=>> Building biology/mrbayes build started at Sat Jan 24 09:07:14 EST 2026 port directory: /usr/ports/biology/mrbayes package name: mrbayes-3.2.7_2 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1064 Aug 27 2024 /usr/ports/biology/mrbayes/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 06 ---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/06/.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 mrbayes-3.2.7_2: AVX=off: Use AVX optimized routines DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples FMA=off: Use FMA optimized routines SSE=on: Use SSE optimized routines ====> 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-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-avx --disable-fma --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mrbayes/work/.cache HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mrbayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mrbayes/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mrbayes/work/.cache HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mrbayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mrbayes/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="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib " 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/mrbayes" EXAMPLESDIR="share/examples/mrbayes" DATADIR="share/mrbayes" WWWDIR="www/mrbayes" ETCDIR="etc/mrbayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mrbayes DOCSDIR=/usr/local/share/doc/mrbayes EXAMPLESDIR=/usr/local/share/examples/mrbayes WWWDIR=/usr/local/www/mrbayes ETCDIR=/usr/local/etc/mrbayes --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 ===> mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mrbayes-3.2.7_2 =========================================================================== =================================================== ===== 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 mrbayes-3.2.7_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mrbayes-3.2.7_2 for building => SHA256 Checksum OK for NBISweden-MrBayes-v3.2.7_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 mrbayes-3.2.7_2 for building ===> Extracting for mrbayes-3.2.7_2 => SHA256 Checksum OK for NBISweden-MrBayes-v3.2.7_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 mrbayes-3.2.7_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mrbayes-3.2.7_2 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. ===> mrbayes-3.2.7_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of mrbayes-3.2.7_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mrbayes-3.2.7_2 depends on shared library: libreadline.so.8 - not found ===> Installing existing package /packages/All/readline-8.3.3.pkg [pkg.DaveG.ca] Installing readline-8.3.3... [pkg.DaveG.ca] `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] Extracting readline-8.3.3: .......... done ===> mrbayes-3.2.7_2 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8) ===> Returning to build of mrbayes-3.2.7_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for mrbayes-3.2.7_2 configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 whether to enable maintainer-specific portions of Makefiles... no checking build system type... amd64-portbld-freebsd13.5 checking host system type... amd64-portbld-freebsd13.5 checking for pkg-config... no checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking for style of include used by make... GNU checking whether to compile using MPI... no checking for gcc... cc 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 we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for sqrt in -lm... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes configure: Trying to locate Beagle (hmsbeagle-1) in '/usr/local' checking libhmsbeagle/beagle.h usability... no checking libhmsbeagle/beagle.h presence... no checking for libhmsbeagle/beagle.h... no checking for beagleCreateInstance in -lhmsbeagle... no configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking libhmsbeagle/beagle.h usability... no checking libhmsbeagle/beagle.h presence... no checking for libhmsbeagle/beagle.h... no checking for beagleCreateInstance in -lhmsbeagle... (cached) no configure: WARNING: Failed to locate Beagle, falling back on pkg-config checking for BEAGLE... no checking for a readline compatible library... -lreadline checking readline.h usability... no checking readline.h presence... no checking for readline.h... no checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking whether readline supports history... yes checking history.h usability... no checking history.h presence... no checking for history.h... no checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for memory.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for C compiler vendor... clang checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for C compiler version... 19.1.7 checking CFLAGS for maximum warnings... -Wall checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:68747541:444d4163:69746e65 checking for x86 cpuid 0x80000000 output... 8000001f:68747541:444d4163:69746e65 checking for x86 cpuid 0x00000001 output... 800f82:25400800:7ed8320b:178bfbff checking for x86 cpuid 0x00000007 output... 0:209c01a9:0:0 checking for x86 cpuid 0x80000001 output... 800f82:70000000:35c233ff:2fd3fbff checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C compiler accepts -mabm... no configure: WARNING: Your processor and OS supports ABM instructions but not your compiler, can you try another compiler? checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... yes checking whether SSE4a is supported by the processor and OS... yes checking whether C compiler accepts -msse4a... yes checking whether SHA is supported by the processor... yes checking whether SHA is supported by the processor and OS... yes checking whether C compiler accepts -msha... yes checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for floor... yes checking for memset... (cached) yes checking for pow... yes checking for sqrt... yes checking for strchr... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for mrbayes-3.2.7_2 --- all-recursive --- Making all in src --- all --- /usr/bin/make all-am --- mb-bayes.o --- --- mb-best.o --- --- mb-command.o --- --- mb-likelihood.o --- --- mb-mbbeagle.o --- --- mb-mcmc.o --- --- mb-model.o --- --- mb-proposal.o --- --- mb-sumpt.o --- --- mb-utils.o --- --- mb-bayes.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-bayes.o -MD -MP -MF .deps/mb-bayes.Tpo -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c --- mb-best.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-best.o -MD -MP -MF .deps/mb-best.Tpo -c -o mb-best.o `test -f 'best.c' || echo './'`best.c --- mb-command.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-command.o -MD -MP -MF .deps/mb-command.Tpo -c -o mb-command.o `test -f 'command.c' || echo './'`command.c --- mb-likelihood.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-likelihood.o -MD -MP -MF .deps/mb-likelihood.Tpo -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c --- mb-mbbeagle.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-mbbeagle.o -MD -MP -MF .deps/mb-mbbeagle.Tpo -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c --- mb-mcmc.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-mcmc.o -MD -MP -MF .deps/mb-mcmc.Tpo -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c --- mb-model.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-model.o -MD -MP -MF .deps/mb-model.Tpo -c -o mb-model.o `test -f 'model.c' || echo './'`model.c --- mb-proposal.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-proposal.o -MD -MP -MF .deps/mb-proposal.Tpo -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c --- mb-sumpt.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-sumpt.o -MD -MP -MF .deps/mb-sumpt.Tpo -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c --- mb-utils.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -MT mb-utils.o -MD -MP -MF .deps/mb-utils.Tpo -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c --- mb-mbbeagle.o --- mbbeagle.c:2997:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2997 | void BeagleNotLinked() | ^ | void mbbeagle.c:3003:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3003 | void BeagleThreadsNotAvailable() | ^ | void 2 warnings generated. mv -f .deps/mb-mbbeagle.Tpo .deps/mb-mbbeagle.Po --- mb-bayes.o --- mv -f .deps/mb-bayes.Tpo .deps/mb-bayes.Po --- mb-best.o --- mv -f .deps/mb-best.Tpo .deps/mb-best.Po --- mb-sumpt.o --- sumpt.c:3063:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3063 | PartCtr *AllocPartCtr () | ^ | void sumpt.c:3125:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3125 | TreeCtr *AllocTreeCtr () | ^ | void 2 warnings generated. mv -f .deps/mb-sumpt.Tpo .deps/mb-sumpt.Po --- mb-command.o --- mv -f .deps/mb-command.Tpo .deps/mb-command.Po --- mb-likelihood.o --- likelihood.c:5920:57: warning: variable 'lnLI_SSE' set but not used [-Wunused-but-set-variable] 5920 | CLFlt *lnScaler, *nSitesOfPat, *lnL_SSE, *lnLI_SSE; | ^ 1 warning generated. mv -f .deps/mb-likelihood.Tpo .deps/mb-likelihood.Po --- mb-proposal.o --- proposal.c:9189:17: warning: variable 'minLenCur' set but not used [-Wunused-but-set-variable] 9189 | minLenCur, minLenNew, f; | ^ 1 warning generated. mv -f .deps/mb-proposal.Tpo .deps/mb-proposal.Po --- mb-utils.o --- mv -f .deps/mb-utils.Tpo .deps/mb-utils.Po --- mb-mcmc.o --- mcmc.c:4110:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 4110 | int ExtendChainQuery () | ^ | void mcmc.c:8794:20: warning: variable 'n' set but not used [-Wunused-but-set-variable] 8794 | int i, n, m; | ^ mcmc.c:8931:41: warning: variable 'K' set but not used [-Wunused-but-set-variable] 8931 | int i, j, i1, i2, i3, sl, K, M, E; | ^ mcmc.c:9116:41: warning: variable 'K' set but not used [-Wunused-but-set-variable] 9116 | int i, j, i1, i2, i3, sl, K, M, E; | ^ 4 warnings generated. mv -f .deps/mb-mcmc.Tpo .deps/mb-mcmc.Po --- mb-model.o --- model.c:178:58: warning: variable 'numStdChars' set but not used [-Wunused-but-set-variable] 178 | int i, j, k, d, numIncompatible, numDeleted, numStdChars, oldRowSize, | ^ model.c:1951:33: warning: variable 's' set but not used [-Wunused-but-set-variable] 1951 | int c, d, i, t, s, s1, s2, s3, whichNuc, uniqueId, numCharsInPart, | ^ model.c:1954:57: warning: variable 'allCheckedOut' set but not used [-Wunused-but-set-variable] 1954 | oneGoodCodon, foundUnpaired, nPair, allCheckedOut; | ^ model.c:11824:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 11824 | int PruneConstraintPartitions() | ^ | void model.c:12912:21: warning: variable 'numActiveHardConstraints' set but not used [-Wunused-but-set-variable] 12912 | numActiveHardConstraints = 0; | ^ model.c:17446:31: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 17446 | int i, s, s1, s2, s3, ns; | ^ 6 warnings generated. mv -f .deps/mb-model.Tpo .deps/mb-model.Po --- mb --- cc -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -O3 -DNDEBUG -std=c99 -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -L/usr/local/lib -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -lm -lreadline Making all in doc --- all-recursive --- Making all in manual Making all in tutorial Making all in examples =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mrbayes-3.2.7_2 ===> Generating temporary packing list Making install in src /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/bin' install -s -m 555 mb '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/bin' Making install in doc Making install in manual /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' install -m 0644 Manual_MrBayes_v3.2.pdf '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' Making install in tutorial /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' install -m 0644 hym.nex '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' install -m 0644 MBDating.pdf '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' Making install in examples /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/examples/mrbayes' install -m 0644 avian_ovomucoids.nex codon.nex cynmix.nex finch.nex hymfossil.nex primates.nex replicase.nex sceloporus.nex '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/examples/mrbayes' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' install -m 0644 COPYING README NEWS '/wrkdirs/usr/ports/biology/mrbayes/work/stage/usr/local/share/doc/mrbayes' ====> 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=2026-01-24T14:07:14+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' '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 mrbayes-3.2.7_2 ===> Building mrbayes-3.2.7_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mrbayes-3.2.7_2 build of biology/mrbayes | mrbayes-3.2.7_2 ended at Sat Jan 24 09:07:38 EST 2026 build time: 00:00:25