=>> Building biology/phyml build started at Fri Dec 12 14:40:19 EST 2025 port directory: /usr/ports/biology/phyml package name: phyml-3.3.20220408_1,1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1458 Aug 27 2024 /usr/ports/biology/phyml/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 90c6e11540a6 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 12 ---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/12/.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 phyml-3.3.20220408_1,1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ====> MPI (Message Passing Interface) support: you can only select none or one of them MPICH=off: Parallel processing support via MPICH OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-beagle --disable-native --disable-mpi --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/phyml/work/.cache HOME=/wrkdirs/usr/ports/biology/phyml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phyml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/phyml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/phyml/work/.cache HOME=/wrkdirs/usr/ports/biology/phyml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phyml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/phyml/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 DEFAULT_AUTOCONF=2.72 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/phyml" EXAMPLESDIR="share/examples/phyml" DATADIR="share/phyml" WWWDIR="www/phyml" ETCDIR="etc/phyml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/phyml DOCSDIR=/usr/local/share/doc/phyml EXAMPLESDIR=/usr/local/share/examples/phyml WWWDIR=/usr/local/www/phyml ETCDIR=/usr/local/etc/phyml --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 ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> phyml-3.3.20220408_1,1 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 ===> phyml-3.3.20220408_1,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of phyml-3.3.20220408_1,1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building => SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20220408_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 ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building ===> Extracting for phyml-3.3.20220408_1,1 => SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20220408_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 phyml-3.3.20220408_1,1 ===> Applying FreeBSD patches for phyml-3.3.20220408_1,1 from /usr/ports/biology/phyml/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> phyml-3.3.20220408_1,1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> phyml-3.3.20220408_1,1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of phyml-3.3.20220408_1,1 ===> phyml-3.3.20220408_1,1 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg.DaveG.ca] Installing autoconf-2.72... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72: .......... done ===> phyml-3.3.20220408_1,1 depends on package: autoconf>=2.72 - found ===> Returning to build of phyml-3.3.20220408_1,1 ===> phyml-3.3.20220408_1,1 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg.DaveG.ca] Installing automake-1.17... [pkg.DaveG.ca] Extracting automake-1.17: .......... done ===> phyml-3.3.20220408_1,1 depends on package: automake>=1.17 - found ===> Returning to build of phyml-3.3.20220408_1,1 ===> phyml-3.3.20220408_1,1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> phyml-3.3.20220408_1,1 depends on executable: libtoolize - found ===> Returning to build of phyml-3.3.20220408_1,1 ===> phyml-3.3.20220408_1,1 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. ===> phyml-3.3.20220408_1,1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of phyml-3.3.20220408_1,1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for phyml-3.3.20220408_1,1 configure.ac:21: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:21: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:21: the top level configure.ac:42: warning: The macro 'AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED. ./lib/autoconf/functions.m4:1785: AC_FUNC_SETVBUF_REVERSED is expanded from... configure.ac:42: the top level configure.ac:14: installing './compile' configure.ac:12: installing './config.guess' configure.ac:12: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' configure: WARNING: unrecognized options: --disable-beagle, --disable-mpi configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking build system type... amd64-portbld-freebsd13.5 checking host system type... amd64-portbld-freebsd13.5 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking for log in -lm... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for float.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... (cached) yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... (cached) yes checking for strstr... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-beagle, --disable-mpi =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for phyml-3.3.20220408_1,1 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in src --- intro --- --- main.o --- --- utilities.o --- --- optimiz.o --- --- lk.o --- --- bionj.o --- --- models.o --- --- free.o --- --- help.o --- --- simu.o --- --- eigen.o --- --- pars.o --- --- alrt.o --- --- interface.o --- --- cl.o --- --- spr.o --- --- draw.o --- --- stats.o --- --- io.o --- --- make.o --- --- nexus.o --- --- init.o --- --- xml.o --- --- sse.o --- --- avx.o --- --- tbe.o --- --- ancestral.o --- --- mixt.o --- .: Building [phyml]. Version 3.3.20220408 :. --- main.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c --- utilities.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c --- optimiz.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c --- lk.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c --- bionj.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c --- models.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c --- free.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c --- help.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c --- simu.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c --- eigen.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c --- pars.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c --- alrt.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c --- interface.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c --- cl.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c --- spr.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c --- draw.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c --- stats.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c --- io.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c --- make.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c --- nexus.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c --- init.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c --- xml.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c --- sse.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c --- avx.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c --- ancestral.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c --- mixt.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c --- tbe.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c --- help.o --- mv -f .deps/help.Tpo .deps/help.Po --- avx.o --- mv -f .deps/avx.Tpo .deps/avx.Po --- main.o --- mv -f .deps/main.Tpo .deps/main.Po --- tbe.o --- mv -f .deps/tbe.Tpo .deps/tbe.Po --- nexus.o --- mv -f .deps/nexus.Tpo .deps/nexus.Po --- bionj.o --- mv -f .deps/bionj.Tpo .deps/bionj.Po --- draw.o --- mv -f .deps/draw.Tpo .deps/draw.Po --- simu.o --- simu.c:82:19: warning: variable 'n_iter' set but not used [-Wunused-but-set-variable] 82 | phydbl old_pars,n_iter,lambda; | ^ simu.c:83:24: warning: variable 'n_without_swap' set but not used [-Wunused-but-set-variable] 83 | int i,n_neg,n_tested,n_without_swap,n_tot_swap,step; | ^ simu.c:83:39: warning: variable 'n_tot_swap' set but not used [-Wunused-but-set-variable] 83 | int i,n_neg,n_tested,n_without_swap,n_tot_swap,step; | ^ simu.c:85:7: warning: variable 'each' set but not used [-Wunused-but-set-variable] 85 | int each; | ^ 4 warnings generated. mv -f .deps/simu.Tpo .deps/simu.Po --- interface.o --- mv -f .deps/interface.Tpo .deps/interface.Po --- sse.o --- mv -f .deps/sse.Tpo .deps/sse.Po --- make.o --- In file included from make.c:13: ./make.h:70:15: 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] 70 | t_phyrex_mod *PHYREX_Make_Migrep_Model(); | ^ make.c:1713:15: note: conflicting prototype is here 1713 | t_phyrex_mod *PHYREX_Make_Migrep_Model(int n_otu,int dim) | ^ 1 warning generated. --- cl.o --- mv -f .deps/cl.Tpo .deps/cl.Po --- make.o --- mv -f .deps/make.Tpo .deps/make.Po --- alrt.o --- mv -f .deps/alrt.Tpo .deps/alrt.Po --- free.o --- mv -f .deps/free.Tpo .deps/free.Po --- spr.o --- spr.c:735:10: warning: variable 'mean_delta_lnL_spr' set but not used [-Wunused-but-set-variable] 735 | phydbl mean_delta_lnL_spr,max_delta_lnL_spr,tune_l_mult; | ^ spr.c:739:16: warning: variable 'hit_zero_improv' set but not used [-Wunused-but-set-variable] 739 | unsigned int hit_zero_improv = 0; | ^ spr.c:1951:31: warning: variable 'no_improvement' set but not used [-Wunused-but-set-variable] 1951 | int step,i,n_targets,n_rand,no_improvement; | ^ 3 warnings generated. mv -f .deps/spr.Tpo .deps/spr.Po --- ancestral.o --- mv -f .deps/ancestral.Tpo .deps/ancestral.Po --- pars.o --- mv -f .deps/pars.Tpo .deps/pars.Po --- xml.o --- mv -f .deps/xml.Tpo .deps/xml.Po --- eigen.o --- mv -f .deps/eigen.Tpo .deps/eigen.Po --- models.o --- models.c:1106:10: warning: variable 'sum' set but not used [-Wunused-but-set-variable] 1106 | phydbl sum; | ^ models.c:1107:10: warning: variable 'sum_ev' set but not used [-Wunused-but-set-variable] 1107 | phydbl sum_ev; | ^ models.c:1200:10: warning: variable 'sum' set but not used [-Wunused-but-set-variable] 1200 | phydbl sum; | ^ 3 warnings generated. mv -f .deps/models.Tpo .deps/models.Po --- mixt.o --- mixt.c:3862:7: warning: variable 'i' set but not used [-Wunused-but-set-variable] 3862 | int i; | ^ mixt.c:3932:27: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3932 | (*Task_Function)(tree); | ^ 2 warnings generated. mv -f .deps/mixt.Tpo .deps/mixt.Po --- lk.o --- mv -f .deps/lk.Tpo .deps/lk.Po --- init.o --- mv -f .deps/init.Tpo .deps/init.Po --- io.o --- mv -f .deps/io.Tpo .deps/io.Po --- stats.o --- stats.c:3293:11: warning: variable 'det' set but not used [-Wunused-but-set-variable] 3293 | phydbl det; | ^ 1 warning generated. mv -f .deps/stats.Tpo .deps/stats.Po --- optimiz.o --- optimiz.c:285:7: warning: variable 'n_opt_step' set but not used [-Wunused-but-set-variable] 285 | int n_opt_step; | ^ 1 warning generated. mv -f .deps/optimiz.Tpo .deps/optimiz.Po --- utilities.o --- utilities.c:2147:7: warning: variable 'diff' set but not used [-Wunused-but-set-variable] 2147 | int diff; | ^ utilities.c:4118:7: warning: variable 'different' set but not used [-Wunused-but-set-variable] 4118 | int different,identical; | ^ utilities.c:6548:22: warning: variable 'sd' set but not used [-Wunused-but-set-variable] 6548 | phydbl *delta,mean,sd,obs_stat,threshold; | ^ 3 warnings generated. mv -f .deps/utilities.Tpo .deps/utilities.Po --- phyml --- cc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm --- all-am --- Done. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for phyml-3.3.20220408_1,1 ===> Generating temporary packing list Making install in src .: Building [phyml]. Version 3.3.20220408 :. Done. /bin/mkdir -p '/wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/bin' install -s -m 555 phyml '/wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/bin' (cd /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/doc && install -m 0644 *.pdf /wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/share/doc/phyml) ====> 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=2025-12-12T19:40:19+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=90c6e11540a6' '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 phyml-3.3.20220408_1,1 ===> Building phyml-3.3.20220408_1,1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for phyml-3.3.20220408_1,1 build of biology/phyml | phyml-3.3.20220408_1,1 ended at Fri Dec 12 14:40:34 EST 2025 build time: 00:00:17