rpm          920 kB/s | 344 kB     00:00    
(87/153): debugedit-5.0-12.fc39.x86_64.rpm      471 kB/s |  79 kB     00:00    
(88/153): elfutils-0.191-2.fc39.x86_64.rpm      458 kB/s | 559 kB     00:01    
(89/153): elfutils-debuginfod-client-0.191-2.fc 638 kB/s |  38 kB     00:00    
(90/153): elfutils-default-yama-scope-0.191-2.f 221 kB/s |  13 kB     00:00    
(91/153): coreutils-common-9.3-5.fc39.x86_64.rp 757 kB/s | 2.1 MB     00:02    
(92/153): elfutils-libelf-0.191-2.fc39.x86_64.r 1.2 MB/s | 209 kB     00:00    
(93/153): fedora-gpg-keys-39-2.noarch.rpm       344 kB/s | 130 kB     00:00    
(94/153): elfutils-libs-0.191-2.fc39.x86_64.rpm 604 kB/s | 263 kB     00:00    
(95/153): fedora-release-39-36.noarch.rpm        67 kB/s | 8.6 kB     00:00    
(96/153): fedora-release-common-39-36.noarch.rp  64 kB/s |  19 kB     00:00    
(97/153): fedora-release-identity-basic-39-36.n  26 kB/s | 9.4 kB     00:00    
(98/153): fedora-repos-39-2.noarch.rpm           40 kB/s | 9.3 kB     00:00    
(99/153): forge-srpm-macros-0.3.1-1.fc39.noarch 190 kB/s |  19 kB     00:00    
(100/153): binutils-2.40-14.fc39.x86_64.rpm     561 kB/s | 5.6 MB     00:10    
(101/153): glibc-common-2.38-18.fc39.x86_64.rpm 156 kB/s | 353 kB     00:02    
(102/153): glibc-2.38-18.fc39.x86_64.rpm        179 kB/s | 2.2 MB     00:12    
(103/153): glibc-minimal-langpack-2.38-18.fc39. 170 kB/s |  73 kB     00:00    
(104/153): go-srpm-macros-3.5.0-1.fc39.noarch.r  21 kB/s |  28 kB     00:01    
(105/153): keyutils-libs-1.6.3-1.fc39.x86_64.rp 117 kB/s |  31 kB     00:00    
(106/153): glibc-gconv-extra-2.38-18.fc39.x86_6 158 kB/s | 1.6 MB     00:10    
(107/153): libacl-2.3.1-9.fc39.x86_64.rpm       127 kB/s |  23 kB     00:00    
(108/153): krb5-libs-1.21.2-3.fc39.x86_64.rpm   459 kB/s | 765 kB     00:01    
(109/153): libblkid-2.39.4-1.fc39.x86_64.rpm    479 kB/s | 116 kB     00:00    
(110/153): libcap-2.48-9.fc39.x86_64.rpm        397 kB/s |  68 kB     00:00    
(111/153): libarchive-3.7.1-2.fc39.x86_64.rpm   552 kB/s | 407 kB     00:00    
(112/153): libeconf-0.5.2-2.fc39.x86_64.rpm     123 kB/s |  30 kB     00:00    
(113/153): libfdisk-2.39.4-1.fc39.x86_64.rpm    559 kB/s | 161 kB     00:00    
(114/153): libcurl-8.2.1-5.fc39.x86_64.rpm      415 kB/s | 322 kB     00:00    
(115/153): gdb-minimal-14.2-1.fc39.x86_64.rpm   250 kB/s | 4.3 MB     00:17    
(116/153): libgcc-13.3.1-1.fc39.x86_64.rpm      253 kB/s | 118 kB     00:00    
(117/153): libidn2-2.3.7-1.fc39.x86_64.rpm      527 kB/s | 119 kB     00:00    
(118/153): libnghttp2-1.55.1-5.fc39.x86_64.rpm  483 kB/s |  75 kB     00:00    
(119/153): libgomp-13.3.1-1.fc39.x86_64.rpm     455 kB/s | 328 kB     00:00    
(120/153): libmount-2.39.4-1.fc39.x86_64.rpm    600 kB/s | 154 kB     00:00    
(121/153): libsmartcols-2.39.4-1.fc39.x86_64.rp 481 kB/s |  67 kB     00:00    
(122/153): libssh-config-0.10.6-2.fc39.noarch.r  89 kB/s | 9.0 kB     00:00    
(123/153): libssh-0.10.6-2.fc39.x86_64.rpm      1.1 MB/s | 212 kB     00:00    
(124/153): libtirpc-1.3.4-1.rc3.fc39.x86_64.rpm 541 kB/s |  93 kB     00:00    
(125/153): libuuid-2.39.4-1.fc39.x86_64.rpm     248 kB/s |  28 kB     00:00    
(126/153): lua-srpm-macros-1-13.fc39.noarch.rpm 188 kB/s | 8.7 kB     00:00    
(127/153): ncurses-base-6.4-7.20230520.fc39.1.n 440 kB/s |  88 kB     00:00    
(128/153): libzstd-1.5.6-1.fc39.x86_64.rpm      1.0 MB/s | 312 kB     00:00    
(129/153): openldap-2.6.7-1.fc39.x86_64.rpm     1.0 MB/s | 254 kB     00:00    
(130/153): libstdc++-13.3.1-1.fc39.x86_64.rpm   1.1 MB/s | 869 kB     00:00    
(131/153): ncurses-libs-6.4-7.20230520.fc39.1.x 1.1 MB/s | 336 kB     00:00    
(132/153): p11-kit-trust-0.25.3-1.fc39.x86_64.r 439 kB/s | 140 kB     00:00    
(133/153): pam-libs-1.5.3-3.fc39.x86_64.rpm     902 kB/s |  56 kB     00:00    
(134/153): p11-kit-0.25.3-1.fc39.x86_64.rpm     1.1 MB/s | 520 kB     00:00    
(135/153): publicsuffix-list-dafsa-20240107-1.f 690 kB/s |  58 kB     00:00    
(136/153): pyproject-srpm-macros-1.12.0-1.fc39. 219 kB/s |  14 kB     00:00    
(137/153): pam-1.5.3-3.fc39.x86_64.rpm          1.1 MB/s | 542 kB     00:00    
(138/153): qt5-srpm-macros-5.15.13-1.fc39.noarc 239 kB/s | 8.5 kB     00:00    
(139/153): qt6-srpm-macros-6.6.2-1.fc39.noarch. 188 kB/s | 8.9 kB     00:00    
(140/153): readline-8.2-6.fc39.x86_64.rpm       476 kB/s | 212 kB     00:00    
(141/153): redhat-rpm-config-266-1.fc39.noarch. 168 kB/s |  78 kB     00:00    
(142/153): rpm-build-4.19.1.1-1.fc39.x86_64.rpm 288 kB/s |  78 kB     00:00    
(143/153): rpm-build-libs-4.19.1.1-1.fc39.x86_6 364 kB/s |  95 kB     00:00    
(144/153): rpm-4.19.1.1-1.fc39.x86_64.rpm       574 kB/s | 538 kB     00:00    
(145/153): rpm-libs-4.19.1.1-1.fc39.x86_64.rpm  754 kB/s | 312 kB     00:00    
(146/153): rpmautospec-rpm-macros-0.6.3-1.fc39.  49 kB/s |  10 kB     00:00    
(147/153): rust-srpm-macros-26.3-1.fc39.noarch.  44 kB/s |  13 kB     00:00    
(148/153): rpm-sequoia-1.6.0-3.fc39.x86_64.rpm  479 kB/s | 847 kB     00:01    
(149/153): systemd-libs-254.13-1.fc39.x86_64.rp 409 kB/s | 684 kB     00:01    
(150/153): shadow-utils-4.14.0-2.fc39.x86_64.rp 413 kB/s | 1.3 MB     00:03    
(151/153): util-linux-core-2.39.4-1.fc39.x86_64 391 kB/s | 507 kB     00:01    
(152/153): util-linux-2.39.4-1.fc39.x86_64.rpm  376 kB/s | 1.2 MB     00:03    
(153/153): zstd-1.5.6-1.fc39.x86_64.rpm         352 kB/s | 479 kB     00:01    
--------------------------------------------------------------------------------
Total                                           1.5 MB/s |  52 MB     00:33     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x18B8E74C:
 Userid     : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
 Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-6.fc39.x86_64                          1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.3.1-1.fc39.x86_64                          1/153 
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  Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc39.noarc     2/153 
  Installing       : fedora-release-identity-basic-39-36.noarch           3/153 
  Installing       : fedora-gpg-keys-39-2.noarch                          4/153 
  Installing       : fedora-repos-39-2.noarch                             5/153 
  Installing       : fedora-release-common-39-36.noarch                   6/153 
  Installing       : fedora-release-39-36.noarch                          7/153 
  Installing       : setup-2.14.4-1.fc39.noarch                           8/153 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.4-1.fc39.noarch                           8/153 
  Installing       : filesystem-3.18-6.fc39.x86_64                        9/153 
  Installing       : basesystem-11-18.fc39.noarch                        10/153 
  Installing       : rust-srpm-macros-26.3-1.fc39.noarch                 11/153 
  Installing       : qt6-srpm-macros-6.6.2-1.fc39.noarch                 12/153 
  Installing       : qt5-srpm-macros-5.15.13-1.fc39.noarch               13/153 
  Installing       : publicsuffix-list-dafsa-20240107-1.fc39.noarch      14/153 
  Installing       : ncurses-base-6.4-7.20230520.fc39.1.noarch           15/153 
  Installing       : glibc-gconv-extra-2.38-18.fc39.x86_64               16/153 
  Running scriptlet: glibc-gconv-extra-2.38-18.fc39.x86_64               16/153 
  Installing       : glibc-minimal-langpack-2.38-18.fc39.x86_64          17/153 
  Installing       : glibc-common-2.38-18.fc39.x86_64                    18/153 
  Running scriptlet: glibc-2.38-18.fc39.x86_64                           19/153 
  Installing       : glibc-2.38-18.fc39.x86_64                           19/153 
  Running scriptlet: glibc-2.38-18.fc39.x86_64                           19/153 
  Installing       : ncurses-libs-6.4-7.20230520.fc39.1.x86_64           20/153 
  Installing       : bash-5.2.26-1.fc39.x86_64                           21/153 
  Running scriptlet: bash-5.2.26-1.fc39.x86_64                           21/153 
  Installing       : zlib-1.2.13-4.fc39.x86_64                           22/153 
  Installing       : xz-libs-5.4.4-1.fc39.x86_64                         23/153 
  Installing       : bzip2-libs-1.0.8-16.fc39.x86_64                     24/153 
  Installing       : popt-1.19-3.fc39.x86_64                             25/153 
  Installing       : libstdc++-13.3.1-1.fc39.x86_64                      26/153 
  Installing       : libuuid-2.39.4-1.fc39.x86_64                        27/153 
  Installing       : libzstd-1.5.6-1.fc39.x86_64                         28/153 
  Installing       : elfutils-libelf-0.191-2.fc39.x86_64                 29/153 
  Installing       : libblkid-2.39.4-1.fc39.x86_64                       30/153 
  Installing       : readline-8.2-6.fc39.x86_64                          31/153 
  Installing       : gmp-1:6.2.1-5.fc39.x86_64                           32/153 
  Installing       : libattr-2.5.1-8.fc39.x86_64                         33/153 
  Installing       : libacl-2.3.1-9.fc39.x86_64                          34/153 
  Installing       : libxcrypt-4.4.36-2.fc39.x86_64                      35/153 
  Installing       : libcap-2.48-9.fc39.x86_64                           36/153 
  Installing       : lz4-libs-1.9.4-4.fc39.x86_64                        37/153 
  Installing       : libeconf-0.5.2-2.fc39.x86_64                        38/153 
  Installing       : systemd-libs-254.13-1.fc39.x86_64                   39/153 
  Installing       : mpfr-4.2.0-3.fc39.x86_64                            40/153 
  Installing       : dwz-0.15-3.fc39.x86_64                              41/153 
  Installing       : unzip-6.0-62.fc39.x86_64                            42/153 
  Installing       : file-libs-5.44-5.fc39.x86_64                        43/153 
  Installing       : file-5.44-5.fc39.x86_64                             44/153 
  Installing       : jansson-2.13.1-7.fc39.x86_64                        45/153 
  Installing       : libcap-ng-0.8.3-8.fc39.x86_64                       46/153 
  Installing       : audit-libs-3.1.3-1.fc39.x86_64                      47/153 
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  Installing       : libcom_err-1.47.0-2.fc39.x86_64                     49/153 
  Installing       : libsepol-3.5-2.fc39.x86_64                          50/153 
  Installing       : libtasn1-4.19.0-3.fc39.x86_64                       51/153 
  Installing       : libunistring-1.1-5.fc39.x86_64                      52/153 
  Installing       : libidn2-2.3.7-1.fc39.x86_64                         53/153 
  Installing       : lua-libs-5.4.6-3.fc39.x86_64                        54/153 
  Installing       : alternatives-1.26-1.fc39.x86_64                     55/153 
  Installing       : libsmartcols-2.39.4-1.fc39.x86_64                   56/153 
  Installing       : libpsl-0.21.2-4.fc39.x86_64                         57/153 
  Installing       : zip-3.0-39.fc39.x86_64                              58/153 
  Installing       : zstd-1.5.6-1.fc39.x86_64                            59/153 
  Installing       : libfdisk-2.39.4-1.fc39.x86_64                       60/153 
  Installing       : bzip2-1.0.8-16.fc39.x86_64                          61/153 
  Installing       : libxml2-2.10.4-3.fc39.x86_64                        62/153 
  Installing       : sqlite-libs-3.42.0-7.fc39.x86_64                    63/153 
  Installing       : ed-1.19-4.fc39.x86_64                               64/153 
  Installing       : elfutils-default-yama-scope-0.191-2.fc39.noarch     65/153 
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  Installing       : cpio-2.14-4.fc39.x86_64                             66/153 
  Installing       : diffutils-3.10-3.fc39.x86_64                        67/153 
  Installing       : gdbm-libs-1:1.23-4.fc39.x86_64                      68/153 
  Installing       : cyrus-sasl-lib-2.1.28-11.fc39.x86_64                69/153 
  Installing       : libbrotli-1.1.0-1.fc39.x86_64                       70/153 
  Installing       : libdb-5.3.28-56.fc39.x86_64                         71/153 
  Installing       : libffi-3.4.4-4.fc39.x86_64                          72/153 
  Installing       : p11-kit-0.25.3-1.fc39.x86_64                        73/153 
  Installing       : p11-kit-trust-0.25.3-1.fc39.x86_64                  74/153 
  Running scriptlet: p11-kit-trust-0.25.3-1.fc39.x86_64                  74/153 
  Installing       : libpkgconf-1.9.5-2.fc39.x86_64                      75/153 
  Installing       : pkgconf-1.9.5-2.fc39.x86_64                         76/153 
  Installing       : libsigsegv-2.14-5.fc39.x86_64                       77/153 
  Installing       : gawk-5.2.2-2.fc39.x86_64                            78/153 
  Installing       : libtool-ltdl-2.4.7-7.fc39.x86_64                    79/153 
  Installing       : libverto-0.3.2-6.fc39.x86_64                        80/153 
  Installing       : xxhash-libs-0.8.2-1.fc39.x86_64                     81/153 
  Installing       : keyutils-libs-1.6.3-1.fc39.x86_64                   82/153 
  Installing       : libgomp-13.3.1-1.fc39.x86_64                        83/153 
  Installing       : libnghttp2-1.55.1-5.fc39.x86_64                     84/153 
  Installing       : libssh-config-0.10.6-2.fc39.noarch                  85/153 
  Installing       : coreutils-common-9.3-5.fc39.x86_64                  86/153 
  Installing       : ansible-srpm-macros-1-12.fc39.noarch                87/153 
  Installing       : pkgconf-m4-1.9.5-2.fc39.noarch                      88/153 
  Installing       : pkgconf-pkg-config-1.9.5-2.fc39.x86_64              89/153 
  Installing       : perl-srpm-macros-1-51.fc39.noarch                   90/153 
  Installing       : pcre2-syntax-10.42-1.fc39.2.noarch                  91/153 
  Installing       : pcre2-10.42-1.fc39.2.x86_64                         92/153 
  Installing       : libselinux-3.5-5.fc39.x86_64                        93/153 
  Installing       : sed-4.8-14.fc39.x86_64                              94/153 
  Installing       : grep-3.11-3.fc39.x86_64                             95/153 
  Installing       : findutils-1:4.9.0-5.fc39.x86_64                     96/153 
  Installing       : xz-5.4.4-1.fc39.x86_64                              97/153 
  Installing       : libmount-2.39.4-1.fc39.x86_64                       98/153 
  Installing       : util-linux-core-2.39.4-1.fc39.x86_64                99/153 
  Installing       : openssl-libs-1:3.1.1-4.fc39.x86_64                 100/153 
  Installing       : coreutils-9.3-5.fc39.x86_64                        101/153 
  Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch   102/153 
  Installing       : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch   102/153 
  Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch   102/153 
  Installing       : krb5-libs-1.21.2-3.fc39.x86_64                     103/153 
  Installing       : libtirpc-1.3.4-1.rc3.fc39.x86_64                   104/153 
  Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64                105/153 
  Installing       : authselect-libs-1.4.3-1.fc39.x86_64                105/153 
  Installing       : gzip-1.12-6.fc39.x86_64                            106/153 
  Installing       : libarchive-3.7.1-2.fc39.x86_64                     107/153 
  Installing       : cracklib-2.9.11-2.fc39.x86_64                      108/153 
  Installing       : libpwquality-1.4.5-6.fc39.x86_64                   109/153 
  Installing       : authselect-1.4.3-1.fc39.x86_64                     110/153 
  Installing       : libnsl2-2.0.0-6.fc39.x86_64                        111/153 
  Installing       : pam-1.5.3-3.fc39.x86_64                            112/153 
  Installing       : libssh-0.10.6-2.fc39.x86_64                        113/153 
  Installing       : libevent-2.1.12-9.fc39.x86_64                      114/153 
  Installing       : openldap-2.6.7-1.fc39.x86_64                       115/153 
  Installing       : libcurl-8.2.1-5.fc39.x86_64                        116/153 
  Installing       : elfutils-libs-0.191-2.fc39.x86_64                  117/153 
  Installing       : elfutils-debuginfod-client-0.191-2.fc39.x86_64     118/153 
  Installing       : binutils-gold-2.40-14.fc39.x86_64                  119/153 
  Running scriptlet: binutils-gold-2.40-14.fc39.x86_64                  119/153 
  Installing       : binutils-2.40-14.fc39.x86_64                       120/153 
  Running scriptlet: binutils-2.40-14.fc39.x86_64                       120/153 
  Installing       : elfutils-0.191-2.fc39.x86_64                       121/153 
  Installing       : gdb-minimal-14.2-1.fc39.x86_64                     122/153 
  Installing       : debugedit-5.0-12.fc39.x86_64                       123/153 
  Installing       : curl-8.2.1-5.fc39.x86_64                           124/153 
  Installing       : rpm-sequoia-1.6.0-3.fc39.x86_64                    125/153 
  Installing       : rpm-libs-4.19.1.1-1.fc39.x86_64                    126/153 
  Running scriptlet: rpm-4.19.1.1-1.fc39.x86_64                         127/153 
  Installing       : rpm-4.19.1.1-1.fc39.x86_64                         127/153 
  Installing       : efi-srpm-macros-5-9.fc39.noarch                    128/153 
  Installing       : lua-srpm-macros-1-13.fc39.noarch                   129/153 
  Installing       : rpmautospec-rpm-macros-0.6.3-1.fc39.noarch         130/153 
  Installing       : rpm-build-libs-4.19.1.1-1.fc39.x86_64              131/153 
  Installing       : libsemanage-3.5-4.fc39.x86_64                      132/153 
  Installing       : shadow-utils-2:4.14.0-2.fc39.x86_64                133/153 
  Running scriptlet: libutempter-1.2.1-10.fc39.x86_64                   134/153 
  Installing       : libutempter-1.2.1-10.fc39.x86_64                   134/153 
  Installing       : patch-2.7.6-22.fc39.x86_64                         135/153 
  Installing       : tar-2:1.35-2.fc39.x86_64                           136/153 
  Installing       : package-notes-srpm-macros-0.5-9.fc39.noarch        137/153 
  Installing       : openblas-srpm-macros-2-14.fc39.noarch              138/153 
  Installing       : ocaml-srpm-macros-8-2.fc39.noarch                  139/153 
  Installing       : kernel-srpm-macros-1.0-20.fc39.noarch              140/153 
  Installing       : gnat-srpm-macros-6-3.fc39.noarch                   141/153 
  Installing       : ghc-srpm-macros-1.6.1-2.fc39.noarch                142/153 
  Installing       : fpc-srpm-macros-1.3-8.fc39.noarch                  143/153 
  Installing       : fonts-srpm-macros-1:2.0.5-12.fc39.noarch           144/153 
  Installing       : python-srpm-macros-3.12-4.fc39.noarch              145/153 
  Installing       : forge-srpm-macros-0.3.1-1.fc39.noarch              146/153 
  Installing       : go-srpm-macros-3.5.0-1.fc39.noarch                 147/153 
  Installing       : redhat-rpm-config-266-1.fc39.noarch                148/153 
  Installing       : rpm-build-4.19.1.1-1.fc39.x86_64                   149/153 
  Installing       : pyproject-srpm-macros-1.12.0-1.fc39.noarch         150/153 
  Installing       : util-linux-2.39.4-1.fc39.x86_64                    151/153 
  Running scriptlet: util-linux-2.39.4-1.fc39.x86_64                    151/153 
  Installing       : which-2.21-40.fc39.x86_64                          152/153 
  Installing       : info-7.0.3-3.fc39.x86_64                           153/153 
  Running scriptlet: filesystem-3.18-6.fc39.x86_64                      153/153 
  Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch   153/153 
  Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64                153/153 
  Running scriptlet: rpm-4.19.1.1-1.fc39.x86_64                         153/153 
  Running scriptlet: info-7.0.3-3.fc39.x86_64                           153/153 
  Verifying        : authselect-1.4.3-1.fc39.x86_64                       1/153 
  Verifying        : authselect-libs-1.4.3-1.fc39.x86_64                  2/153 
  Verifying        : basesystem-11-18.fc39.noarch                         3/153 
  Verifying        : bzip2-1.0.8-16.fc39.x86_64                           4/153 
  Verifying        : bzip2-libs-1.0.8-16.fc39.x86_64                      5/153 
  Verifying        : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch     6/153 
  Verifying        : cpio-2.14-4.fc39.x86_64                              7/153 
  Verifying        : cracklib-2.9.11-2.fc39.x86_64                        8/153 
  Verifying        : cyrus-sasl-lib-2.1.28-11.fc39.x86_64                 9/153 
  Verifying        : diffutils-3.10-3.fc39.x86_64                        10/153 
  Verifying        : dwz-0.15-3.fc39.x86_64                              11/153 
  Verifying        : ed-1.19-4.fc39.x86_64                               12/153 
  Verifying        : efi-srpm-macros-5-9.fc39.noarch                     13/153 
  Verifying        : file-5.44-5.fc39.x86_64                             14/153 
  Verifying        : file-libs-5.44-5.fc39.x86_64                        15/153 
  Verifying        : filesystem-3.18-6.fc39.x86_64                       16/153 
  Verifying        : findutils-1:4.9.0-5.fc39.x86_64                     17/153 
  Verifying        : fonts-srpm-macros-1:2.0.5-12.fc39.noarch            18/153 
  Verifying        : fpc-srpm-macros-1.3-8.fc39.noarch                   19/153 
  Verifying        : gawk-5.2.2-2.fc39.x86_64                            20/153 
  Verifying        : gdbm-libs-1:1.23-4.fc39.x86_64                      21/153 
  Verifying        : ghc-srpm-macros-1.6.1-2.fc39.noarch                 22/153 
  Verifying        : gmp-1:6.2.1-5.fc39.x86_64                           23/153 
  Verifying        : gnat-srpm-macros-6-3.fc39.noarch                    24/153 
  Verifying        : grep-3.11-3.fc39.x86_64                             25/153 
  Verifying        : gzip-1.12-6.fc39.x86_64                             26/153 
  Verifying        : info-7.0.3-3.fc39.x86_64                            27/153 
  Verifying        : jansson-2.13.1-7.fc39.x86_64                        28/153 
  Verifying        : kernel-srpm-macros-1.0-20.fc39.noarch               29/153 
  Verifying        : libattr-2.5.1-8.fc39.x86_64                         30/153 
  Verifying        : libbrotli-1.1.0-1.fc39.x86_64                       31/153 
  Verifying        : libcap-ng-0.8.3-8.fc39.x86_64                       32/153 
  Verifying        : libcom_err-1.47.0-2.fc39.x86_64                     33/153 
  Verifying        : libdb-5.3.28-56.fc39.x86_64                         34/153 
  Verifying        : libevent-2.1.12-9.fc39.x86_64                       35/153 
  Verifying        : libffi-3.4.4-4.fc39.x86_64                          36/153 
  Verifying        : libnsl2-2.0.0-6.fc39.x86_64                         37/153 
  Verifying        : libpkgconf-1.9.5-2.fc39.x86_64                      38/153 
  Verifying        : libpsl-0.21.2-4.fc39.x86_64                         39/153 
  Verifying        : libpwquality-1.4.5-6.fc39.x86_64                    40/153 
  Verifying        : libselinux-3.5-5.fc39.x86_64                        41/153 
  Verifying        : libsemanage-3.5-4.fc39.x86_64                       42/153 
  Verifying        : libsepol-3.5-2.fc39.x86_64                          43/153 
  Verifying        : libsigsegv-2.14-5.fc39.x86_64                       44/153 
  Verifying        : libtasn1-4.19.0-3.fc39.x86_64                       45/153 
  Verifying        : libtool-ltdl-2.4.7-7.fc39.x86_64                    46/153 
  Verifying        : libunistring-1.1-5.fc39.x86_64                      47/153 
  Verifying        : libutempter-1.2.1-10.fc39.x86_64                    48/153 
  Verifying        : libverto-0.3.2-6.fc39.x86_64                        49/153 
  Verifying        : libxcrypt-4.4.36-2.fc39.x86_64                      50/153 
  Verifying        : libxml2-2.10.4-3.fc39.x86_64                        51/153 
  Verifying        : lua-libs-5.4.6-3.fc39.x86_64                        52/153 
  Verifying        : lz4-libs-1.9.4-4.fc39.x86_64                        53/153 
  Verifying        : mpfr-4.2.0-3.fc39.x86_64                            54/153 
  Verifying        : ocaml-srpm-macros-8-2.fc39.noarch                   55/153 
  Verifying        : openblas-srpm-macros-2-14.fc39.noarch               56/153 
  Verifying        : openssl-libs-1:3.1.1-4.fc39.x86_64                  57/153 
  Verifying        : package-notes-srpm-macros-0.5-9.fc39.noarch         58/153 
  Verifying        : patch-2.7.6-22.fc39.x86_64                          59/153 
  Verifying        : pcre2-10.42-1.fc39.2.x86_64                         60/153 
  Verifying        : pcre2-syntax-10.42-1.fc39.2.noarch                  61/153 
  Verifying        : perl-srpm-macros-1-51.fc39.noarch                   62/153 
  Verifying        : pkgconf-1.9.5-2.fc39.x86_64                         63/153 
  Verifying        : pkgconf-m4-1.9.5-2.fc39.noarch                      64/153 
  Verifying        : pkgconf-pkg-config-1.9.5-2.fc39.x86_64              65/153 
  Verifying        : popt-1.19-3.fc39.x86_64                             66/153 
  Verifying        : python-srpm-macros-3.12-4.fc39.noarch               67/153 
  Verifying        : sed-4.8-14.fc39.x86_64                              68/153 
  Verifying        : setup-2.14.4-1.fc39.noarch                          69/153 
  Verifying        : sqlite-libs-3.42.0-7.fc39.x86_64                    70/153 
  Verifying        : tar-2:1.35-2.fc39.x86_64                            71/153 
  Verifying        : unzip-6.0-62.fc39.x86_64                            72/153 
  Verifying        : which-2.21-40.fc39.x86_64                           73/153 
  Verifying        : xxhash-libs-0.8.2-1.fc39.x86_64                     74/153 
  Verifying        : xz-5.4.4-1.fc39.x86_64                              75/153 
  Verifying        : xz-libs-5.4.4-1.fc39.x86_64                         76/153 
  Verifying        : zip-3.0-39.fc39.x86_64                              77/153 
  Verifying        : zlib-1.2.13-4.fc39.x86_64                           78/153 
  Verifying        : alternatives-1.26-1.fc39.x86_64                     79/153 
  Verifying        : ansible-srpm-macros-1-12.fc39.noarch                80/153 
  Verifying        : audit-libs-3.1.3-1.fc39.x86_64                      81/153 
  Verifying        : bash-5.2.26-1.fc39.x86_64                           82/153 
  Verifying        : binutils-2.40-14.fc39.x86_64                        83/153 
  Verifying        : binutils-gold-2.40-14.fc39.x86_64                   84/153 
  Verifying        : coreutils-9.3-5.fc39.x86_64                         85/153 
  Verifying        : coreutils-common-9.3-5.fc39.x86_64                  86/153 
  Verifying        : crypto-policies-20231204-1.git1e3a2e4.fc39.noarc    87/153 
  Verifying        : curl-8.2.1-5.fc39.x86_64                            88/153 
  Verifying        : debugedit-5.0-12.fc39.x86_64                        89/153 
  Verifying        : elfutils-0.191-2.fc39.x86_64                        90/153 
  Verifying        : elfutils-debuginfod-client-0.191-2.fc39.x86_64      91/153 
  Verifying        : elfutils-default-yama-scope-0.191-2.fc39.noarch     92/153 
  Verifying        : elfutils-libelf-0.191-2.fc39.x86_64                 93/153 
  Verifying        : elfutils-libs-0.191-2.fc39.x86_64                   94/153 
  Verifying        : fedora-gpg-keys-39-2.noarch                         95/153 
  Verifying        : fedora-release-39-36.noarch                         96/153 
  Verifying        : fedora-release-common-39-36.noarch                  97/153 
  Verifying        : fedora-release-identity-basic-39-36.noarch          98/153 
  Verifying        : fedora-repos-39-2.noarch                            99/153 
  Verifying        : forge-srpm-macros-0.3.1-1.fc39.noarch              100/153 
  Verifying        : gdb-minimal-14.2-1.fc39.x86_64                     101/153 
  Verifying        : glibc-2.38-18.fc39.x86_64                          102/153 
  Verifying        : glibc-common-2.38-18.fc39.x86_64                   103/153 
  Verifying        : glibc-gconv-extra-2.38-18.fc39.x86_64              104/153 
  Verifying        : glibc-minimal-langpack-2.38-18.fc39.x86_64         105/153 
  Verifying        : go-srpm-macros-3.5.0-1.fc39.noarch                 106/153 
  Verifying        : keyutils-libs-1.6.3-1.fc39.x86_64                  107/153 
  Verifying        : krb5-libs-1.21.2-3.fc39.x86_64                     108/153 
  Verifying        : libacl-2.3.1-9.fc39.x86_64                         109/153 
  Verifying        : libarchive-3.7.1-2.fc39.x86_64                     110/153 
  Verifying        : libblkid-2.39.4-1.fc39.x86_64                      111/153 
  Verifying        : libcap-2.48-9.fc39.x86_64                          112/153 
  Verifying        : libcurl-8.2.1-5.fc39.x86_64                        113/153 
  Verifying        : libeconf-0.5.2-2.fc39.x86_64                       114/153 
  Verifying        : libfdisk-2.39.4-1.fc39.x86_64                      115/153 
  Verifying        : libgcc-13.3.1-1.fc39.x86_64                        116/153 
  Verifying        : libgomp-13.3.1-1.fc39.x86_64                       117/153 
  Verifying        : libidn2-2.3.7-1.fc39.x86_64                        118/153 
  Verifying        : libmount-2.39.4-1.fc39.x86_64                      119/153 
  Verifying        : libnghttp2-1.55.1-5.fc39.x86_64                    120/153 
  Verifying        : libsmartcols-2.39.4-1.fc39.x86_64                  121/153 
  Verifying        : libssh-0.10.6-2.fc39.x86_64                        122/153 
  Verifying        : libssh-config-0.10.6-2.fc39.noarch                 123/153 
  Verifying        : libstdc++-13.3.1-1.fc39.x86_64                     124/153 
  Verifying        : libtirpc-1.3.4-1.rc3.fc39.x86_64                   125/153 
  Verifying        : libuuid-2.39.4-1.fc39.x86_64                       126/153 
  Verifying        : libzstd-1.5.6-1.fc39.x86_64                        127/153 
  Verifying        : lua-srpm-macros-1-13.fc39.noarch                   128/153 
  Verifying        : ncurses-base-6.4-7.20230520.fc39.1.noarch          129/153 
  Verifying        : ncurses-libs-6.4-7.20230520.fc39.1.x86_64          130/153 
  Verifying        : openldap-2.6.7-1.fc39.x86_64                       131/153 
  Verifying        : p11-kit-0.25.3-1.fc39.x86_64                       132/153 
  Verifying        : p11-kit-trust-0.25.3-1.fc39.x86_64                 133/153 
  Verifying        : pam-1.5.3-3.fc39.x86_64                            134/153 
  Verifying        : pam-libs-1.5.3-3.fc39.x86_64                       135/153 
  Verifying        : publicsuffix-list-dafsa-20240107-1.fc39.noarch     136/153 
  Verifying        : pyproject-srpm-macros-1.12.0-1.fc39.noarch         137/153 
  Verifying        : qt5-srpm-macros-5.15.13-1.fc39.noarch              138/153 
  Verifying        : qt6-srpm-macros-6.6.2-1.fc39.noarch                139/153 
  Verifying        : readline-8.2-6.fc39.x86_64                         140/153 
  Verifying        : redhat-rpm-config-266-1.fc39.noarch                141/153 
  Verifying        : rpm-4.19.1.1-1.fc39.x86_64                         142/153 
  Verifying        : rpm-build-4.19.1.1-1.fc39.x86_64                   143/153 
  Verifying        : rpm-build-libs-4.19.1.1-1.fc39.x86_64              144/153 
  Verifying        : rpm-libs-4.19.1.1-1.fc39.x86_64                    145/153 
  Verifying        : rpm-sequoia-1.6.0-3.fc39.x86_64                    146/153 
  Verifying        : rpmautospec-rpm-macros-0.6.3-1.fc39.noarch         147/153 
  Verifying        : rust-srpm-macros-26.3-1.fc39.noarch                148/153 
  Verifying        : shadow-utils-2:4.14.0-2.fc39.x86_64                149/153 
  Verifying        : systemd-libs-254.13-1.fc39.x86_64                  150/153 
  Verifying        : util-linux-2.39.4-1.fc39.x86_64                    151/153 
  Verifying        : util-linux-core-2.39.4-1.fc39.x86_64               152/153 
  Verifying        : zstd-1.5.6-1.fc39.x86_64                           153/153 
Installed products updated.

Installed:
  alternatives-1.26-1.fc39.x86_64                                               
  ansible-srpm-macros-1-12.fc39.noarch                                          
  audit-libs-3.1.3-1.fc39.x86_64                                                
  authselect-1.4.3-1.fc39.x86_64                                                
  authselect-libs-1.4.3-1.fc39.x86_64                                           
  basesystem-11-18.fc39.noarch                                                  
  bash-5.2.26-1.fc39.x86_64                                                     
  binutils-2.40-14.fc39.x86_64                                                  
  binutils-gold-2.40-14.fc39.x86_64                                             
  bzip2-1.0.8-16.fc39.x86_64                                                    
  bzip2-libs-1.0.8-16.fc39.x86_64                                               
  ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch                              
  coreutils-9.3-5.fc39.x86_64                                                   
  coreutils-common-9.3-5.fc39.x86_64                                            
  cpio-2.14-4.fc39.x86_64                                                       
  cracklib-2.9.11-2.fc39.x86_64                                                 
  crypto-policies-20231204-1.git1e3a2e4.fc39.noarch                             
  curl-8.2.1-5.fc39.x86_64                                                      
  cyrus-sasl-lib-2.1.28-11.fc39.x86_64                                          
  debugedit-5.0-12.fc39.x86_64                                                  
  diffutils-3.10-3.fc39.x86_64                                                  
  dwz-0.15-3.fc39.x86_64                                                        
  ed-1.19-4.fc39.x86_64                                                         
  efi-srpm-macros-5-9.fc39.noarch                                               
  elfutils-0.191-2.fc39.x86_64                                                  
  elfutils-debuginfod-client-0.191-2.fc39.x86_64                                
  elfutils-default-yama-scope-0.191-2.fc39.noarch                               
  elfutils-libelf-0.191-2.fc39.x86_64                                           
  elfutils-libs-0.191-2.fc39.x86_64                                             
  fedora-gpg-keys-39-2.noarch                                                   
  fedora-release-39-36.noarch                                                   
  fedora-release-common-39-36.noarch                                            
  fedora-release-identity-basic-39-36.noarch                                    
  fedora-repos-39-2.noarch                                                      
  file-5.44-5.fc39.x86_64                                                       
  file-libs-5.44-5.fc39.x86_64                                                  
  filesystem-3.18-6.fc39.x86_64                                                 
  findutils-1:4.9.0-5.fc39.x86_64                                               
  fonts-srpm-macros-1:2.0.5-12.fc39.noarch                                      
  forge-srpm-macros-0.3.1-1.fc39.noarch                                         
  fpc-srpm-macros-1.3-8.fc39.noarch                                             
  gawk-5.2.2-2.fc39.x86_64                                                      
  gdb-minimal-14.2-1.fc39.x86_64                                                
  gdbm-libs-1:1.23-4.fc39.x86_64                                                
  ghc-srpm-macros-1.6.1-2.fc39.noarch                                           
  glibc-2.38-18.fc39.x86_64                                                     
  glibc-common-2.38-18.fc39.x86_64                                              
  glibc-gconv-extra-2.38-18.fc39.x86_64                                         
  glibc-minimal-langpack-2.38-18.fc39.x86_64                                    
  gmp-1:6.2.1-5.fc39.x86_64                                                     
  gnat-srpm-macros-6-3.fc39.noarch                                              
  go-srpm-macros-3.5.0-1.fc39.noarch                                            
  grep-3.11-3.fc39.x86_64                                                       
  gzip-1.12-6.fc39.x86_64                                                       
  info-7.0.3-3.fc39.x86_64                                                      
  jansson-2.13.1-7.fc39.x86_64                                                  
  kernel-srpm-macros-1.0-20.fc39.noarch                                         
  keyutils-libs-1.6.3-1.fc39.x86_64                                             
  krb5-libs-1.21.2-3.fc39.x86_64                                                
  libacl-2.3.1-9.fc39.x86_64                                                    
  libarchive-3.7.1-2.fc39.x86_64                                                
  libattr-2.5.1-8.fc39.x86_64                                                   
  libblkid-2.39.4-1.fc39.x86_64                                                 
  libbrotli-1.1.0-1.fc39.x86_64                                                 
  libcap-2.48-9.fc39.x86_64                                                     
  libcap-ng-0.8.3-8.fc39.x86_64                                                 
  libcom_err-1.47.0-2.fc39.x86_64                                               
  libcurl-8.2.1-5.fc39.x86_64                                                   
  libdb-5.3.28-56.fc39.x86_64                                                   
  libeconf-0.5.2-2.fc39.x86_64                                                  
  libevent-2.1.12-9.fc39.x86_64                                                 
  libfdisk-2.39.4-1.fc39.x86_64                                                 
  libffi-3.4.4-4.fc39.x86_64                                                    
  libgcc-13.3.1-1.fc39.x86_64                                                   
  libgomp-13.3.1-1.fc39.x86_64                                                  
  libidn2-2.3.7-1.fc39.x86_64                                                   
  libmount-2.39.4-1.fc39.x86_64                                                 
  libnghttp2-1.55.1-5.fc39.x86_64                                               
  libnsl2-2.0.0-6.fc39.x86_64                                                   
  libpkgconf-1.9.5-2.fc39.x86_64                                                
  libpsl-0.21.2-4.fc39.x86_64                                                   
  libpwquality-1.4.5-6.fc39.x86_64                                              
  libselinux-3.5-5.fc39.x86_64                                                  
  libsemanage-3.5-4.fc39.x86_64                                                 
  libsepol-3.5-2.fc39.x86_64                                                    
  libsigsegv-2.14-5.fc39.x86_64                                                 
  libsmartcols-2.39.4-1.fc39.x86_64                                             
  libssh-0.10.6-2.fc39.x86_64                                                   
  libssh-config-0.10.6-2.fc39.noarch                                            
  libstdc++-13.3.1-1.fc39.x86_64                                                
  libtasn1-4.19.0-3.fc39.x86_64                                                 
  libtirpc-1.3.4-1.rc3.fc39.x86_64                                              
  libtool-ltdl-2.4.7-7.fc39.x86_64                                              
  libunistring-1.1-5.fc39.x86_64                                                
  libutempter-1.2.1-10.fc39.x86_64                                              
  libuuid-2.39.4-1.fc39.x86_64                                                  
  libverto-0.3.2-6.fc39.x86_64                                                  
  libxcrypt-4.4.36-2.fc39.x86_64                                                
  libxml2-2.10.4-3.fc39.x86_64                                                  
  libzstd-1.5.6-1.fc39.x86_64                                                   
  lua-libs-5.4.6-3.fc39.x86_64                                                  
  lua-srpm-macros-1-13.fc39.noarch                                              
  lz4-libs-1.9.4-4.fc39.x86_64                                                  
  mpfr-4.2.0-3.fc39.x86_64                                                      
  ncurses-base-6.4-7.20230520.fc39.1.noarch                                     
  ncurses-libs-6.4-7.20230520.fc39.1.x86_64                                     
  ocaml-srpm-macros-8-2.fc39.noarch                                             
  openblas-srpm-macros-2-14.fc39.noarch                                         
  openldap-2.6.7-1.fc39.x86_64                                                  
  openssl-libs-1:3.1.1-4.fc39.x86_64                                            
  p11-kit-0.25.3-1.fc39.x86_64                                                  
  p11-kit-trust-0.25.3-1.fc39.x86_64                                            
  package-notes-srpm-macros-0.5-9.fc39.noarch                                   
  pam-1.5.3-3.fc39.x86_64                                                       
  pam-libs-1.5.3-3.fc39.x86_64                                                  
  patch-2.7.6-22.fc39.x86_64                                                    
  pcre2-10.42-1.fc39.2.x86_64                                                   
  pcre2-syntax-10.42-1.fc39.2.noarch                                            
  perl-srpm-macros-1-51.fc39.noarch                                             
  pkgconf-1.9.5-2.fc39.x86_64                                                   
  pkgconf-m4-1.9.5-2.fc39.noarch                                                
  pkgconf-pkg-config-1.9.5-2.fc39.x86_64                                        
  popt-1.19-3.fc39.x86_64                                                       
  publicsuffix-list-dafsa-20240107-1.fc39.noarch                                
  pyproject-srpm-macros-1.12.0-1.fc39.noarch                                    
  python-srpm-macros-3.12-4.fc39.noarch                                         
  qt5-srpm-macros-5.15.13-1.fc39.noarch                                         
  qt6-srpm-macros-6.6.2-1.fc39.noarch                                           
  readline-8.2-6.fc39.x86_64                                                    
  redhat-rpm-config-266-1.fc39.noarch                                           
  rpm-4.19.1.1-1.fc39.x86_64                                                    
  rpm-build-4.19.1.1-1.fc39.x86_64                                              
  rpm-build-libs-4.19.1.1-1.fc39.x86_64                                         
  rpm-libs-4.19.1.1-1.fc39.x86_64                                               
  rpm-sequoia-1.6.0-3.fc39.x86_64                                               
  rpmautospec-rpm-macros-0.6.3-1.fc39.noarch                                    
  rust-srpm-macros-26.3-1.fc39.noarch                                           
  sed-4.8-14.fc39.x86_64                                                        
  setup-2.14.4-1.fc39.noarch                                                    
  shadow-utils-2:4.14.0-2.fc39.x86_64                                           
  sqlite-libs-3.42.0-7.fc39.x86_64                                              
  systemd-libs-254.13-1.fc39.x86_64                                             
  tar-2:1.35-2.fc39.x86_64                                                      
  unzip-6.0-62.fc39.x86_64                                                      
  util-linux-2.39.4-1.fc39.x86_64                                               
  util-linux-core-2.39.4-1.fc39.x86_64                                          
  which-2.21-40.fc39.x86_64                                                     
  xxhash-libs-0.8.2-1.fc39.x86_64                                               
  xz-5.4.4-1.fc39.x86_64                                                        
  xz-libs-5.4.4-1.fc39.x86_64                                                   
  zip-3.0-39.fc39.x86_64                                                        
  zlib-1.2.13-4.fc39.x86_64                                                     
  zstd-1.5.6-1.fc39.x86_64                                                      

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.26-1.fc39.x86_64
ansible-srpm-macros-1-12.fc39.noarch
audit-libs-3.1.3-1.fc39.x86_64
authselect-1.4.3-1.fc39.x86_64
authselect-libs-1.4.3-1.fc39.x86_64
basesystem-11-18.fc39.noarch
bash-5.2.26-1.fc39.x86_64
binutils-2.40-14.fc39.x86_64
binutils-gold-2.40-14.fc39.x86_64
bzip2-1.0.8-16.fc39.x86_64
bzip2-libs-1.0.8-16.fc39.x86_64
ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch
coreutils-9.3-5.fc39.x86_64
coreutils-common-9.3-5.fc39.x86_64
cpio-2.14-4.fc39.x86_64
cracklib-2.9.11-2.fc39.x86_64
crypto-policies-20231204-1.git1e3a2e4.fc39.noarch
curl-8.2.1-5.fc39.x86_64
cyrus-sasl-lib-2.1.28-11.fc39.x86_64
debugedit-5.0-12.fc39.x86_64
diffutils-3.10-3.fc39.x86_64
dwz-0.15-3.fc39.x86_64
ed-1.19-4.fc39.x86_64
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.191-2.fc39.x86_64
elfutils-debuginfod-client-0.191-2.fc39.x86_64
elfutils-default-yama-scope-0.191-2.fc39.noarch
elfutils-libelf-0.191-2.fc39.x86_64
elfutils-libs-0.191-2.fc39.x86_64
fedora-gpg-keys-39-2.noarch
fedora-release-39-36.noarch
fedora-release-common-39-36.noarch
fedora-release-identity-basic-39-36.noarch
fedora-repos-39-2.noarch
file-5.44-5.fc39.x86_64
file-libs-5.44-5.fc39.x86_64
filesystem-3.18-6.fc39.x86_64
findutils-4.9.0-5.fc39.x86_64
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.3.1-1.fc39.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.x86_64
gdb-minimal-14.2-1.fc39.x86_64
gdbm-libs-1.23-4.fc39.x86_64
ghc-srpm-macros-1.6.1-2.fc39.noarch
glibc-2.38-18.fc39.x86_64
glibc-common-2.38-18.fc39.x86_64
glibc-gconv-extra-2.38-18.fc39.x86_64
glibc-minimal-langpack-2.38-18.fc39.x86_64
gmp-6.2.1-5.fc39.x86_64
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.5.0-1.fc39.noarch
gpg-pubkey-18b8e74c-62f2920f
grep-3.11-3.fc39.x86_64
gzip-1.12-6.fc39.x86_64
info-7.0.3-3.fc39.x86_64
jansson-2.13.1-7.fc39.x86_64
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.3-1.fc39.x86_64
krb5-libs-1.21.2-3.fc39.x86_64
libacl-2.3.1-9.fc39.x86_64
libarchive-3.7.1-2.fc39.x86_64
libattr-2.5.1-8.fc39.x86_64
libblkid-2.39.4-1.fc39.x86_64
libbrotli-1.1.0-1.fc39.x86_64
libcap-2.48-9.fc39.x86_64
libcap-ng-0.8.3-8.fc39.x86_64
libcom_err-1.47.0-2.fc39.x86_64
libcurl-8.2.1-5.fc39.x86_64
libdb-5.3.28-56.fc39.x86_64
libeconf-0.5.2-2.fc39.x86_64
libevent-2.1.12-9.fc39.x86_64
libfdisk-2.39.4-1.fc39.x86_64
libffi-3.4.4-4.fc39.x86_64
libgcc-13.3.1-1.fc39.x86_64
libgomp-13.3.1-1.fc39.x86_64
libidn2-2.3.7-1.fc39.x86_64
libmount-2.39.4-1.fc39.x86_64
libnghttp2-1.55.1-5.fc39.x86_64
libnsl2-2.0.0-6.fc39.x86_64
libpkgconf-1.9.5-2.fc39.x86_64
libpsl-0.21.2-4.fc39.x86_64
libpwquality-1.4.5-6.fc39.x86_64
libselinux-3.5-5.fc39.x86_64
libsemanage-3.5-4.fc39.x86_64
libsepol-3.5-2.fc39.x86_64
libsigsegv-2.14-5.fc39.x86_64
libsmartcols-2.39.4-1.fc39.x86_64
libssh-0.10.6-2.fc39.x86_64
libssh-config-0.10.6-2.fc39.noarch
libstdc++-13.3.1-1.fc39.x86_64
libtasn1-4.19.0-3.fc39.x86_64
libtirpc-1.3.4-1.rc3.fc39.x86_64
libtool-ltdl-2.4.7-7.fc39.x86_64
libunistring-1.1-5.fc39.x86_64
libutempter-1.2.1-10.fc39.x86_64
libuuid-2.39.4-1.fc39.x86_64
libverto-0.3.2-6.fc39.x86_64
libxcrypt-4.4.36-2.fc39.x86_64
libxml2-2.10.4-3.fc39.x86_64
libzstd-1.5.6-1.fc39.x86_64
lua-libs-5.4.6-3.fc39.x86_64
lua-srpm-macros-1-13.fc39.noarch
lz4-libs-1.9.4-4.fc39.x86_64
mpfr-4.2.0-3.fc39.x86_64
ncurses-base-6.4-7.20230520.fc39.1.noarch
ncurses-libs-6.4-7.20230520.fc39.1.x86_64
ocaml-srpm-macros-8-2.fc39.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.7-1.fc39.x86_64
openssl-libs-3.1.1-4.fc39.x86_64
p11-kit-0.25.3-1.fc39.x86_64
p11-kit-trust-0.25.3-1.fc39.x86_64
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-3.fc39.x86_64
pam-libs-1.5.3-3.fc39.x86_64
patch-2.7.6-22.fc39.x86_64
pcre2-10.42-1.fc39.2.x86_64
pcre2-syntax-10.42-1.fc39.2.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.x86_64
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.x86_64
popt-1.19-3.fc39.x86_64
publicsuffix-list-dafsa-20240107-1.fc39.noarch
pyproject-srpm-macros-1.12.0-1.fc39.noarch
python-srpm-macros-3.12-4.fc39.noarch
qt5-srpm-macros-5.15.13-1.fc39.noarch
qt6-srpm-macros-6.6.2-1.fc39.noarch
readline-8.2-6.fc39.x86_64
redhat-rpm-config-266-1.fc39.noarch
rpm-4.19.1.1-1.fc39.x86_64
rpm-build-4.19.1.1-1.fc39.x86_64
rpm-build-libs-4.19.1.1-1.fc39.x86_64
rpm-libs-4.19.1.1-1.fc39.x86_64
rpm-sequoia-1.6.0-3.fc39.x86_64
rpmautospec-rpm-macros-0.6.3-1.fc39.noarch
rust-srpm-macros-26.3-1.fc39.noarch
sed-4.8-14.fc39.x86_64
setup-2.14.4-1.fc39.noarch
shadow-utils-4.14.0-2.fc39.x86_64
sqlite-libs-3.42.0-7.fc39.x86_64
systemd-libs-254.13-1.fc39.x86_64
tar-1.35-2.fc39.x86_64
unzip-6.0-62.fc39.x86_64
util-linux-2.39.4-1.fc39.x86_64
util-linux-core-2.39.4-1.fc39.x86_64
which-2.21-40.fc39.x86_64
xxhash-libs-0.8.2-1.fc39.x86_64
xz-5.4.4-1.fc39.x86_64
xz-libs-5.4.4-1.fc39.x86_64
zip-3.0-39.fc39.x86_64
zlib-1.2.13-4.fc39.x86_64
zstd-1.5.6-1.fc39.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-1.8.2-1.fc39.copr7692640.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-39-x86_64-1719710865.390544/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.log
/var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.rpm.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-nycz4ntb/R-CRAN-castor/R-CRAN-castor.spec) Config(child) 3 minutes 6 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-1.8.2-1.fc39.copr7692640.src.rpm)  Config(fedora-39-x86_64)
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1719710865.390544/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-1.8.2-1.fc39.copr7692640.src.rpm
Start: build setup for R-CRAN-castor-1.8.2-1.fc39.copr7692640.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-1.8.2-1.fc39.copr7692640.src.rpm

RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered with an entitlement server. You can use subscription-manager to register.

Copr repository                                  33 kB/s | 1.5 kB     00:00    
Copr repository                                  62 MB/s |  26 MB     00:00    
fedora                                          1.2 MB/s |  30 kB     00:00    
updates                                         1.0 MB/s |  27 kB     00:00    
Dependencies resolved.
========================================================================================
 Package                       Arch    Version                          Repo        Size
========================================================================================
Installing:
 R-CRAN-Matrix                 x86_64  1.6.5-1.fc39.copr6886765         copr_base  4.1 M
 R-CRAN-RSpectra               x86_64  0.16.1-1.fc39.copr6664807        copr_base  425 k
 R-CRAN-Rcpp                   x86_64  1.0.12-1.fc39.copr6877523        copr_base  2.0 M
 R-CRAN-jsonlite               x86_64  1.8.8-1.fc39.copr6724909         copr_base  636 k
 R-CRAN-naturalsort            noarch  0.1.3-1.fc39.copr6279895         copr_base   27 k
 R-core                        x86_64  4.3.3-2.fc39                     updates     64 M
 R-devel                       x86_64  4.3.3-2.fc39                     updates     10 k
Installing dependencies:
 R-CRAN-lattice                x86_64  0.22.6-1.fc39.copr7307082        copr_base  1.4 M
 R-core-devel                  x86_64  4.3.3-2.fc39                     updates     93 k
 R-java                        x86_64  4.3.3-2.fc39                     updates     11 k
 R-java-devel                  x86_64  4.3.3-2.fc39                     updates     10 k
 R-littler                     x86_64  0.3.19-1.fc39                    updates     76 k
 R-rpm-macros                  noarch  1.2.1-7.fc39                     fedora      11 k
 abattis-cantarell-vf-fonts    noarch  0.301-10.fc39                    fedora     121 k
 alsa-lib                      x86_64  1.2.12-1.fc39                    updates    521 k
 annobin-docs                  noarch  12.57-1.fc39                     updates     89 k
 annobin-plugin-gcc            x86_64  12.57-1.fc39                     updates    964 k
 avahi-libs                    x86_64  0.8-24.fc39                      fedora      67 k
 brotli                        x86_64  1.1.0-1.fc39                     fedora      20 k
 brotli-devel                  x86_64  1.1.0-1.fc39                     fedora      34 k
 bzip2-devel                   x86_64  1.0.8-16.fc39                    fedora     214 k
 cairo                         x86_64  1.18.0-1.fc39                    fedora     710 k
 cmake-filesystem              x86_64  3.27.7-1.fc39                    fedora      19 k
 copy-jdk-configs              noarch  4.1-3.fc39                       fedora      28 k
 cpp                           x86_64  13.3.1-1.fc39                    updates     11 M
 crypto-policies-scripts       noarch  20231204-1.git1e3a2e4.fc39       updates    117 k
 cups-libs                     x86_64  1:2.4.8-3.fc39                   updates    267 k
 dbus-libs                     x86_64  1:1.14.10-1.fc39                 fedora     156 k
 default-fonts-core-sans       noarch  4.0-9.fc39                       fedora      32 k
 desktop-file-utils            x86_64  0.26-9.fc39                      fedora      72 k
 emacs-filesystem              noarch  1:29.3-1.fc39                    updates    7.2 k
 expat                         x86_64  2.6.2-1.fc39                     updates    114 k
 flexiblas                     x86_64  3.4.4-1.fc39                     updates     25 k
 flexiblas-devel               x86_64  3.4.4-1.fc39                     updates    121 k
 flexiblas-netlib              x86_64  3.4.4-1.fc39                     updates    3.1 M
 flexiblas-netlib64            x86_64  3.4.4-1.fc39                     updates    3.0 M
 flexiblas-openblas-openmp     x86_64  3.4.4-1.fc39                     updates     17 k
 flexiblas-openblas-openmp64   x86_64  3.4.4-1.fc39                     updates     17 k
 fontconfig                    x86_64  2.14.2-6.fc39                    updates    296 k
 fontconfig-devel              x86_64  2.14.2-6.fc39                    updates    164 k
 fonts-filesystem              noarch  1:2.0.5-12.fc39                  fedora     8.2 k
 freetype                      x86_64  2.13.1-2.fc39                    fedora     414 k
 freetype-devel                x86_64  2.13.1-2.fc39                    fedora     950 k
 fribidi                       x86_64  1.0.13-2.fc39                    fedora      91 k
 gc                            x86_64  8.2.2-4.fc39                     fedora     110 k
 gcc                           x86_64  13.3.1-1.fc39                    updates     34 M
 gcc-c++                       x86_64  13.3.1-1.fc39                    updates     13 M
 gcc-gfortran                  x86_64  13.3.1-1.fc39                    updates     12 M
 gcc-plugin-annobin            x86_64  13.3.1-1.fc39                    updates     56 k
 gettext                       x86_64  0.22-2.fc39                      fedora     1.1 M
 gettext-envsubst              x86_64  0.22-2.fc39                      fedora      36 k
 gettext-libs                  x86_64  0.22-2.fc39                      fedora     328 k
 gettext-runtime               x86_64  0.22-2.fc39                      fedora     120 k
 glib2                         x86_64  2.78.6-1.fc39                    updates    2.8 M
 glib2-devel                   x86_64  2.78.6-1.fc39                    updates    594 k
 glibc-devel                   x86_64  2.38-18.fc39                     updates     86 k
 glibc-headers-x86             noarch  2.38-18.fc39                     updates    571 k
 gnutls                        x86_64  3.8.5-1.fc39                     updates    1.1 M
 google-noto-fonts-common      noarch  20240101-1.fc39                  updates     17 k
 google-noto-sans-vf-fonts     noarch  20240101-1.fc39                  updates    593 k
 graphite2                     x86_64  1.3.14-12.fc39                   fedora      95 k
 graphite2-devel               x86_64  1.3.14-12.fc39                   fedora      20 k
 guile22                       x86_64  2.2.7-9.fc39                     fedora     6.5 M
 harfbuzz                      x86_64  8.2.1-2.fc39                     fedora     975 k
 harfbuzz-devel                x86_64  8.2.1-2.fc39                     fedora     450 k
 harfbuzz-icu                  x86_64  8.2.1-2.fc39                     fedora      17 k
 java-17-openjdk               x86_64  1:17.0.11.0.9-1.fc39             updates    404 k
 java-17-openjdk-devel         x86_64  1:17.0.11.0.9-1.fc39             updates    4.7 M
 java-17-openjdk-headless      x86_64  1:17.0.11.0.9-1.fc39             updates     44 M
 javapackages-filesystem       noarch  6.1.0-10.fc39                    fedora      12 k
 jbigkit-libs                  x86_64  2.1-26.fc39                      fedora      53 k
 kernel-headers                x86_64  6.9.4-100.fc39                   updates    1.6 M
 libICE                        x86_64  1.0.10-11.fc39                   fedora      70 k
 libRmath                      x86_64  4.3.3-2.fc39                     updates    121 k
 libRmath-devel                x86_64  4.3.3-2.fc39                     updates     16 k
 libSM                         x86_64  1.2.3-13.fc39                    fedora      41 k
 libX11                        x86_64  1.8.9-1.fc39                     updates    650 k
 libX11-common                 noarch  1.8.9-1.fc39                     updates    176 k
 libX11-devel                  x86_64  1.8.9-1.fc39                     updates    1.0 M
 libX11-xcb                    x86_64  1.8.9-1.fc39                     updates     12 k
 libXau                        x86_64  1.0.11-3.fc39                    fedora      31 k
 libXau-devel                  x86_64  1.0.11-3.fc39                    fedora      14 k
 libXcomposite                 x86_64  0.4.5-10.fc39                    fedora      23 k
 libXext                       x86_64  1.3.5-3.fc39                     fedora      39 k
 libXft                        x86_64  2.3.8-3.fc39                     fedora      72 k
 libXft-devel                  x86_64  2.3.8-3.fc39                     fedora      50 k
 libXi                         x86_64  1.8.1-2.fc39                     fedora      40 k
 libXmu                        x86_64  1.1.4-3.fc39                     fedora      76 k
 libXrender                    x86_64  0.9.11-3.fc39                    fedora      27 k
 libXrender-devel              x86_64  0.9.11-3.fc39                    fedora      19 k
 libXt                         x86_64  1.2.1-5.fc39                     fedora     178 k
 libXtst                       x86_64  1.2.4-3.fc39                     fedora      20 k
 libb2                         x86_64  0.98.1-9.fc39                    fedora      25 k
 libblkid-devel                x86_64  2.39.4-1.fc39                    updates     18 k
 libdatrie                     x86_64  0.2.13-7.fc39                    fedora      32 k
 libffi-devel                  x86_64  3.4.4-4.fc39                     fedora      29 k
 libfontenc                    x86_64  1.1.6-3.fc39                     fedora      32 k
 libgfortran                   x86_64  13.3.1-1.fc39                    updates    906 k
 libicu                        x86_64  73.2-2.fc39                      fedora      11 M
 libicu-devel                  x86_64  73.2-2.fc39                      fedora     924 k
 libjpeg-turbo                 x86_64  2.1.4-3.fc39                     fedora     183 k
 liblerc                       x86_64  4.0.0-4.fc39                     fedora     201 k
 libmount-devel                x86_64  2.39.4-1.fc39                    updates     18 k
 libmpc                        x86_64  1.3.1-3.fc39                     fedora      70 k
 libpng                        x86_64  2:1.6.37-15.fc39                 fedora     119 k
 libpng-devel                  x86_64  2:1.6.37-15.fc39                 fedora     291 k
 libquadmath                   x86_64  13.3.1-1.fc39                    updates    203 k
 libquadmath-devel             x86_64  13.3.1-1.fc39                    updates     45 k
 libselinux-devel              x86_64  3.5-5.fc39                       fedora     151 k
 libsepol-devel                x86_64  3.5-2.fc39                       fedora      49 k
 libstdc++-devel               x86_64  13.3.1-1.fc39                    updates    2.6 M
 libthai                       x86_64  0.1.29-6.fc39                    fedora     213 k
 libtiff                       x86_64  4.4.0-8.fc39                     fedora     202 k
 libtirpc-devel                x86_64  1.3.4-1.rc3.fc39                 updates    124 k
 libwebp                       x86_64  1.3.2-2.fc39                     fedora     284 k
 libxcb                        x86_64  1.13.1-12.fc39                   fedora     233 k
 libxcb-devel                  x86_64  1.13.1-12.fc39                   fedora     1.4 M
 libxcrypt-devel               x86_64  4.4.36-2.fc39                    fedora      30 k
 libxml2-devel                 x86_64  2.10.4-3.fc39                    fedora     527 k
 lksctp-tools                  x86_64  1.0.19-4.fc39                    fedora      92 k
 lua                           x86_64  5.4.6-3.fc39                     fedora     191 k
 lua-posix                     x86_64  36.2.1-3.fc39                    fedora     143 k
 make                          x86_64  1:4.4.1-2.fc39                   fedora     589 k
 mkfontscale                   x86_64  1.2.2-4.fc39                     fedora      32 k
 mpdecimal                     x86_64  2.5.1-7.fc39                     fedora      89 k
 nettle                        x86_64  3.9.1-2.fc39                     fedora     425 k
 nspr                          x86_64  4.35.0-21.fc39                   updates    137 k
 nss                           x86_64  3.101.0-1.fc39                   updates    707 k
 nss-softokn                   x86_64  3.101.0-1.fc39                   updates    417 k
 nss-softokn-freebl            x86_64  3.101.0-1.fc39                   updates    299 k
 nss-sysinit                   x86_64  3.101.0-1.fc39                   updates     18 k
 nss-util                      x86_64  3.101.0-1.fc39                   updates     88 k
 openblas                      x86_64  0.3.21-6.fc39                    fedora      35 k
 openblas-openmp               x86_64  0.3.21-6.fc39                    fedora     4.9 M
 openblas-openmp64             x86_64  0.3.21-6.fc39                    fedora     4.8 M
 pango                         x86_64  1.51.0-1.fc39                    fedora     343 k
 pcre2-devel                   x86_64  10.42-1.fc39.2                   fedora     505 k
 pcre2-utf16                   x86_64  10.42-1.fc39.2                   fedora     212 k
 pcre2-utf32                   x86_64  10.42-1.fc39.2                   fedora     200 k
 pixman                        x86_64  0.42.2-2.fc39                    fedora     288 k
 python-pip-wheel              noarch  23.2.1-2.fc39                    updates    1.5 M
 python3                       x86_64  3.12.3-2.fc39                    updates     27 k
 python3-libs                  x86_64  3.12.3-2.fc39                    updates    9.2 M
 python3-setuptools            noarch  67.7.2-7.fc39                    fedora     1.5 M
 sysprof-capture-devel         x86_64  45.1-1.fc39                      updates     59 k
 tcl                           x86_64  1:8.6.12-5.fc39                  fedora     1.1 M
 tcl-devel                     x86_64  1:8.6.12-5.fc39                  fedora     169 k
 tk                            x86_64  1:8.6.12-5.fc39                  fedora     1.6 M
 tk-devel                      x86_64  1:8.6.12-5.fc39                  fedora     537 k
 tre                           x86_64  0.8.0-41.20140228gitc2f5d13.fc39 fedora      43 k
 tre-common                    noarch  0.8.0-41.20140228gitc2f5d13.fc39 fedora      31 k
 tre-devel                     x86_64  0.8.0-41.20140228gitc2f5d13.fc39 fedora      12 k
 ttmkfdir                      x86_64  3.0.9-69.fc39                    fedora      56 k
 tzdata                        noarch  2024a-2.fc39                     updates    715 k
 tzdata-java                   noarch  2024a-2.fc39                     updates    208 k
 xdg-utils                     noarch  1.1.3-15.fc39                    fedora      77 k
 xml-common                    noarch  0.6.3-61.fc39                    fedora      31 k
 xorg-x11-fonts-Type1          noarch  7.5-36.fc39                      fedora     504 k
 xorg-x11-proto-devel          noarch  2023.2-2.fc39                    fedora     298 k
 xz-devel                      x86_64  5.4.4-1.fc39                     fedora      66 k
 zlib-devel                    x86_64  1.2.13-4.fc39                    fedora      45 k

Transaction Summary
========================================================================================
Install  161 Packages

Total download size: 275 M
Installed size: 871 M
Downloading Packages:
(1/161): R-CRAN-RSpectra-0.16.1-1.fc39.copr6664 3.9 MB/s | 425 kB     00:00    
(2/161): R-CRAN-Rcpp-1.0.12-1.fc39.copr6877523.  12 MB/s | 2.0 MB     00:00    
(3/161): R-CRAN-Matrix-1.6.5-1.fc39.copr6886765  21 MB/s | 4.1 MB     00:00    
(4/161): R-CRAN-jsonlite-1.8.8-1.fc39.copr67249 6.8 MB/s | 636 kB     00:00    
(5/161): R-CRAN-lattice-0.22.6-1.fc39.copr73070  33 MB/s | 1.4 MB     00:00    
(6/161): R-CRAN-naturalsort-0.1.3-1.fc39.copr62 1.2 MB/s |  27 kB     00:00    
(7/161): R-rpm-macros-1.2.1-7.fc39.noarch.rpm   164 kB/s |  11 kB     00:00    
(8/161): brotli-1.1.0-1.fc39.x86_64.rpm         1.0 MB/s |  20 kB     00:00    
(9/161): avahi-libs-0.8-24.fc39.x86_64.rpm      844 kB/s |  67 kB     00:00    
(10/161): abattis-cantarell-vf-fonts-0.301-10.f 1.1 MB/s | 121 kB     00:00    
(11/161): brotli-devel-1.1.0-1.fc39.x86_64.rpm  930 kB/s |  34 kB     00:00    
(12/161): cmake-filesystem-3.27.7-1.fc39.x86_64 1.0 MB/s |  19 kB     00:00    
(13/161): bzip2-devel-1.0.8-16.fc39.x86_64.rpm  3.8 MB/s | 214 kB     00:00    
(14/161): copy-jdk-configs-4.1-3.fc39.noarch.rp 1.4 MB/s |  28 kB     00:00    
(15/161): dbus-libs-1.14.10-1.fc39.x86_64.rpm   4.8 MB/s | 156 kB     00:00    
(16/161): default-fonts-core-sans-4.0-9.fc39.no 983 kB/s |  32 kB     00:00    
(17/161): desktop-file-utils-0.26-9.fc39.x86_64 2.0 MB/s |  72 kB     00:00    
(18/161): fonts-filesystem-2.0.5-12.fc39.noarch 301 kB/s | 8.2 kB     00:00    
(19/161): cairo-1.18.0-1.fc39.x86_64.rpm        6.6 MB/s | 710 kB     00:00    
(20/161): fribidi-1.0.13-2.fc39.x86_64.rpm      2.9 MB/s |  91 kB     00:00    
(21/161): freetype-2.13.1-2.fc39.x86_64.rpm     9.6 MB/s | 414 kB     00:00    
(22/161): gc-8.2.2-4.fc39.x86_64.rpm            4.5 MB/s | 110 kB     00:00    
(23/161): gettext-envsubst-0.22-2.fc39.x86_64.r 1.7 MB/s |  36 kB     00:00    
(24/161): freetype-devel-2.13.1-2.fc39.x86_64.r 9.7 MB/s | 950 kB     00:00    
(25/161): gettext-0.22-2.fc39.x86_64.rpm         15 MB/s | 1.1 MB     00:00    
(26/161): gettext-libs-0.22-2.fc39.x86_64.rpm   9.1 MB/s | 328 kB     00:00    
(27/161): gettext-runtime-0.22-2.fc39.x86_64.rp 4.9 MB/s | 120 kB     00:00    
(28/161): graphite2-devel-1.3.14-12.fc39.x86_64 1.0 MB/s |  20 kB     00:00    
(29/161): graphite2-1.3.14-12.fc39.x86_64.rpm   4.1 MB/s |  95 kB     00:00    
(30/161): harfbuzz-devel-8.2.1-2.fc39.x86_64.rp 9.2 MB/s | 450 kB     00:00    
(31/161): harfbuzz-icu-8.2.1-2.fc39.x86_64.rpm  520 kB/s |  17 kB     00:00    
(32/161): harfbuzz-8.2.1-2.fc39.x86_64.rpm       11 MB/s | 975 kB     00:00    
(33/161): javapackages-filesystem-6.1.0-10.fc39 561 kB/s |  12 kB     00:00    
(34/161): libICE-1.0.10-11.fc39.x86_64.rpm      2.5 MB/s |  70 kB     00:00    
(35/161): libSM-1.2.3-13.fc39.x86_64.rpm        1.1 MB/s |  41 kB     00:00    
(36/161): libXau-1.0.11-3.fc39.x86_64.rpm       1.4 MB/s |  31 kB     00:00    
(37/161): libXau-devel-1.0.11-3.fc39.x86_64.rpm 626 kB/s |  14 kB     00:00    
(38/161): libXcomposite-0.4.5-10.fc39.x86_64.rp 1.2 MB/s |  23 kB     00:00    
(39/161): libXext-1.3.5-3.fc39.x86_64.rpm       1.2 MB/s |  39 kB     00:00    
(40/161): libXft-2.3.8-3.fc39.x86_64.rpm        3.2 MB/s |  72 kB     00:00    
(41/161): libXft-devel-2.3.8-3.fc39.x86_64.rpm  2.4 MB/s |  50 kB     00:00    
(42/161): libXi-1.8.1-2.fc39.x86_64.rpm         1.9 MB/s |  40 kB     00:00    
(43/161): jbigkit-libs-2.1-26.fc39.x86_64.rpm   215 kB/s |  53 kB     00:00    
(44/161): libXmu-1.1.4-3.fc39.x86_64.rpm        3.6 MB/s |  76 kB     00:00    
(45/161): libXrender-0.9.11-3.fc39.x86_64.rpm   1.4 MB/s |  27 kB     00:00    
(46/161): libXrender-devel-0.9.11-3.fc39.x86_64 1.0 MB/s |  19 kB     00:00    
(47/161): libXt-1.2.1-5.fc39.x86_64.rpm         7.3 MB/s | 178 kB     00:00    
(48/161): libXtst-1.2.4-3.fc39.x86_64.rpm       1.0 MB/s |  20 kB     00:00    
(49/161): guile22-2.2.7-9.fc39.x86_64.rpm        16 MB/s | 6.5 MB     00:00    
(50/161): libb2-0.98.1-9.fc39.x86_64.rpm        981 kB/s |  25 kB     00:00    
(51/161): libdatrie-0.2.13-7.fc39.x86_64.rpm    1.6 MB/s |  32 kB     00:00    
(52/161): libffi-devel-3.4.4-4.fc39.x86_64.rpm  1.5 MB/s |  29 kB     00:00    
(53/161): libfontenc-1.1.6-3.fc39.x86_64.rpm    1.6 MB/s |  32 kB     00:00    
(54/161): libjpeg-turbo-2.1.4-3.fc39.x86_64.rpm 6.8 MB/s | 183 kB     00:00    
(55/161): liblerc-4.0.0-4.fc39.x86_64.rpm       7.5 MB/s | 201 kB     00:00    
(56/161): libicu-devel-73.2-2.fc39.x86_64.rpm    15 MB/s | 924 kB     00:00    
(57/161): libmpc-1.3.1-3.fc39.x86_64.rpm        3.3 MB/s |  70 kB     00:00    
(58/161): libpng-1.6.37-15.fc39.x86_64.rpm      5.0 MB/s | 119 kB     00:00    
(59/161): libpng-devel-1.6.37-15.fc39.x86_64.rp 9.5 MB/s | 291 kB     00:00    
(60/161): libselinux-devel-3.5-5.fc39.x86_64.rp 6.2 MB/s | 151 kB     00:00    
(61/161): libsepol-devel-3.5-2.fc39.x86_64.rpm  2.2 MB/s |  49 kB     00:00    
(62/161): libthai-0.1.29-6.fc39.x86_64.rpm      6.6 MB/s | 213 kB     00:00    
(63/161): libtiff-4.4.0-8.fc39.x86_64.rpm       7.4 MB/s | 202 kB     00:00    
(64/161): libwebp-1.3.2-2.fc39.x86_64.rpm       9.5 MB/s | 284 kB     00:00    
(65/161): libxcb-1.13.1-12.fc39.x86_64.rpm      8.0 MB/s | 233 kB     00:00    
(66/161): libxcrypt-devel-4.4.36-2.fc39.x86_64. 1.4 MB/s |  30 kB     00:00    
(67/161): libxml2-devel-2.10.4-3.fc39.x86_64.rp  13 MB/s | 527 kB     00:00    
(68/161): libxcb-devel-1.13.1-12.fc39.x86_64.rp  17 MB/s | 1.4 MB     00:00    
(69/161): lksctp-tools-1.0.19-4.fc39.x86_64.rpm 4.2 MB/s |  92 kB     00:00    
(70/161): lua-5.4.6-3.fc39.x86_64.rpm           6.9 MB/s | 191 kB     00:00    
(71/161): lua-posix-36.2.1-3.fc39.x86_64.rpm    5.7 MB/s | 143 kB     00:00    
(72/161): mkfontscale-1.2.2-4.fc39.x86_64.rpm   1.4 MB/s |  32 kB     00:00    
(73/161): make-4.4.1-2.fc39.x86_64.rpm           12 MB/s | 589 kB     00:00    
(74/161): mpdecimal-2.5.1-7.fc39.x86_64.rpm     3.8 MB/s |  89 kB     00:00    
(75/161): openblas-0.3.21-6.fc39.x86_64.rpm     1.3 MB/s |  35 kB     00:00    
(76/161): nettle-3.9.1-2.fc39.x86_64.rpm        9.5 MB/s | 425 kB     00:00    
(77/161): openblas-openmp64-0.3.21-6.fc39.x86_6 9.3 MB/s | 4.8 MB     00:00    
(78/161): pango-1.51.0-1.fc39.x86_64.rpm        3.7 MB/s | 343 kB     00:00    
(79/161): openblas-openmp-0.3.21-6.fc39.x86_64. 7.7 MB/s | 4.9 MB     00:00    
(80/161): pcre2-utf16-10.42-1.fc39.2.x86_64.rpm 3.9 MB/s | 212 kB     00:00    
(81/161): pcre2-devel-10.42-1.fc39.2.x86_64.rpm 5.7 MB/s | 505 kB     00:00    
(82/161): pcre2-utf32-10.42-1.fc39.2.x86_64.rpm 4.3 MB/s | 200 kB     00:00    
(83/161): pixman-0.42.2-2.fc39.x86_64.rpm       3.7 MB/s | 288 kB     00:00    
(84/161): tcl-8.6.12-5.fc39.x86_64.rpm          5.6 MB/s | 1.1 MB     00:00    
(85/161): python3-setuptools-67.7.2-7.fc39.noar 5.3 MB/s | 1.5 MB     00:00    
(86/161): tcl-devel-8.6.12-5.fc39.x86_64.rpm    3.2 MB/s | 169 kB     00:00    
(87/161): libicu-73.2-2.fc39.x86_64.rpm         6.9 MB/s |  11 MB     00:01    
(88/161): tre-0.8.0-41.20140228gitc2f5d13.fc39. 620 kB/s |  43 kB     00:00    
(89/161): tre-common-0.8.0-41.20140228gitc2f5d1 379 kB/s |  31 kB     00:00    
(90/161): tre-devel-0.8.0-41.20140228gitc2f5d13 224 kB/s |  12 kB     00:00    
(91/161): ttmkfdir-3.0.9-69.fc39.x86_64.rpm     2.2 MB/s |  56 kB     00:00    
(92/161): xdg-utils-1.1.3-15.fc39.noarch.rpm    3.3 MB/s |  77 kB     00:00    
(93/161): xml-common-0.6.3-61.fc39.noarch.rpm   1.0 MB/s |  31 kB     00:00    
(94/161): tk-8.6.12-5.fc39.x86_64.rpm           3.8 MB/s | 1.6 MB     00:00    
(95/161): xorg-x11-proto-devel-2023.2-2.fc39.no 6.6 MB/s | 298 kB     00:00    
(96/161): xorg-x11-fonts-Type1-7.5-36.fc39.noar 6.2 MB/s | 504 kB     00:00    
(97/161): xz-devel-5.4.4-1.fc39.x86_64.rpm      3.2 MB/s |  66 kB     00:00    
(98/161): zlib-devel-1.2.13-4.fc39.x86_64.rpm   1.9 MB/s |  45 kB     00:00    
(99/161): tk-devel-8.6.12-5.fc39.x86_64.rpm     878 kB/s | 537 kB     00:00    
(100/161): R-core-devel-4.3.3-2.fc39.x86_64.rpm 442 kB/s |  93 kB     00:00    
(101/161): R-devel-4.3.3-2.fc39.x86_64.rpm       80 kB/s |  10 kB     00:00    
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Total                                            11 MB/s | 275 MB     00:24     
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  Verifying        : tzdata-java-2024a-2.fc39.noarch                    161/161 
Installed products updated.

Installed:
  R-CRAN-Matrix-1.6.5-1.fc39.copr6886765.x86_64                                 
  R-CRAN-RSpectra-0.16.1-1.fc39.copr6664807.x86_64                              
  R-CRAN-Rcpp-1.0.12-1.fc39.copr6877523.x86_64                                  
  R-CRAN-jsonlite-1.8.8-1.fc39.copr6724909.x86_64                               
  R-CRAN-lattice-0.22.6-1.fc39.copr7307082.x86_64                               
  R-CRAN-naturalsort-0.1.3-1.fc39.copr6279895.noarch                            
  R-core-4.3.3-2.fc39.x86_64                                                    
  R-core-devel-4.3.3-2.fc39.x86_64                                              
  R-devel-4.3.3-2.fc39.x86_64                                                   
  R-java-4.3.3-2.fc39.x86_64                                                    
  R-java-devel-4.3.3-2.fc39.x86_64                                              
  R-littler-0.3.19-1.fc39.x86_64                                                
  R-rpm-macros-1.2.1-7.fc39.noarch                                              
  abattis-cantarell-vf-fonts-0.301-10.fc39.noarch                               
  alsa-lib-1.2.12-1.fc39.x86_64                                                 
  annobin-docs-12.57-1.fc39.noarch                                              
  annobin-plugin-gcc-12.57-1.fc39.x86_64                                        
  avahi-libs-0.8-24.fc39.x86_64                                                 
  brotli-1.1.0-1.fc39.x86_64                                                    
  brotli-devel-1.1.0-1.fc39.x86_64                                              
  bzip2-devel-1.0.8-16.fc39.x86_64                                              
  cairo-1.18.0-1.fc39.x86_64                                                    
  cmake-filesystem-3.27.7-1.fc39.x86_64                                         
  copy-jdk-configs-4.1-3.fc39.noarch                                            
  cpp-13.3.1-1.fc39.x86_64                                                      
  crypto-policies-scripts-20231204-1.git1e3a2e4.fc39.noarch                     
  cups-libs-1:2.4.8-3.fc39.x86_64                                               
  dbus-libs-1:1.14.10-1.fc39.x86_64                                             
  default-fonts-core-sans-4.0-9.fc39.noarch                                     
  desktop-file-utils-0.26-9.fc39.x86_64                                         
  emacs-filesystem-1:29.3-1.fc39.noarch                                         
  expat-2.6.2-1.fc39.x86_64                                                     
  flexiblas-3.4.4-1.fc39.x86_64                                                 
  flexiblas-devel-3.4.4-1.fc39.x86_64                                           
  flexiblas-netlib-3.4.4-1.fc39.x86_64                                          
  flexiblas-netlib64-3.4.4-1.fc39.x86_64                                        
  flexiblas-openblas-openmp-3.4.4-1.fc39.x86_64                                 
  flexiblas-openblas-openmp64-3.4.4-1.fc39.x86_64                               
  fontconfig-2.14.2-6.fc39.x86_64                                               
  fontconfig-devel-2.14.2-6.fc39.x86_64                                         
  fonts-filesystem-1:2.0.5-12.fc39.noarch                                       
  freetype-2.13.1-2.fc39.x86_64                                                 
  freetype-devel-2.13.1-2.fc39.x86_64                                           
  fribidi-1.0.13-2.fc39.x86_64                                                  
  gc-8.2.2-4.fc39.x86_64                                                        
  gcc-13.3.1-1.fc39.x86_64                                                      
  gcc-c++-13.3.1-1.fc39.x86_64                                                  
  gcc-gfortran-13.3.1-1.fc39.x86_64                                             
  gcc-plugin-annobin-13.3.1-1.fc39.x86_64                                       
  gettext-0.22-2.fc39.x86_64                                                    
  gettext-envsubst-0.22-2.fc39.x86_64                                           
  gettext-libs-0.22-2.fc39.x86_64                                               
  gettext-runtime-0.22-2.fc39.x86_64                                            
  glib2-2.78.6-1.fc39.x86_64                                                    
  glib2-devel-2.78.6-1.fc39.x86_64                                              
  glibc-devel-2.38-18.fc39.x86_64                                               
  glibc-headers-x86-2.38-18.fc39.noarch                                         
  gnutls-3.8.5-1.fc39.x86_64                                                    
  google-noto-fonts-common-20240101-1.fc39.noarch                               
  google-noto-sans-vf-fonts-20240101-1.fc39.noarch                              
  graphite2-1.3.14-12.fc39.x86_64                                               
  graphite2-devel-1.3.14-12.fc39.x86_64                                         
  guile22-2.2.7-9.fc39.x86_64                                                   
  harfbuzz-8.2.1-2.fc39.x86_64                                                  
  harfbuzz-devel-8.2.1-2.fc39.x86_64                                            
  harfbuzz-icu-8.2.1-2.fc39.x86_64                                              
  java-17-openjdk-1:17.0.11.0.9-1.fc39.x86_64                                   
  java-17-openjdk-devel-1:17.0.11.0.9-1.fc39.x86_64                             
  java-17-openjdk-headless-1:17.0.11.0.9-1.fc39.x86_64                          
  javapackages-filesystem-6.1.0-10.fc39.noarch                                  
  jbigkit-libs-2.1-26.fc39.x86_64                                               
  kernel-headers-6.9.4-100.fc39.x86_64                                          
  libICE-1.0.10-11.fc39.x86_64                                                  
  libRmath-4.3.3-2.fc39.x86_64                                                  
  libRmath-devel-4.3.3-2.fc39.x86_64                                            
  libSM-1.2.3-13.fc39.x86_64                                                    
  libX11-1.8.9-1.fc39.x86_64                                                    
  libX11-common-1.8.9-1.fc39.noarch                                             
  libX11-devel-1.8.9-1.fc39.x86_64                                              
  libX11-xcb-1.8.9-1.fc39.x86_64                                                
  libXau-1.0.11-3.fc39.x86_64                                                   
  libXau-devel-1.0.11-3.fc39.x86_64                                             
  libXcomposite-0.4.5-10.fc39.x86_64                                            
  libXext-1.3.5-3.fc39.x86_64                                                   
  libXft-2.3.8-3.fc39.x86_64                                                    
  libXft-devel-2.3.8-3.fc39.x86_64                                              
  libXi-1.8.1-2.fc39.x86_64                                                     
  libXmu-1.1.4-3.fc39.x86_64                                                    
  libXrender-0.9.11-3.fc39.x86_64                                               
  libXrender-devel-0.9.11-3.fc39.x86_64                                         
  libXt-1.2.1-5.fc39.x86_64                                                     
  libXtst-1.2.4-3.fc39.x86_64                                                   
  libb2-0.98.1-9.fc39.x86_64                                                    
  libblkid-devel-2.39.4-1.fc39.x86_64                                           
  libdatrie-0.2.13-7.fc39.x86_64                                                
  libffi-devel-3.4.4-4.fc39.x86_64                                              
  libfontenc-1.1.6-3.fc39.x86_64                                                
  libgfortran-13.3.1-1.fc39.x86_64                                              
  libicu-73.2-2.fc39.x86_64                                                     
  libicu-devel-73.2-2.fc39.x86_64                                               
  libjpeg-turbo-2.1.4-3.fc39.x86_64                                             
  liblerc-4.0.0-4.fc39.x86_64                                                   
  libmount-devel-2.39.4-1.fc39.x86_64                                           
  libmpc-1.3.1-3.fc39.x86_64                                                    
  libpng-2:1.6.37-15.fc39.x86_64                                                
  libpng-devel-2:1.6.37-15.fc39.x86_64                                          
  libquadmath-13.3.1-1.fc39.x86_64                                              
  libquadmath-devel-13.3.1-1.fc39.x86_64                                        
  libselinux-devel-3.5-5.fc39.x86_64                                            
  libsepol-devel-3.5-2.fc39.x86_64                                              
  libstdc++-devel-13.3.1-1.fc39.x86_64                                          
  libthai-0.1.29-6.fc39.x86_64                                                  
  libtiff-4.4.0-8.fc39.x86_64                                                   
  libtirpc-devel-1.3.4-1.rc3.fc39.x86_64                                        
  libwebp-1.3.2-2.fc39.x86_64                                                   
  libxcb-1.13.1-12.fc39.x86_64                                                  
  libxcb-devel-1.13.1-12.fc39.x86_64                                            
  libxcrypt-devel-4.4.36-2.fc39.x86_64                                          
  libxml2-devel-2.10.4-3.fc39.x86_64                                            
  lksctp-tools-1.0.19-4.fc39.x86_64                                             
  lua-5.4.6-3.fc39.x86_64                                                       
  lua-posix-36.2.1-3.fc39.x86_64                                                
  make-1:4.4.1-2.fc39.x86_64                                                    
  mkfontscale-1.2.2-4.fc39.x86_64                                               
  mpdecimal-2.5.1-7.fc39.x86_64                                                 
  nettle-3.9.1-2.fc39.x86_64                                                    
  nspr-4.35.0-21.fc39.x86_64                                                    
  nss-3.101.0-1.fc39.x86_64                                                     
  nss-softokn-3.101.0-1.fc39.x86_64                                             
  nss-softokn-freebl-3.101.0-1.fc39.x86_64                                      
  nss-sysinit-3.101.0-1.fc39.x86_64                                             
  nss-util-3.101.0-1.fc39.x86_64                                                
  openblas-0.3.21-6.fc39.x86_64                                                 
  openblas-openmp-0.3.21-6.fc39.x86_64                                          
  openblas-openmp64-0.3.21-6.fc39.x86_64                                        
  pango-1.51.0-1.fc39.x86_64                                                    
  pcre2-devel-10.42-1.fc39.2.x86_64                                             
  pcre2-utf16-10.42-1.fc39.2.x86_64                                             
  pcre2-utf32-10.42-1.fc39.2.x86_64                                             
  pixman-0.42.2-2.fc39.x86_64                                                   
  python-pip-wheel-23.2.1-2.fc39.noarch                                         
  python3-3.12.3-2.fc39.x86_64                                                  
  python3-libs-3.12.3-2.fc39.x86_64                                             
  python3-setuptools-67.7.2-7.fc39.noarch                                       
  sysprof-capture-devel-45.1-1.fc39.x86_64                                      
  tcl-1:8.6.12-5.fc39.x86_64                                                    
  tcl-devel-1:8.6.12-5.fc39.x86_64                                              
  tk-1:8.6.12-5.fc39.x86_64                                                     
  tk-devel-1:8.6.12-5.fc39.x86_64                                               
  tre-0.8.0-41.20140228gitc2f5d13.fc39.x86_64                                   
  tre-common-0.8.0-41.20140228gitc2f5d13.fc39.noarch                            
  tre-devel-0.8.0-41.20140228gitc2f5d13.fc39.x86_64                             
  ttmkfdir-3.0.9-69.fc39.x86_64                                                 
  tzdata-2024a-2.fc39.noarch                                                    
  tzdata-java-2024a-2.fc39.noarch                                               
  xdg-utils-1.1.3-15.fc39.noarch                                                
  xml-common-0.6.3-61.fc39.noarch                                               
  xorg-x11-fonts-Type1-7.5-36.fc39.noarch                                       
  xorg-x11-proto-devel-2023.2-2.fc39.noarch                                     
  xz-devel-5.4.4-1.fc39.x86_64                                                  
  zlib-devel-1.2.13-4.fc39.x86_64                                               

Complete!
Finish: build setup for R-CRAN-castor-1.8.2-1.fc39.copr7692640.src.rpm
Start: rpmbuild R-CRAN-castor-1.8.2-1.fc39.copr7692640.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.Kim1tP
+ 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_1.8.2.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.Gfjfcw
+ 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   -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   -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   -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   -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,now -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.6Ltxl3
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64
++ dirname /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.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   -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   -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   -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   -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,now -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-1.8.2-1.fc39.copr7692640.x86_64/usr/local/lib/R/library
+ /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.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) 13.3.1 20240522 (Red Hat 13.3.1-1)’
using C++ compiler: ‘g++ (GCC) 13.3.1 20240522 (Red Hat 13.3.1-1)’
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   -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   -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: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   -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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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:8956:25:   required from here
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:8956:25:   required from here
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:8956:25:   required from here
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:21465:94:   required from here
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:23339:141:   required from here
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:23441:9:   required from here
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 ‘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 ‘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 ‘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: ‘best_error’ may be used uninitialized [-Wmaybe-uninitialized]
 6031 |         return (best_error<tolerance);
      |                                     ^
phylogenetics_cpp_routines.cpp:5961:43: note: ‘best_error’ was declared here
 5961 |         double XAX, error, best_lambda=0, best_error=INFTY_D;
      |                                           ^~~~~~~~~~
In file included from /usr/include/c++/13/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++/13/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:4667:39: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized]
 4667 |                 pivoting_indices[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   -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,now -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-1.8.2-1.fc39.copr7692640.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_from_taxa                          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-1.8.2-1.fc39.copr7692640.x86_64/usr/local/lib/R/library/R.css
+ find /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64@@g '{}' ';'
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.8.2-1.fc39.copr7692640 --unique-debug-suffix -1.8.2-1.fc39.copr7692640.x86_64 --unique-debug-src-base R-CRAN-castor-1.8.2-1.fc39.copr7692640.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-1.8.2-1.fc39.copr7692640.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 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64
Provides: R-CRAN-castor = 1.8.2-1.fc39.copr7692640 R-CRAN-castor(x86-64) = 1.8.2-1.fc39.copr7692640
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) 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_1.3.9)(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-1.8.2-1.fc39.copr7692640.x86_64
Provides: R-CRAN-castor-debugsource = 1.8.2-1.fc39.copr7692640 R-CRAN-castor-debugsource(x86-64) = 1.8.2-1.fc39.copr7692640
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-1.8.2-1.fc39.copr7692640.x86_64
Provides: R-CRAN-castor-debuginfo = 1.8.2-1.fc39.copr7692640 R-CRAN-castor-debuginfo(x86-64) = 1.8.2-1.fc39.copr7692640 debuginfo(build-id) = 8ecadec0c632c860b119064b0a6e4d2ae9e6e32a
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) = 1.8.2-1.fc39.copr7692640
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64
Wrote: /builddir/build/RPMS/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-castor-debugsource-1.8.2-1.fc39.copr7692640.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-castor-debuginfo-1.8.2-1.fc39.copr7692640.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Ip6BdY
+ umask 022
+ cd /builddir/build/BUILD
+ cd castor
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-castor-1.8.2-1.fc39.copr7692640.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.SVS6In
+ 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-1.8.2-1.fc39.copr7692640.src.rpm
Finish: build phase for R-CRAN-castor-1.8.2-1.fc39.copr7692640.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.log
/var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-39-x86_64-1719710865.390544/root/var/log/dnf.rpm.log
INFO: Done(/var/lib/copr-rpmbuild/results/R-CRAN-castor-1.8.2-1.fc39.copr7692640.src.rpm) Config(child) 2 minutes 36 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",
            "epoch": null,
            "version": "1.8.2",
            "release": "1.fc39.copr7692640",
            "arch": "x86_64"
        },
        {
            "name": "R-CRAN-castor-debuginfo",
            "epoch": null,
            "version": "1.8.2",
            "release": "1.fc39.copr7692640",
            "arch": "x86_64"
        },
        {
            "name": "R-CRAN-castor-debugsource",
            "epoch": null,
            "version": "1.8.2",
            "release": "1.fc39.copr7692640",
            "arch": "x86_64"
        },
        {
            "name": "R-CRAN-castor",
            "epoch": null,
            "version": "1.8.2",
            "release": "1.fc39.copr7692640",
            "arch": "src"
        }
    ]
}
RPMResults finished