------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/science/mmdb2 XDG_CONFIG_HOME=/construction/science/mmdb2 XDG_CACHE_HOME=/construction/science/mmdb2/.cache HOME=/construction/science/mmdb2 TMPDIR="/tmp" PATH=/construction/science/mmdb2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/mmdb2/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --enable-shared --disable-static --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/mmdb2 XDG_CONFIG_HOME=/construction/science/mmdb2 XDG_CACHE_HOME=/construction/science/mmdb2/.cache HOME=/construction/science/mmdb2 TMPDIR="/tmp" PATH=/construction/science/mmdb2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/mmdb2/.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 CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/mmdb2/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mmdb2" EXAMPLESDIR="share/examples/mmdb2" DATADIR="share/mmdb2" WWWDIR="www/mmdb2" ETCDIR="etc/mmdb2" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mmdb2 DOCSDIR=/usr/local/share/doc/mmdb2 EXAMPLESDIR=/usr/local/share/examples/mmdb2 WWWDIR=/usr/local/www/mmdb2 ETCDIR=/usr/local/etc/mmdb2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/ccache-3.7.12_4.pkg 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 gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.22 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.22 for building => SHA256 Checksum OK for mmdb2-2.0.22.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mmdb2-2.0.22 for building ===> Extracting for mmdb2-2.0.22 => SHA256 Checksum OK for mmdb2-2.0.22.tar.gz. Extracted Memory Use: 3.62M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mmdb2-2.0.22 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on package: gmake>=4.3 - found ===> mmdb2-2.0.22 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mmdb2-2.0.22 depends on package: gmake>=4.3 - found ===> mmdb2-2.0.22 depends on file: /usr/local/bin/ccache - found ===> Configuring for mmdb2-2.0.22 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/mmdb2-2.0.22/build-aux/missing: Unknown `--is-lightweight' option Try `/construction/science/mmdb2/mmdb2-2.0.22/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 whether gmake supports the include directive... yes (GNU style) 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 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-dragonfly6.5 checking host system type... x86_64-portbld-dragonfly6.5 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-dragonfly6.5 file names to x86_64-portbld-dragonfly6.5 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly6.5 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... dragonfly6.5 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... dragonfly6.5 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 00:00:05 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mmdb2-2.0.22 gmake[1]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.22' gmake all-am gmake[2]: Entering directory '/construction/science/mmdb2/mmdb2-2.0.22' 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++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_manager.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_manager.lo mmdb2/mmdb_manager.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_mattype.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_title.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_chain.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_io_stream.lo -MD -MP -MF mmdb2/.deps/mmdb_io_stream.Tpo -c mmdb2/mmdb_io_stream.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_io_stream.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/hybrid_36.lo -MD -MP -MF mmdb2/.deps/hybrid_36.Tpo -c mmdb2/hybrid_36.cpp -fPIC -DPIC -o mmdb2/.libs/hybrid_36.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_symop.lo -MD -MP -MF mmdb2/.deps/mmdb_symop.Tpo -c mmdb2/mmdb_symop.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_symop.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_chain.lo -MD -MP -MF mmdb2/.deps/mmdb_chain.Tpo -c mmdb2/mmdb_chain.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_chain.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_tables.lo -MD -MP -MF mmdb2/.deps/mmdb_tables.Tpo -c mmdb2/mmdb_tables.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_tables.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_linalg.lo -MD -MP -MF mmdb2/.deps/mmdb_math_linalg.Tpo -c mmdb2/mmdb_math_linalg.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_linalg.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_manager.lo -MD -MP -MF mmdb2/.deps/mmdb_manager.Tpo -c mmdb2/mmdb_manager.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_manager.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mattype.lo -MD -MP -MF mmdb2/.deps/mmdb_mattype.Tpo -c mmdb2/mmdb_mattype.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_mattype.o depbase=`echo mmdb2/mmdb_mask.lo | sed 's|[^/]*$|.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 -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_mask.lo mmdb2/mmdb_mask.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_mmcif_.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mmcif_.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_mmcif_.lo mmdb2/mmdb_mmcif_.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_title.lo -MD -MP -MF mmdb2/.deps/mmdb_title.Tpo -c mmdb2/mmdb_title.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_title.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_machine_.lo -MD -MP -MF mmdb2/.deps/mmdb_machine_.Tpo -c mmdb2/mmdb_machine_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_machine_.o depbase=`echo mmdb2/mmdb_uddata.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_uddata.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_uddata.lo mmdb2/mmdb_uddata.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mmdb2/mmdb_cifdefs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_cifdefs.lo -MD -MP -MF $depbase.Tpo -c -o mmdb2/mmdb_cifdefs.lo mmdb2/mmdb_cifdefs.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_atom.lo -MDdepbase=`echo mmdb2/mmdb_math_.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ -MP -MF mmdb2/.deps/mmdb_atom.Tpo -c mmdb2/mmdb_atom.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_atom.o /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -pipe -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 $depbase.Plo depbase=`echo mmdb2/mmdb_model.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_utils.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_rand.lo -MD -MP -MF mmdb2/.deps/mmdb_math_rand.Tpo -c mmdb2/mmdb_math_rand.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_rand.o depbase=`echo mmdb2/mmdb_coormngr.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_math_align.lo | sed 's|[^/]*$|.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_mask.lo -MD -MP -MF mmdb2/.deps/mmdb_mask.Tpo -c mmdb2/mmdb_mask.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_mask.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_mmcif_.lo -MD -MP -MF mmdb2/.deps/mmdb_mmcif_.Tpo -c mmdb2/mmdb_mmcif_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_mmcif_.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) ); ~~~~~~^~~ 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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_cifdefs.lo -MD -MP -MF mmdb2/.deps/mmdb_cifdefs.Tpo -c mmdb2/mmdb_cifdefs.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_cifdefs.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)) ); ~~~~~~^~~~~~~~ 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_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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_model.lo -MD -MP -MF mmdb2/.deps/mmdb_model.Tpo -c mmdb2/mmdb_model.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_model.o depbase=`echo mmdb2/mmdb_xml_.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_uddata.lo -MD -MP -MF mmdb2/.deps/mmdb_uddata.Tpo -c mmdb2/mmdb_uddata.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_uddata.o depbase=`echo mmdb2/mmdb_cryst.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_.lo -MD -MP -MF mmdb2/.deps/mmdb_math_.Tpo -c mmdb2/mmdb_math_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_.o depbase=`echo mmdb2/mmdb_math_bfgsmin.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_coormngr.lo -MD -MP -MF mmdb2/.deps/mmdb_coormngr.Tpo -c mmdb2/mmdb_coormngr.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_coormngr.o depbase=`echo mmdb2/mmdb_rwbrook.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_math_align.lo -MD -MP -MF mmdb2/.deps/mmdb_math_align.Tpo -c mmdb2/mmdb_math_align.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_math_align.o depbase=`echo mmdb2/mmdb_ficif.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_math_fft.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_selmngr.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_io_file.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT mmdb2/mmdb_root.lo -MD -MP -MF mmdb2/.deps/mmdb_root.Tpo -c mmdb2/mmdb_root.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_root.o depbase=`echo mmdb2/mmdb_math_graph.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo mmdb2/mmdb_seqsuperpose.lo | sed 's|[^/]*$|.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_xml_.lo -MD -MP -MF mmdb2/.deps/mmdb_xml_.Tpo -c mmdb2/mmdb_xml_.cpp -fPIC -DPIC -o mmdb2/.libs/mmdb_xml_.o 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 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 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 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 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 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 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)) ); ~~~~~~^~~~~~~~~~~~ In file included from mmdb2/mmdb_machine_.cpp:41: mmdb2/mmdb_machine_.h:296:13: error: 'size_t' does not name a type typedef size_t fpstr_size_t; ^~~~~~ mmdb2/mmdb_machine_.h:296:13: note: 'size_t' is defined in header ''; did you forget to '#include '? mmdb2/mmdb_machine_.h:45:1: +#include mmdb2/mmdb_machine_.h:296:13: typedef size_t fpstr_size_t; ^~~~~~ 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 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 gmake[2]: *** [Makefile:665: mmdb2/mmdb_machine_.lo] Error 1 gmake[2]: *** Waiting for unfinished jobs.... 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 gmake[2]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.22' gmake[1]: *** [Makefile:435: all] Error 2 gmake[1]: Leaving directory '/construction/science/mmdb2/mmdb2-2.0.22' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/science/mmdb2 FAILED 00:00:00