------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3.txz SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.20 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.20 for building => SHA256 Checksum OK for mmdb2-2.0.20.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.20 for building ===> Extracting for mmdb2-2.0.20 => SHA256 Checksum OK for mmdb2-2.0.20.tar.gz. Extracted Memory Use: 3.57M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mmdb2-2.0.20 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mmdb2-2.0.20 depends on package: gmake>=4.3 - found ===> Configuring for mmdb2-2.0.20 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 /construction/science/mmdb2/mmdb2-2.0.20/build-aux/missing: Unknown `--is-lightweight' option Try `/construction/science/mmdb2/mmdb2-2.0.20/build-aux/missing --help' for more information configure: WARNING: 'missing' script is too old or missing 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 for style of include used by gmake... GNU checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking 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 whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 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 that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating mmdb2.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mmdb2-2.0.20 gmake[1]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.20' gmake all-am gmake[2]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.20' depbase=`echo mmdb2/hybrid_36.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/hybrid_36.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/hybrid_36.lo mmdb2/hybrid_36.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_io_stream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_io_stream.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_io_stream.lo mmdb2/mmdb_io_stream.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_math_linalg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_linalg.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_linalg.lo mmdb2/mmdb_math_linalg.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_symop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_symop.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_symop.lo mmdb2/mmdb_symop.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_atom.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_atom.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_atom.lo mmdb2/mmdb_atom.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_machine_.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_machine_.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_machine_.lo mmdb2/mmdb_machine_.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_math_rand.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_rand.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_rand.lo mmdb2/mmdb_math_rand.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_tables.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_tables.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_tables.lo mmdb2/mmdb_tables.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_bondmngr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_bondmngr.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_bondmngr.lo mmdb2/mmdb_bondmngr.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_manager.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ 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mmdb2/.libs/mmdb_machine_.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_manager.lo -MD -MP -MF mmdb2/.deps/mmdb_manager.Tpo -c mmdb2/mmdb_manager.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_manager.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_atom.lo -MD -MP -MF mmdb2/.deps/mmdb_atom.Tpo -c mmdb2/mmdb_atom.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_atom.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_symop.lo -MD -MP -MF mmdb2/.deps/mmdb_symop.Tpo -c mmdb2/mmdb_symop.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_symop.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_linalg.lo -MD -MP -MF mmdb2/.deps/mmdb_math_linalg.Tpo -c mmdb2/mmdb_math_linalg.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_linalg.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_tables.lo -MD -MP -MF mmdb2/.deps/mmdb_tables.Tpo -c mmdb2/mmdb_tables.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_tables.o depbase=`echo mmdb2/mmdb_mattype.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mattype.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_mattype.lo mmdb2/mmdb_mattype.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mattype.lo -MD -MP -MF mmdb2/.deps/mmdb_mattype.Tpo -c mmdb2/mmdb_mattype.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_mattype.o depbase=`echo mmdb2/mmdb_title.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_title.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_title.lo mmdb2/mmdb_title.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_bondmngr.lo -MD -MP -MF mmdb2/.deps/mmdb_bondmngr.Tpo -c mmdb2/mmdb_bondmngr.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_bondmngr.o depbase=`echo mmdb2/mmdb_chain.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_chain.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_chain.lo mmdb2/mmdb_chain.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_title.lo -MD -MP -MF mmdb2/.deps/mmdb_title.Tpo -c mmdb2/mmdb_title.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_title.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_chain.lo -MD -MP -MF mmdb2/.deps/mmdb_chain.Tpo -c mmdb2/mmdb_chain.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_chain.o depbase=`echo mmdb2/mmdb_mask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mask.lo -MD 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-O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_.lo mmdb2/mmdb_math_.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_.lo -MD -MP -MF mmdb2/.deps/mmdb_math_.Tpo -c mmdb2/mmdb_math_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_.o depbase=`echo mmdb2/mmdb_model.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_model.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_model.lo mmdb2/mmdb_model.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_model.lo -MD -MP -MF mmdb2/.deps/mmdb_model.Tpo -c mmdb2/mmdb_model.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_model.o depbase=`echo mmdb2/mmdb_utils.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_utils.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_utils.lo mmdb2/mmdb_utils.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_utils.lo -MD -MP -MF mmdb2/.deps/mmdb_utils.Tpo -c mmdb2/mmdb_utils.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_utils.o depbase=`echo mmdb2/mmdb_coormngr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_coormngr.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_coormngr.lo mmdb2/mmdb_coormngr.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_coormngr.lo -MD -MP -MF mmdb2/.deps/mmdb_coormngr.Tpo -c mmdb2/mmdb_coormngr.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_coormngr.o depbase=`echo mmdb2/mmdb_math_align.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_align.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_align.lo mmdb2/mmdb_math_align.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_align.lo -MD -MP -MF mmdb2/.deps/mmdb_math_align.Tpo -c mmdb2/mmdb_math_align.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_align.o In function 'virtual void mmdb::Remark::PDBASCIIDump(mmdb::pstr, int)', inlined from 'virtual void mmdb::Remark::PDBASCIIDump(mmdb::pstr, int)' at mmdb2/mmdb_title.cpp:1357:9: mmdb2/mmdb_title.cpp:1364:18: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy ( &(S[11]),remark,IMin(68,strlen(remark)) ); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdb2/mmdb_title.cpp: In member function 'virtual void mmdb::Remark::PDBASCIIDump(mmdb::pstr, int)': mmdb2/mmdb_title.cpp:1364:50: note: length computed here strncpy ( &(S[11]),remark,IMin(68,strlen(remark)) ); ~~~~~~^~~~~~~~ depbase=`echo mmdb2/mmdb_root.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_root.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_root.lo mmdb2/mmdb_root.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_xml_.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_xml_.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_xml_.lo mmdb2/mmdb_xml_.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_root.lo -MD -MP -MF mmdb2/.deps/mmdb_root.Tpo -c mmdb2/mmdb_root.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_root.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_xml_.lo -MD -MP -MF mmdb2/.deps/mmdb_xml_.Tpo -c mmdb2/mmdb_xml_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_xml_.o depbase=`echo mmdb2/mmdb_cryst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_cryst.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_cryst.lo mmdb2/mmdb_cryst.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_cryst.lo -MD -MP -MF mmdb2/.deps/mmdb_cryst.Tpo -c mmdb2/mmdb_cryst.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_cryst.o depbase=`echo mmdb2/mmdb_math_bfgsmin.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_bfgsmin.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_bfgsmin.lo mmdb2/mmdb_math_bfgsmin.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_bfgsmin.lo -MD -MP -MF mmdb2/.deps/mmdb_math_bfgsmin.Tpo -c mmdb2/mmdb_math_bfgsmin.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_bfgsmin.o mmdb2/mmdb_mmcif_.cpp: In member function 'void mmdb::mmcif::Loop::CopyString(mmdb::pstr, int, mmdb::cpstr, int, int&)': mmdb2/mmdb_mmcif_.cpp:1058:17: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy ( buf,p,IMin(maxlength,strlen(p)+1) ); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdb2/mmdb_mmcif_.cpp:1058:46: note: length computed here strncpy ( buf,p,IMin(maxlength,strlen(p)+1) ); ~~~~~~^~~ depbase=`echo mmdb2/mmdb_rwbrook.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_rwbrook.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_rwbrook.lo mmdb2/mmdb_rwbrook.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_rwbrook.lo -MD -MP -MF mmdb2/.deps/mmdb_rwbrook.Tpo -c mmdb2/mmdb_rwbrook.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_rwbrook.o depbase=`echo mmdb2/mmdb_ficif.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_ficif.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_ficif.lo mmdb2/mmdb_ficif.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_ficif.lo -MD -MP -MF mmdb2/.deps/mmdb_ficif.Tpo -c mmdb2/mmdb_ficif.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_ficif.o depbase=`echo mmdb2/mmdb_math_fft.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_fft.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_fft.lo mmdb2/mmdb_math_fft.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_fft.lo -MD -MP -MF mmdb2/.deps/mmdb_math_fft.Tpo -c mmdb2/mmdb_math_fft.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_fft.o mmdb2/mmdb_cryst.cpp: In member function 'virtual void mmdb::TVect::PDBASCIIDump(mmdb::pstr, int)': mmdb2/mmdb_cryst.cpp:412:15: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy ( &(S[40]),comment,IMin(30,strlen(comment)) ); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdb2/mmdb_cryst.cpp:412:48: note: length computed here strncpy ( &(S[40]),comment,IMin(30,strlen(comment)) ); ~~~~~~^~~~~~~~~ mmdb2/mmdb_cryst.cpp: In member function 'void mmdb::Cryst::PDBASCIIDump(mmdb::io::RFile)': mmdb2/mmdb_cryst.cpp:877:17: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy ( &(S[55]),spaceGroup,IMin(11,strlen(spaceGroup)) ); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdb2/mmdb_cryst.cpp:877:53: note: length computed here strncpy ( &(S[55]),spaceGroup,IMin(11,strlen(spaceGroup)) ); ~~~~~~^~~~~~~~~~~~ depbase=`echo mmdb2/mmdb_selmngr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_selmngr.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_selmngr.lo mmdb2/mmdb_selmngr.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_selmngr.lo -MD -MP -MF mmdb2/.deps/mmdb_selmngr.Tpo -c mmdb2/mmdb_selmngr.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_selmngr.o depbase=`echo mmdb2/mmdb_io_file.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_io_file.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_io_file.lo mmdb2/mmdb_io_file.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_io_file.lo -MD -MP -MF mmdb2/.deps/mmdb_io_file.Tpo -c mmdb2/mmdb_io_file.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_io_file.o depbase=`echo mmdb2/mmdb_math_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_graph.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_math_graph.lo mmdb2/mmdb_math_graph.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_graph.lo -MD -MP -MF mmdb2/.deps/mmdb_math_graph.Tpo -c mmdb2/mmdb_math_graph.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_graph.o depbase=`echo mmdb2/mmdb_seqsuperpose.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_seqsuperpose.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_seqsuperpose.lo mmdb2/mmdb_seqsuperpose.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_seqsuperpose.lo -MD -MP -MF mmdb2/.deps/mmdb_seqsuperpose.Tpo -c mmdb2/mmdb_seqsuperpose.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_seqsuperpose.o /bin/sh ./libtool --tag=CXX --mode=link c++ -pipe -O2 -fno-strict-aliasing -no-undefined -o mmdb2/libmmdb2.la -rpath /usr/local/lib mmdb2/hybrid_36.lo mmdb2/mmdb_io_stream.lo mmdb2/mmdb_math_linalg.lo mmdb2/mmdb_symop.lo mmdb2/mmdb_atom.lo mmdb2/mmdb_machine_.lo mmdb2/mmdb_math_rand.lo mmdb2/mmdb_tables.lo mmdb2/mmdb_bondmngr.lo mmdb2/mmdb_manager.lo mmdb2/mmdb_mattype.lo mmdb2/mmdb_title.lo mmdb2/mmdb_chain.lo mmdb2/mmdb_mask.lo mmdb2/mmdb_mmcif_.lo mmdb2/mmdb_uddata.lo mmdb2/mmdb_cifdefs.lo mmdb2/mmdb_math_.lo mmdb2/mmdb_model.lo mmdb2/mmdb_utils.lo mmdb2/mmdb_coormngr.lo mmdb2/mmdb_math_align.lo mmdb2/mmdb_root.lo mmdb2/mmdb_xml_.lo mmdb2/mmdb_cryst.lo mmdb2/mmdb_math_bfgsmin.lo mmdb2/mmdb_rwbrook.lo mmdb2/mmdb_ficif.lo mmdb2/mmdb_math_fft.lo mmdb2/mmdb_selmngr.lo mmdb2/mmdb_io_file.lo mmdb2/mmdb_math_graph.lo mmdb2/mmdb_seqsuperpose.lo -lm libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o mmdb2/.libs/hybrid_36.o mmdb2/.libs/mmdb_io_stream.o mmdb2/.libs/mmdb_math_linalg.o mmdb2/.libs/mmdb_symop.o mmdb2/.libs/mmdb_atom.o mmdb2/.libs/mmdb_machine_.o mmdb2/.libs/mmdb_math_rand.o mmdb2/.libs/mmdb_tables.o mmdb2/.libs/mmdb_bondmngr.o mmdb2/.libs/mmdb_manager.o mmdb2/.libs/mmdb_mattype.o mmdb2/.libs/mmdb_title.o mmdb2/.libs/mmdb_chain.o mmdb2/.libs/mmdb_mask.o mmdb2/.libs/mmdb_mmcif_.o mmdb2/.libs/mmdb_uddata.o mmdb2/.libs/mmdb_cifdefs.o mmdb2/.libs/mmdb_math_.o mmdb2/.libs/mmdb_model.o mmdb2/.libs/mmdb_utils.o mmdb2/.libs/mmdb_coormngr.o mmdb2/.libs/mmdb_math_align.o mmdb2/.libs/mmdb_root.o mmdb2/.libs/mmdb_xml_.o mmdb2/.libs/mmdb_cryst.o mmdb2/.libs/mmdb_math_bfgsmin.o mmdb2/.libs/mmdb_rwbrook.o mmdb2/.libs/mmdb_ficif.o mmdb2/.libs/mmdb_math_fft.o mmdb2/.libs/mmdb_selmngr.o mmdb2/.libs/mmdb_io_file.o mmdb2/.libs/mmdb_math_graph.o mmdb2/.libs/mmdb_seqsuperpose.o -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-soname -Wl,libmmdb2.so.0 -o mmdb2/.libs/libmmdb2.so.0.0.0 libtool: link: (cd "mmdb2/.libs" && rm -f "libmmdb2.so.0" && ln -s "libmmdb2.so.0.0.0" "libmmdb2.so.0") libtool: link: (cd "mmdb2/.libs" && rm -f "libmmdb2.so" && ln -s "libmmdb2.so.0.0.0" "libmmdb2.so") libtool: link: ( cd "mmdb2/.libs" && rm -f "libmmdb2.la" && ln -s "../libmmdb2.la" "libmmdb2.la" ) gmake[2]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.20' gmake[1]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.20' SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for mmdb2-2.0.20 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.20' gmake[2]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.20' /bin/mkdir -p '/construction/science/mmdb2/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c mmdb2/libmmdb2.la '/construction/science/mmdb2/stage/usr/local/lib' libtool: install: /usr/bin/install -c mmdb2/.libs/libmmdb2.so.0.0.0 /construction/science/mmdb2/stage/usr/local/lib/libmmdb2.so.0.0.0 libtool: install: (cd /construction/science/mmdb2/stage/usr/local/lib && { ln -s -f libmmdb2.so.0.0.0 libmmdb2.so.0 || { rm -f libmmdb2.so.0 && ln -s libmmdb2.so.0.0.0 libmmdb2.so.0; }; }) libtool: install: (cd /construction/science/mmdb2/stage/usr/local/lib && { ln -s -f libmmdb2.so.0.0.0 libmmdb2.so || { rm -f libmmdb2.so && ln -s libmmdb2.so.0.0.0 libmmdb2.so; }; }) libtool: install: /usr/bin/install -c mmdb2/.libs/libmmdb2.lai /construction/science/mmdb2/stage/usr/local/lib/libmmdb2.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/science/mmdb2/stage/usr/local/lib/pkgconfig' install -m 0644 mmdb2.pc '/construction/science/mmdb2/stage/usr/local/lib/pkgconfig' /bin/mkdir -p '/construction/science/mmdb2/stage/usr/local/include/mmdb2' install -m 0644 mmdb2/hybrid_36.h mmdb2/mmdb_io_file.h mmdb2/mmdb_math_graph.h mmdb2/mmdb_seqsuperpose.h mmdb2/mmdb_atom.h mmdb2/mmdb_io_stream.h mmdb2/mmdb_math_linalg.h mmdb2/mmdb_symop.h mmdb2/mmdb_bondmngr.h mmdb2/mmdb_machine_.h mmdb2/mmdb_math_rand.h mmdb2/mmdb_tables.h mmdb2/mmdb_chain.h mmdb2/mmdb_manager.h mmdb2/mmdb_mattype.h mmdb2/mmdb_title.h mmdb2/mmdb_cifdefs.h mmdb2/mmdb_mask.h mmdb2/mmdb_mmcif_.h mmdb2/mmdb_uddata.h mmdb2/mmdb_coormngr.h mmdb2/mmdb_math_.h mmdb2/mmdb_model.h mmdb2/mmdb_utils.h mmdb2/mmdb_cryst.h mmdb2/mmdb_math_align.h mmdb2/mmdb_root.h mmdb2/mmdb_xml_.h mmdb2/mmdb_defs.h mmdb2/mmdb_math_bfgsmin.h mmdb2/mmdb_rwbrook.h mmdb2/mmdb_ficif.h mmdb2/mmdb_math_fft.h mmdb2/mmdb_selmngr.h '/construction/science/mmdb2/stage/usr/local/include/mmdb2' gmake[2]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.20' gmake[1]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.20' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: 'lib/libmmdb2.so.0.0.0' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for mmdb2-2.0.20 file sizes/checksums [38]: 0% file sizes/checksums [38]: 100% packing files [38]: 0% packing files [38]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:00:25