=>> Building science/libssm build started at Thu Jan 22 06:45:56 EST 2026 port directory: /usr/ports/science/libssm package name: libssm-1.4.0_4 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 606 Jan 31 2025 /usr/ports/science/libssm/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: a8674e05484a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-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_14_3_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_14_3_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-shared --disable-static --enable-ccp4 --with-mmdb=/usr/local --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/science/libssm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/libssm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/libssm/work/.cache HOME=/wrkdirs/usr/ports/science/libssm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/libssm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/libssm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" 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/science/libssm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/libssm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/libssm/work/.cache HOME=/wrkdirs/usr/ports/science/libssm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/libssm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/libssm/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/libssm" EXAMPLESDIR="share/examples/libssm" DATADIR="share/libssm" WWWDIR="www/libssm" ETCDIR="etc/libssm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/libssm DOCSDIR=/usr/local/share/doc/libssm EXAMPLESDIR=/usr/local/share/examples/libssm WWWDIR=/usr/local/www/libssm ETCDIR=/usr/local/etc/libssm --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 pipebuf (-y) 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 ===> libssm-1.4.0_4 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 ===> libssm-1.4.0_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of libssm-1.4.0_4 =========================================================================== =================================================== ===== 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 libssm-1.4.0_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by libssm-1.4.0_4 for building => SHA256 Checksum OK for ssm-1.4.0.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 libssm-1.4.0_4 for building ===> Extracting for libssm-1.4.0_4 => SHA256 Checksum OK for ssm-1.4.0.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 libssm-1.4.0_4 ===> Applying FreeBSD patches for libssm-1.4.0_4 from /usr/ports/science/libssm/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libssm-1.4.0_4 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> libssm-1.4.0_4 depends on package: gmake>=4.4.1 - found ===> Returning to build of libssm-1.4.0_4 ===> libssm-1.4.0_4 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. ===> libssm-1.4.0_4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of libssm-1.4.0_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libssm-1.4.0_4 depends on shared library: libccp4c.so - not found ===> Installing existing package /packages/All/libccp4-8.0.0.pkg [pkg.DaveG.ca] Installing libccp4-8.0.0... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] `-- Installing mmdb2-2.0.22... [pkg.DaveG.ca] `-- Extracting mmdb2-2.0.22: .......... done [pkg.DaveG.ca] Extracting libccp4-8.0.0: .......... done ===== Message from gcc14-14.2.0_4: -- 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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> libssm-1.4.0_4 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> Returning to build of libssm-1.4.0_4 ===> libssm-1.4.0_4 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for libssm-1.4.0_4 configure: WARNING: unrecognized options: --with-mmdb 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 /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes 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 ar... ar checking the archiver (ar) interface... ar checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm -B checking the name lister (/usr/local/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert amd64-portbld-freebsd14.3 file names to amd64-portbld-freebsd14.3 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.3 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/local/bin/nm -B output from cc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp 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 dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking for library containing cos... -lm checking for MMDB_CCIF_Init in -lmmdb2... yes checking mmdb2/mmdb_manager.h usability... yes checking mmdb2/mmdb_manager.h presence... yes checking for mmdb2/mmdb_manager.h... yes checking for ccp4_banner in -lccp4c... yes checking ccp4/ccp4_general.h usability... yes checking ccp4/ccp4_general.h presence... yes checking for ccp4/ccp4_general.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ssm.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --with-mmdb =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for libssm-1.4.0_4 /usr/local/bin/gmake all-am gmake[1]: Entering directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' c++ -DHAVE_CONFIG_H -I. -D_ccp4_ -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT superpose-superpose.o -MD -MP -MF .deps/superpose-superpose.Tpo -c -o superpose-superpose.o `test -f 'superpose.cpp' || echo './'`superpose.cpp c++ -DHAVE_CONFIG_H -I. -D_ccp4_ -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT superpose-sup_pairwise.o -MD -MP -MF .deps/superpose-sup_pairwise.Tpo -c -o superpose-sup_pairwise.o `test -f 'sup_pairwise.cpp' || echo './'`sup_pairwise.cpp c++ -DHAVE_CONFIG_H -I. -D_ccp4_ -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT superpose-sup_multiple.o -MD -MP -MF .deps/superpose-sup_multiple.Tpo -c -o superpose-sup_multiple.o `test -f 'sup_multiple.cpp' || echo './'`sup_multiple.cpp depbase=`echo ssm/ssm_superpose.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_superpose.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_superpose.lo ssm/ssm_superpose.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ssm/ssm_csia.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_csia.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_csia.lo ssm/ssm_csia.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ssm/ssm_vxedge.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_vxedge.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_vxedge.lo ssm/ssm_vxedge.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ssm/ssm_align.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_align.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_align.lo ssm/ssm_align.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ssm/ssm_malign.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_malign.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_malign.lo ssm/ssm_malign.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ssm/ssm_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_graph.lo -MD -MP -MF $depbase.Tpo -c -o ssm/ssm_graph.lo ssm/ssm_graph.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_graph.lo -MD -MP -MF ssm/.deps/ssm_graph.Tpo -c ssm/ssm_graph.cpp -fPIC -DPIC -o ssm/.libs/ssm_graph.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_superpose.lo -MD -MP -MF ssm/.deps/ssm_superpose.Tpo -c ssm/ssm_superpose.cpp -fPIC -DPIC -o ssm/.libs/ssm_superpose.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_csia.lo -MD -MP -MF ssm/.deps/ssm_csia.Tpo -c ssm/ssm_csia.cpp -fPIC -DPIC -o ssm/.libs/ssm_csia.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_align.lo -MD -MP -MF ssm/.deps/ssm_align.Tpo -c ssm/ssm_align.cpp -fPIC -DPIC -o ssm/.libs/ssm_align.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_malign.lo -MD -MP -MF ssm/.deps/ssm_malign.Tpo -c ssm/ssm_malign.cpp -fPIC -DPIC -o ssm/.libs/ssm_malign.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_vxedge.lo -MD -MP -MF ssm/.deps/ssm_vxedge.Tpo -c ssm/ssm_vxedge.cpp -fPIC -DPIC -o ssm/.libs/ssm_vxedge.o mv -f .deps/superpose-sup_pairwise.Tpo .deps/superpose-sup_pairwise.Po mv -f .deps/superpose-superpose.Tpo .deps/superpose-superpose.Po mv -f .deps/superpose-sup_multiple.Tpo .deps/superpose-sup_multiple.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -no-undefined -version-info 2:0:0 -L/usr/local/lib -o libssm.la -rpath /usr/local/lib ssm/ssm_superpose.lo ssm/ssm_csia.lo ssm/ssm_vxedge.lo ssm/ssm_align.lo ssm/ssm_malign.lo ssm/ssm_graph.lo -lmmdb2 -lm libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o ssm/.libs/ssm_superpose.o ssm/.libs/ssm_csia.o ssm/.libs/ssm_vxedge.o ssm/.libs/ssm_align.o ssm/.libs/ssm_malign.o ssm/.libs/ssm_graph.o -L/usr/local/lib -lmmdb2 -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-soname -Wl,libssm.so.2 -o .libs/libssm.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libssm.so.2" && ln -s "libssm.so.2.0.0" "libssm.so.2") libtool: link: (cd ".libs" && rm -f "libssm.so" && ln -s "libssm.so.2.0.0" "libssm.so") libtool: link: ( cd ".libs" && rm -f "libssm.la" && ln -s "../libssm.la" "libssm.la" ) /bin/sh ./libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o superpose superpose-superpose.o superpose-sup_pairwise.o superpose-sup_multiple.o libssm.la -lmmdb2 -lccp4c -lm libtool: link: c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o .libs/superpose superpose-superpose.o superpose-sup_pairwise.o superpose-sup_multiple.o -L/usr/local/lib ./.libs/libssm.so -lccp4c -lm -lmmdb2 -Wl,-rpath -Wl,/usr/local/lib gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for libssm-1.4.0_4 ===> Generating temporary packing list if test -z 'strip'; then \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[1]: Entering directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' gmake[2]: Entering directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' /bin/mkdir -p '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libssm.la '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libssm.so.2.0.0 /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib/libssm.so.2.0.0 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib/libssm.so.2.0.0 libtool: install: (cd /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib && { ln -s -f libssm.so.2.0.0 libssm.so.2 || { rm -f libssm.so.2 && ln -s libssm.so.2.0.0 libssm.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib && { ln -s -f libssm.so.2.0.0 libssm.so || { rm -f libssm.so && ln -s libssm.so.2.0.0 libssm.so; }; }) libtool: install: /usr/bin/install -c .libs/libssm.lai /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib/libssm.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s superpose '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/bin' libtool: install: warning: `libssm.la' has not been installed in `/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0/build-aux/install-sh -c -s .libs/superpose /wrkdirs/usr/ports/science/libssm/work/stage/usr/local/bin/superpose /bin/mkdir -p '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib/pkgconfig' install -m 0644 ssm.pc '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/lib/pkgconfig' /bin/mkdir -p '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/include/ssm' install -m 0644 ssm/ssm_superpose.h ssm/ssm_csia.h ssm/ssm_vxedge.h ssm/ssm_align.h ssm/ssm_malign.h ssm/ssm_graph.h ssm/ssm_defs.h '/wrkdirs/usr/ports/science/libssm/work/stage/usr/local/include/ssm' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/libssm/work/ssm-1.4.0' ====> 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=2026-01-22T11:45:56+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=a8674e05484a' '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 libssm-1.4.0_4 ===> Building libssm-1.4.0_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for libssm-1.4.0_4 build of science/libssm | libssm-1.4.0_4 ended at Thu Jan 22 06:46:06 EST 2026 build time: 00:00:11