=>> Building biology/paml build started at Thu Dec 11 02:58:21 EST 2025 port directory: /usr/ports/biology/paml package name: paml-4.10.9 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1384 Jun 29 20:14 /usr/ports/biology/paml/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 5fd436fa038a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for paml-4.10.9: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/paml/work/.cache HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/paml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/paml/work/.cache HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/paml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" PORTEXAMPLES="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> paml-4.10.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> paml-4.10.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.10.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by paml-4.10.9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by paml-4.10.9 for building => SHA256 Checksum OK for abacus-gene-paml-v4.10.9_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by paml-4.10.9 for building ===> Extracting for paml-4.10.9 => SHA256 Checksum OK for abacus-gene-paml-v4.10.9_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for paml-4.10.9 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for paml-4.10.9 from /usr/ports/biology/paml/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> paml-4.10.9 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> paml-4.10.9 depends on package: gmake>=4.4.1 - found ===> Returning to build of paml-4.10.9 ===> paml-4.10.9 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> paml-4.10.9 depends on file: /usr/local/bin/ccache - found ===> Returning to build of paml-4.10.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for paml-4.10.9 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for paml-4.10.9 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c baseml.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c tools.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o baseml baseml.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c codeml.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o codeml codeml.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c basemlg.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o basemlg basemlg.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c mcmctree.c mcmctree.c:45:5: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 45 | int ProcessNodeAnnotation(); | ^ ./treesub.c:8653:5: note: conflicting prototype is here 8653 | int ProcessNodeAnnotation(int* haslabel) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o mcmctree mcmctree.c tools.o -lm mcmctree.c:45:5: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 45 | int ProcessNodeAnnotation(); | ^ ./treesub.c:8653:5: note: conflicting prototype is here 8653 | int ProcessNodeAnnotation(int* haslabel) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o infinitesites -D INFINITESITES mcmctree.c tools.o -lm mcmctree.c:45:5: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 45 | int ProcessNodeAnnotation(); | ^ ./treesub.c:8653:5: note: conflicting prototype is here 8653 | int ProcessNodeAnnotation(int* haslabel) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c pamp.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o pamp pamp.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c evolver.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o evolver evolver.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c yn00.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o yn00 yn00.o tools.o -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -o chi2.o chi2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o chi2 chi2.c -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for paml-4.10.9 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/baseml /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/basemlg /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/chi2 /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/codeml /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/evolver /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/evolverNSbranches /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/evolverNSbranchsites /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/evolverNSsites /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/infinitesites /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/mcmctree /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/pamp /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/src/yn00 /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin install -m 0644 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/doc/* /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/doc/paml install -m 0644 /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/README.md /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/doc/paml (cd /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9 && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "dat Technical" /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/examples/paml) (cd /wrkdirs/usr/ports/biology/paml/work/paml-4.10.9/examples && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/examples/paml) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-11T07:58:21+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=5fd436fa038a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for paml-4.10.9 ===> Building paml-4.10.9 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for paml-4.10.9 build of biology/paml | paml-4.10.9 ended at Thu Dec 11 02:59:52 EST 2025 build time: 00:01:33