=>> Building biology/phyml build started at Sat Apr 6 21:24:43 BST 2024 port directory: /usr/ports/biology/phyml package name: phyml-3.3.20220408_1,1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1441 May 9 2023 /usr/ports/biology/phyml/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 8e2ec289a2 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---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/18/.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 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 3 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=/ccache/libexec/ccache:/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 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/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=/ccache/libexec/ccache:/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=" -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/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--- 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 ===> 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-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 ===> 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-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... 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-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [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] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> 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>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> phyml-3.3.20220408_1,1 depends on package: automake>=1.16.5 - 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-2.4.7_2.pkg [pkg-builder.dan.net.uk] Installing libtool-2.4.7_2... [pkg-builder.dan.net.uk] Extracting libtool-2.4.7_2: .......... done ===> phyml-3.3.20220408_1,1 depends on executable: libtoolize - 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 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 build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 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 /usr/bin/make all-recursive Making all in src 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 mv -f .deps/main.Tpo .deps/main.Po 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 utilities.c:6548:22: warning: variable 'sd' set but not used [-Wunused-but-set-variable] phydbl *delta,mean,sd,obs_stat,threshold; ^ 1 warning generated. mv -f .deps/utilities.Tpo .deps/utilities.Po 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 mv -f .deps/optimiz.Tpo .deps/optimiz.Po 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 mv -f .deps/lk.Tpo .deps/lk.Po 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 mv -f .deps/bionj.Tpo .deps/bionj.Po 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 models.c:1107:10: warning: variable 'sum_ev' set but not used [-Wunused-but-set-variable] phydbl sum_ev; ^ models.c:1106:10: warning: variable 'sum' set but not used [-Wunused-but-set-variable] phydbl sum; ^ models.c:1200:10: warning: variable 'sum' set but not used [-Wunused-but-set-variable] phydbl sum; ^ 3 warnings generated. mv -f .deps/models.Tpo .deps/models.Po 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 mv -f .deps/free.Tpo .deps/free.Po 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 mv -f .deps/help.Tpo .deps/help.Po 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 simu.c:82:19: warning: variable 'n_iter' set but not used [-Wunused-but-set-variable] phydbl old_pars,n_iter,lambda; ^ simu.c:83:39: warning: variable 'n_tot_swap' set but not used [-Wunused-but-set-variable] int i,n_neg,n_tested,n_without_swap,n_tot_swap,step; ^ 2 warnings generated. mv -f .deps/simu.Tpo .deps/simu.Po 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 mv -f .deps/eigen.Tpo .deps/eigen.Po 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 mv -f .deps/pars.Tpo .deps/pars.Po 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 mv -f .deps/alrt.Tpo .deps/alrt.Po 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 mv -f .deps/interface.Tpo .deps/interface.Po 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 mv -f .deps/cl.Tpo .deps/cl.Po 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 spr.c:735:10: warning: variable 'mean_delta_lnL_spr' set but not used [-Wunused-but-set-variable] phydbl mean_delta_lnL_spr,max_delta_lnL_spr,tune_l_mult; ^ 1 warning generated. mv -f .deps/spr.Tpo .deps/spr.Po 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 mv -f .deps/draw.Tpo .deps/draw.Po 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 stats.c:3293:11: warning: variable 'det' set but not used [-Wunused-but-set-variable] phydbl det; ^ 1 warning generated. mv -f .deps/stats.Tpo .deps/stats.Po 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 mv -f .deps/io.Tpo .deps/io.Po 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 mv -f .deps/make.Tpo .deps/make.Po 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 mv -f .deps/nexus.Tpo .deps/nexus.Po 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 mv -f .deps/init.Tpo .deps/init.Po 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 mv -f .deps/xml.Tpo .deps/xml.Po 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 mv -f .deps/sse.Tpo .deps/sse.Po 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 mv -f .deps/avx.Tpo .deps/avx.Po 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 mv -f .deps/tbe.Tpo .deps/tbe.Po 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 mv -f .deps/ancestral.Tpo .deps/ancestral.Po 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 mv -f .deps/mixt.Tpo .deps/mixt.Po 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 .: Building [phyml]. Version 3.3.20220408 :. 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=2024-04-06T20:24:43+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=8e2ec289a2' '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 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 Sat Apr 6 21:25:51 BST 2024 build time: 00:01:09