------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/gmake-4.2.1_3.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/mmdb2-2.0.20.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/gmp-6.2.0.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/mpfr-4.0.2.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/mpc-1.1.0_2.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_2,1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/gcc8-8.4.0.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor ===== Message from gcc8-8.4.0: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/libccp4-6.5.1_4.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:26 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libssm-1.4.0_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libssm-1.4.0_2 for building => SHA256 Checksum OK for ssm-1.4.0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libssm-1.4.0_2 for building ===> Extracting for libssm-1.4.0_2 => SHA256 Checksum OK for ssm-1.4.0.tar.gz. Extracted Memory Use: 1.81M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for libssm-1.4.0_2 ===> Applying ports patches for libssm-1.4.0_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on executable: gmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> libssm-1.4.0_2 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> libssm-1.4.0_2 depends on executable: gmake - found ===> libssm-1.4.0_2 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> libssm-1.4.0_2 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) ===> Configuring for libssm-1.4.0_2 configure: WARNING: unrecognized options: --with-mmdb configure: loading site script /xports/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 gmake sets $(MAKE)... yes checking whether 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 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... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 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/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64-portbld-dragonfly5.9 file names to x86_64-portbld-dragonfly5.9 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.9 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... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/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... no 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... dragonfly5.9 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... dragonfly5.9 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 SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for libssm-1.4.0_2 gmake[1]: Entering directory '/construction/science/libssm/ssm-1.4.0' gmake all-am gmake[2]: Entering directory '/construction/science/libssm/ssm-1.4.0' c++ -DHAVE_CONFIG_H -I. -D_ccp4_ -isystem /usr/local/include -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ssm/ssm_superpose.lo -MD -MP -MF ssm/.deps/ssm_superpose.Tpo -c ssm/ssm_superpose.cpp -fPIC -DPIC -o ssm/.libs/ssm_superpose.o depbase=`echo ssm/ssm_align.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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 -pipe -O2 -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-superpose.Tpo .deps/superpose-superpose.Po mv -f .deps/superpose-sup_pairwise.Tpo .deps/superpose-sup_pairwise.Po mv -f .deps/superpose-sup_multiple.Tpo .deps/superpose-sup_multiple.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -pipe -O2 -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/gcc80/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/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -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++ -pipe -O2 -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++ -pipe -O2 -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[2]: Leaving directory '/construction/science/libssm/ssm-1.4.0' gmake[1]: Leaving directory '/construction/science/libssm/ssm-1.4.0' SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for libssm-1.4.0_2 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/science/libssm/ssm-1.4.0' if test -z 'strip'; then \ gmake INSTALL_PROGRAM="/bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[2]: Entering directory '/construction/science/libssm/ssm-1.4.0' gmake[3]: Entering directory '/construction/science/libssm/ssm-1.4.0' /bin/mkdir -p '/construction/science/libssm/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libssm.la '/construction/science/libssm/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libssm.so.2.0.0 /construction/science/libssm/stage/usr/local/lib/libssm.so.2.0.0 libtool: install: strip --strip-unneeded /construction/science/libssm/stage/usr/local/lib/libssm.so.2.0.0 libtool: install: (cd /construction/science/libssm/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 /construction/science/libssm/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 /construction/science/libssm/stage/usr/local/lib/libssm.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/science/libssm/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s superpose '/construction/science/libssm/stage/usr/local/bin' libtool: install: warning: `libssm.la' has not been installed in `/usr/local/lib' libtool: install: /bin/sh /construction/science/libssm/ssm-1.4.0/build-aux/install-sh -c -s .libs/superpose /construction/science/libssm/stage/usr/local/bin/superpose /bin/mkdir -p '/construction/science/libssm/stage/usr/local/lib/pkgconfig' install -m 0644 ssm.pc '/construction/science/libssm/stage/usr/local/lib/pkgconfig' /bin/mkdir -p '/construction/science/libssm/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 '/construction/science/libssm/stage/usr/local/include/ssm' gmake[3]: Leaving directory '/construction/science/libssm/ssm-1.4.0' gmake[2]: Leaving directory '/construction/science/libssm/ssm-1.4.0' gmake[1]: Leaving directory '/construction/science/libssm/ssm-1.4.0' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for libssm-1.4.0_2 file sizes/checksums [12]: 0% file sizes/checksums [12]: 100% packing files [12]: 0% packing files [12]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:43