=>> Building biology/mrbayes build started at Tue Apr 2 13:28:56 BST 2024 port directory: /usr/ports/biology/mrbayes package name: mrbayes-3.2.7_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1064 Mar 8 2023 /usr/ports/biology/mrbayes/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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 3 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=/ccache/libexec/ccache:/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 CCACHE_DIR="/root/.ccache" 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=/ccache/libexec/ccache:/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 -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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=13.2 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_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 =========================================================================== =================================================== ===== 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-8.2.10.pkg [pkg-builder.dan.net.uk] Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] Extracting readline-8.2.10: .......... 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-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 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... 14.0.5 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... 14:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 406f1:6200800:fefa3203:1f8bfbff checking for x86 cpuid 0x00000007 output... 0:1c2fb9:0:bc000400 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 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... no checking whether SHA is supported by the processor... no 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 Making all in src /usr/bin/make all-am cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-bayes.Tpo .deps/mb-bayes.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-best.Tpo .deps/mb-best.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-command.Tpo .deps/mb-command.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 likelihood.c:5920:57: warning: variable 'lnLI_SSE' set but not used [-Wunused-but-set-variable] CLFlt *lnScaler, *nSitesOfPat, *lnL_SSE, *lnLI_SSE; ^ 1 warning generated. mv -f .deps/mb-likelihood.Tpo .deps/mb-likelihood.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-mbbeagle.Tpo .deps/mb-mbbeagle.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-mcmc.Tpo .deps/mb-mcmc.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 model.c:178:58: warning: variable 'numStdChars' set but not used [-Wunused-but-set-variable] int i, j, k, d, numIncompatible, numDeleted, numStdChars, oldRowSize, ^ 1 warning generated. mv -f .deps/mb-model.Tpo .deps/mb-model.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 proposal.c:9189:17: warning: variable 'minLenCur' set but not used [-Wunused-but-set-variable] minLenCur, minLenNew, f; ^ 1 warning generated. mv -f .deps/mb-proposal.Tpo .deps/mb-proposal.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-sumpt.Tpo .deps/mb-sumpt.Po cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 mv -f .deps/mb-utils.Tpo .deps/mb-utils.Po cc -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 -fstack-protector-strong -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 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=2024-04-02T12:28:56+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' 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 Tue Apr 2 13:30:13 BST 2024 build time: 00:01:18