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Gentoo's Bugzilla – Attachment 448904 Details for
Bug 595986
sci-libs/libmems-1.6_p1-r2 : /.../remove_pointer.hpp:21:21: error: missing binary operator before token "("
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sci-libs:libmems-1.6_p1-r2:20161002-202815.log
sci-libs:libmems-1.6_p1-r2:20161002-202815.log (text/plain), 11.93 KB, created by
Toralf Förster
on 2016-10-02 21:09:08 UTC
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Description:
sci-libs:libmems-1.6_p1-r2:20161002-202815.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-10-02 21:09:08 UTC
Size:
11.93 KB
patch
obsolete
> * Package: sci-libs/libmems-1.6_p1-r2 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking libmems-1.6_p1.tar.xz to /var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work >>>> Source unpacked in /var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work >>>> Preparing source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1 ... > * Applying libmems-1.6_p1-build.patch ... > [ ok ] > * Applying libmems-1.6_p1-boost.patch ... > [ ok ] > * Applying libmems-1.6_p1-gcc-4.7.patch ... > [ ok ] > * Applying libmems-1.6_p1-broken-constness.patch ... > [ ok ] > * Applying libmems-1.6_p1-format-security.patch ... > [ ok ] > * Applying libmems-1.6_p1-fix-c++14.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: libmems-1.6_p1/ > * Running elibtoolize in: libmems-1.6_p1/config/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1 ... > * econf: updating libmems-1.6_p1/config/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating libmems-1.6_p1/config/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/libmems-1.6_p1-r2 --htmldir=/usr/share/doc/libmems-1.6_p1-r2/html --libdir=/usr/lib64 --enable-shared --disable-static >checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports nested variables... yes >checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ >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 x86_64-pc-linux-gnu-g++ accepts -g... yes >checking for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-g++... none >checking whether ln -s works... yes >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking how to print strings... printf >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... mt >checking if mt is a manifest tool... no >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux 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... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking for special C compiler options needed for large files... no >checking for _FILE_OFFSET_BITS value needed for large files... no >checking for ANSI C header files... (cached) yes >checking for boostlib >= 1.34.0... yes >checking whether the compiler implements namespaces... yes >checking whether the Boost::Filesystem library is available... yes >checking for exit in -lboost_filesystem-mt... yes >checking whether the Boost::Program_Options library is available... yes >checking for exit in -lboost_program_options-mt... yes >checking whether the Boost::IOStreams library is available... yes >checking for exit in -lboost_iostreams-mt... yes >checking whether the Boost::System library is available... yes >checking for exit in -lboost_system-mt... yes >checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config >checking pkg-config is at least version 0.9.0... yes >checking for DEPS... yes >checking for sys/types.h... (cached) yes >checking sys/aio.h usability... no >checking sys/aio.h presence... no >checking for sys/aio.h... no >checking aio.h usability... yes >checking aio.h presence... yes >checking for aio.h... yes >checking features.h usability... yes >checking features.h presence... yes >checking for features.h... yes >checking for pthread_mutex_unlock in -lpthread... yes >checking for aio_write in -lrt... yes >checking for x86_64-pc-linux-gnu-doxygen... no >checking for doxygen... no >configure: WARNING: doxygen not found - will not generate any doxygen documentation >checking for x86_64-pc-linux-gnu-perl... no >checking for perl... /usr/bin/perl >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking whether time.h and sys/time.h may both be included... yes >checking whether x86_64-pc-linux-gnu-gcc needs -traditional... no >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating libMems/Makefile >config.status: creating libMems-1.6.pc >config.status: creating config.h >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1 ... >make -j1 >make all-recursive >make[1]: Entering directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1' >Making all in libMems >make[2]: Entering directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1/libMems' >/bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o RepeatHash.lo RepeatHash.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o >In file included from ../libMems/AbstractMatch.h:19:0, > from ../libMems/UngappedLocalAlignment.h:18, > from ../libMems/Match.h:19, > from ../libMems/MatchFinder.h:17, > from ../libMems/MemHash.h:20, > from ../libMems/RepeatHash.h:16, > from RepeatHash.cpp:13: >/usr/include/boost/type_traits/remove_pointer.hpp:21:21: error: missing binary operator before token "(" > #if BOOST_WORKAROUND(BOOST_MSVC, < 1900) > ^ >make[2]: *** [Makefile:759: RepeatHash.lo] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1/libMems' >make[1]: *** [Makefile:540: all-recursive] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1' >make: *** [Makefile:448: all] Error 2 > * ERROR: sci-libs/libmems-1.6_p1-r2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-libs/libmems-1.6_p1-r2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-libs/libmems-1.6_p1-r2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-libs:libmems-1.6_p1-r2:20161002-202815.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1' > * S: '/var/tmp/portage/sci-libs/libmems-1.6_p1-r2/work/libmems-1.6_p1'
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