=>> Building biology/treekin build started at Sun May 4 19:08:22 EDT 2025 port directory: /usr/ports/biology/treekin package name: treekin-0.5.1_7 building for: FreeBSD 13amd64-weekly-desktop-job-03 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 757 Mar 1 07:51 /usr/ports/biology/treekin/Makefile Ports top last git commit: 57a50b106b87 Ports top unclean checkout: yes Port dir last git commit: 6cce1f5b223a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1304000 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1304000 UNAME_v=FreeBSD 13.4-RELEASE-p4 UNAME_r=13.4-RELEASE-p4 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=/mnt/data/.m/13amd64-weekly-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/13amd64-weekly-desktop/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13amd64-weekly-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/13amd64-weekly-desktop/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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/treekin/work/.cache HOME=/wrkdirs/usr/ports/biology/treekin/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/treekin/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/treekin/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/treekin/work/.cache HOME=/wrkdirs/usr/ports/biology/treekin/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/treekin/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/treekin/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- OSREL=13.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/treekin" EXAMPLESDIR="share/examples/treekin" DATADIR="share/treekin" WWWDIR="www/treekin" ETCDIR="etc/treekin" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/treekin DOCSDIR=/usr/local/share/doc/treekin EXAMPLESDIR=/usr/local/share/examples/treekin WWWDIR=/usr/local/www/treekin ETCDIR=/usr/local/etc/treekin --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 #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> treekin-0.5.1_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [13amd64-weekly-desktop-job-03] Installing pkg-2.0.6... [13amd64-weekly-desktop-job-03] Extracting pkg-2.0.6: .......... done ===> treekin-0.5.1_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of treekin-0.5.1_7 =========================================================================== =================================================== ===== 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 treekin-0.5.1_7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by treekin-0.5.1_7 for building => SHA256 Checksum OK for Treekin-0.5.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by treekin-0.5.1_7 for building ===> Extracting for treekin-0.5.1_7 => SHA256 Checksum OK for Treekin-0.5.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for treekin-0.5.1_7 ===> Applying FreeBSD patches for treekin-0.5.1_7 from /usr/ports/biology/treekin/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> treekin-0.5.1_7 depends on package: lapacke>0 - not found ===> Installing existing package /packages/All/lapacke-3.12.1.pkg [13amd64-weekly-desktop-job-03] Installing lapacke-3.12.1... [13amd64-weekly-desktop-job-03] `-- Installing blas-3.12.1... [13amd64-weekly-desktop-job-03] | `-- Installing gcc13-13.3.0_2... [13amd64-weekly-desktop-job-03] | | `-- Installing binutils-2.44,1... [13amd64-weekly-desktop-job-03] | | `-- Installing indexinfo-0.3.1_1... [13amd64-weekly-desktop-job-03] | | `-- Extracting indexinfo-0.3.1_1: . done [13amd64-weekly-desktop-job-03] | | `-- Installing zstd-1.5.7... [13amd64-weekly-desktop-job-03] | | | `-- Installing liblz4-1.10.0,1... [13amd64-weekly-desktop-job-03] | | | `-- Extracting liblz4-1.10.0,1: .......... done [13amd64-weekly-desktop-job-03] | | `-- Extracting zstd-1.5.7: .......... done [13amd64-weekly-desktop-job-03] | | `-- Extracting binutils-2.44,1: .......... done [13amd64-weekly-desktop-job-03] | | `-- Installing gmp-6.3.0... [13amd64-weekly-desktop-job-03] | | `-- Extracting gmp-6.3.0: .......... done [13amd64-weekly-desktop-job-03] | | `-- Installing mpc-1.3.1_1... [13amd64-weekly-desktop-job-03] | | `-- Installing mpfr-4.2.1,1... [13amd64-weekly-desktop-job-03] | | `-- Extracting mpfr-4.2.1,1: .......... done [13amd64-weekly-desktop-job-03] | | `-- Extracting mpc-1.3.1_1: ...... done [13amd64-weekly-desktop-job-03] | `-- Extracting gcc13-13.3.0_2: .......... done [13amd64-weekly-desktop-job-03] `-- Extracting blas-3.12.1: ..... done [13amd64-weekly-desktop-job-03] `-- Installing lapack-3.12.1... [13amd64-weekly-desktop-job-03] `-- Extracting lapack-3.12.1: .......... done [13amd64-weekly-desktop-job-03] Extracting lapacke-3.12.1: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> treekin-0.5.1_7 depends on package: lapacke>0 - found ===> Returning to build of treekin-0.5.1_7 ===> treekin-0.5.1_7 depends on executable: gfortran13 - found ===> treekin-0.5.1_7 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [13amd64-weekly-desktop-job-03] Installing gmake-4.4.1... [13amd64-weekly-desktop-job-03] `-- Installing gettext-runtime-0.23.1... [13amd64-weekly-desktop-job-03] `-- Extracting gettext-runtime-0.23.1: .......... done [13amd64-weekly-desktop-job-03] Extracting gmake-4.4.1: .......... done ===> treekin-0.5.1_7 depends on package: gmake>=4.4.1 - found ===> Returning to build of treekin-0.5.1_7 ===> treekin-0.5.1_7 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> treekin-0.5.1_7 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> treekin-0.5.1_7 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for treekin-0.5.1_7 configure: loading site script /usr/ports/Templates/config.site checking whether /usr/local/bin/gmake supports nested variables... yes 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 /usr/local/bin/gmake sets $(MAKE)... yes checking build system type... amd64-portbld-freebsd13.4 checking host system type... amd64-portbld-freebsd13.4 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 c++ accepts -g... yes checking for style of include used by /usr/local/bin/gmake... GNU checking dependency style of c++... gcc3 checking for gcc... cc 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 ranlib... /usr/local/bin/ranlib checking whether /usr/local/bin/gmake sets $(MAKE)... (cached) yes checking for autoconf... autoconf checking for aclocal... aclocal checking for make... /usr/local/bin/gmake checking for ar... /usr/local/bin/ar checking whether c++ supports C++11 features with -std=gnu++11... yes checking for gengetopt... no checking for sgemm_... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for sgemm_ in -lmkl... no checking for sgemm_... (cached) no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) yes checking for sgemm_ in -lessl... no checking for sgemm_ in -lblas... (cached) yes checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran13 accepts -g... yes checking how to get verbose linking output from gfortran13... -v checking for Fortran 77 libraries of gfortran13... -L/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0/../../../../../x86_64-portbld-freebsd13.4/lib -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore 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 checking for cheev_... no checking for cheev_ in -llapack... yes checking openblas/lapacke.h usability... no checking openblas/lapacke.h presence... no checking for openblas/lapacke.h... no checking lapacke/lapacke.h usability... yes checking lapacke/lapacke.h presence... yes checking for lapacke/lapacke.h... yes checking for ANSI C header files... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for pkg-config... no checking how to run the C++ preprocessor... c++ -std=gnu++11 -E checking for mlapack... no configure: WARNING: ********************************************************************** Failed to setup linking the program against the MLAPACK library. In case you have installed mlapack in a non-standard directory, consider using the --with-mlapack=/path/to/mlapack parameter to specify the location where to find MLAPACK. Otherwise, you can obtain the mlapack library from https://github.com/RaumZeit/mlapack ********************************************************************** checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for help2man... no 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 packaging/treekin.spec config.status: creating packaging/PKGBUILD config.status: creating packaging/treekin-mlapack.spec config.status: creating packaging/PKGBUILD-mlapack config.status: creating man/Makefile config.status: creating man/cmdlopt.sh config.status: creating config.h config.status: executing depfiles commands configure: ====================================== Treekin 0.5.1 ====================================== Configured successful with the following options: Extra Libraries --------------- * MLapack : no ( mlapack library missing or not of version 0.8 or higher ) Install Directories ------------------- * Executables : /usr/local/bin * Libraries : /usr/local/lib * Header files : /usr/local/include * Extra Data : /usr/local/share * Man pages : /usr/local/share/man Note, that the most recent version of the DrTransformer program requires Treekin to be linked against the MLAPACK library! You can run make now. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for treekin-0.5.1_7 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-mxccm.o -MD -MP -MF .deps/treekin-mxccm.Tpo -c -o treekin-mxccm.o `test -f 'mxccm.cpp' || echo './'`mxccm.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-globals.o -MD -MP -MF .deps/treekin-globals.Tpo -c -o treekin-globals.o `test -f 'globals.cpp' || echo './'`globals.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-barparser.o -MD -MP -MF .deps/treekin-barparser.Tpo -c -o treekin-barparser.o `test -f 'barparser.cpp' || echo './'`barparser.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-calcpp.o -MD -MP -MF .deps/treekin-calcpp.Tpo -c -o treekin-calcpp.o `test -f 'calcpp.cpp' || echo './'`calcpp.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-calc.o -MD -MP -MF .deps/treekin-calc.Tpo -c -o treekin-calc.o `test -f 'calc.cpp' || echo './'`calc.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-exp_matrix.o -MD -MP -MF .deps/treekin-exp_matrix.Tpo -c -o treekin-exp_matrix.o `test -f 'exp_matrix.cpp' || echo './'`exp_matrix.cpp cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT treekin-treekin_cmdline.o -MD -MP -MF .deps/treekin-treekin_cmdline.Tpo -c -o treekin-treekin_cmdline.o `test -f 'treekin_cmdline.c' || echo './'`treekin_cmdline.c c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-main.o -MD -MP -MF .deps/treekin-main.Tpo -c -o treekin-main.o `test -f 'main.cpp' || echo './'`main.cpp mv -f .deps/treekin-globals.Tpo .deps/treekin-globals.Po mv -f .deps/treekin-mxccm.Tpo .deps/treekin-mxccm.Po mv -f .deps/treekin-treekin_cmdline.Tpo .deps/treekin-treekin_cmdline.Po mv -f .deps/treekin-barparser.Tpo .deps/treekin-barparser.Po mv -f .deps/treekin-exp_matrix.Tpo .deps/treekin-exp_matrix.Po mv -f .deps/treekin-calcpp.Tpo .deps/treekin-calcpp.Po mv -f .deps/treekin-calc.Tpo .deps/treekin-calc.Po mv -f .deps/treekin-main.Tpo .deps/treekin-main.Po c++ -std=gnu++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o treekin treekin-mxccm.o treekin-globals.o treekin-barparser.o treekin-calcpp.o treekin-calc.o treekin-exp_matrix.o treekin-treekin_cmdline.o treekin-main.o -llapack -lblas -L/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0/../../../../../x86_64-portbld-freebsd13.4/lib -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.4/13.3.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' Making all in man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> treekin-0.5.1_7 depends on executable: gfortran13 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for treekin-0.5.1_7 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/treekin/work/stage/usr/local/bin' install -s -m 555 treekin '/wrkdirs/usr/ports/biology/treekin/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' Making install in man gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/treekin/work/stage/usr/local/share/man/man1' install -m 0644 treekin.1 '/wrkdirs/usr/ports/biology/treekin/work/stage/usr/local/share/man/man1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/man' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' ====> 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=2025-05-04T23:08:22+0000' 'PKG_NOTE_ports_top_git_hash=57a50b106b87' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=6cce1f5b223a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for treekin-0.5.1_7 ===> Building treekin-0.5.1_7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for treekin-0.5.1_7 build of biology/treekin | treekin-0.5.1_7 ended at Sun May 4 19:08:42 EDT 2025 build time: 00:00:21