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Gentoo's Bugzilla – Attachment 390018 Details for
Bug 529770
sci-libs/libmems-1.6_p1: fails to build
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build.log
build.log (text/plain), 86.94 KB, created by
Ian Stakenvicius (RETIRED)
on 2014-11-21 16:48:56 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Ian Stakenvicius (RETIRED)
Created:
2014-11-21 16:48:56 UTC
Size:
86.94 KB
patch
obsolete
> * Package: sci-libs/libmems-1.6_p1 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 doc elibc_glibc kernel_linux test userland_GNU > * FEATURES: sandbox test userpriv usersandbox >Installed LAPACK for library directory lib64 > [1] reference * >Installed BLAS for library directory lib64 > [1] reference * >Installed CBLAS for library directory lib64 > [1] gsl > [2] reference * >>>> Unpacking source... >>>> Unpacking libmems-1.6_p1.tar.xz to /tmp/portage/sci-libs/libmems-1.6_p1/work >>>> Source unpacked in /tmp/portage/sci-libs/libmems-1.6_p1/work >>>> Preparing source in /tmp/portage/sci-libs/libmems-1.6_p1/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 ] > * Running eautoreconf in '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf ... > [ 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 ... >>>> Source prepared. >>>> Configuring source in /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 ... >>>> Working in BUILD_DIR: "/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build" > * 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 >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/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 --libdir=/usr/lib64 --docdir=/usr/share/doc/libmems-1.6_p1 >configure: loading site script /usr/share/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... /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... yes >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... /usr/bin/doxygen >checking for x86_64-pc-linux-gnu-perl... no >checking for perl... /usr/bin/perl >checking for x86_64-pc-linux-gnu-dot... no >checking for dot... /usr/bin/dot >checking for x86_64-pc-linux-gnu-latex... no >checking for latex... /usr/bin/latex >checking for x86_64-pc-linux-gnu-makeindex... no >checking for makeindex... /usr/bin/makeindex >checking for x86_64-pc-linux-gnu-dvips... no >checking for dvips... /usr/bin/dvips >checking for x86_64-pc-linux-gnu-egrep... no >checking for egrep... /bin/egrep >checking for x86_64-pc-linux-gnu-pdflatex... no >checking for pdflatex... /usr/bin/pdflatex >checking for x86_64-pc-linux-gnu-makeindex... /usr/bin/makeindex >checking for x86_64-pc-linux-gnu-egrep... /bin/egrep >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 /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 ... >>>> Working in BUILD_DIR: "/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build" >make -j24 >make all-recursive >make[1]: Entering directory '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build' >Making all in libMems >make[2]: Entering directory '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build/libMems' >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RepeatHash.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatHash.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o DNAFileSML.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/DNAFileSML.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MatchFinder.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchFinder.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o DNAMemorySML.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/DNAMemorySML.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MemorySML.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MemorySML.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o SortedMerList.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SortedMerList.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o FileSML.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/FileSML.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MemHash.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MemHash.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MatchHashEntry.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchHashEntry.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Interval.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Interval.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o IntervalList.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/IntervalList.cpp >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o twister.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/twister.c >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o gnAlignedSequences.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/gnAlignedSequences.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MatchList.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchList.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Aligner.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Islands.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.cpp >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o MaskedMemHash.lo 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-I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/twister.c -o twister.o >/dev/null 2>&1 >In file included from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MuscleInterface.cpp:18:0: >/usr/include/libMUSCLE-3.7/libMUSCLE/muscle.h:54:0: warning: "assert" redefined > #define assert(exp) ((void)0) > ^ >In file included from /usr/include/boost/integer/integer_log2.hpp:18:0, > from /usr/include/boost/pending/integer_log2.hpp:7, > from /usr/include/boost/pending/lowest_bit.hpp:18, > from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:45, > from /usr/include/boost/dynamic_bitset.hpp:15, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/AbstractMatch.h:21, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SparseAbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAlignment.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MuscleInterface.h:19, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MuscleInterface.cpp:13: >/usr/include/assert.h:85:0: note: this is the location of the previous definition > # define assert(expr) \ > ^ >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ProgressiveAligner.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o SuperInterval.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SuperInterval.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o GreedyBreakpointElimination.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GreedyBreakpointElimination.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`HomologyHMM/algebras.cc >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.cpp:13: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:10: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.h:21, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Backbone.cpp:13: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.h:21, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.cpp:14: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`HomologyHMM/homology.cc >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`HomologyHMM/homologymain.cc >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.cc:24: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homologymain.cc:21: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/ext/hash_map:60:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.h:21, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GreedyBreakpointElimination.cpp:7: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] > #warning \ > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Interval.cpp -o Interval.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchList.cpp -o MatchList.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/asyncio.c >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/algorithm:62:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/AbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SparseAbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAlignment.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAligner.h:17, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h: In instantiation of 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LabeledMem*, std::vector<mems::LabeledMem> >; _Compare = mems::LabeledMemComparator]': >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:489:47: required from here >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:78: error: no matching function for call to '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>)' > std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:78: note: candidates are: >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algobase.h:71:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/char_traits.h:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/string:40, > from /usr/include/libGenome-1.3/libGenome/gnSequence.h:22, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:16, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::_Iter_comp_iter(_Compare) [with _Compare = mems::LabeledMemComparator] > _Iter_comp_iter(_Compare __comp) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>' to 'mems::LabeledMemComparator' >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: __gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>&) > struct _Iter_comp_iter > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>&' >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/algorithm:62:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/AbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SparseAbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAlignment.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAligner.h:17, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:1962:5: error: initializing argument 3 of 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LabeledMem*, std::vector<mems::LabeledMem> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>]' > __sort(_RandomAccessIterator __first, _RandomAccessIterator __last, > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h: In instantiation of 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >**, std::vector<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, std::allocator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >; _Compare = mems::MatchLeftEndComparator]': >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:979:40: required from here >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:78: error: no matching function for call to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>)' > std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:78: note: candidates are: >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algobase.h:71:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/char_traits.h:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/string:40, > from /usr/include/libGenome-1.3/libGenome/gnSequence.h:22, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:16, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::_Iter_comp_iter(_Compare) [with _Compare = mems::MatchLeftEndComparator] > _Iter_comp_iter(_Compare __comp) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to 'mems::MatchLeftEndComparator' >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: __gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&) > struct _Iter_comp_iter > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&' >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/algorithm:62:0, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/AbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SparseAbstractMatch.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAlignment.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAligner.h:17, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:18, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:1962:5: error: initializing argument 3 of 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >**, std::vector<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, std::allocator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>]' > __sort(_RandomAccessIterator __first, _RandomAccessIterator __last, > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algobase.h:71:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/char_traits.h:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/string:40, > from /usr/include/libGenome-1.3/libGenome/gnSequence.h:22, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.h:16, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:9: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h: In instantiation of '__gnu_cxx::__ops::_Iter_comp_iter<_Compare> __gnu_cxx::__ops::__iter_comp_iter(_Compare) [with _Compare = mems::LabeledMemComparator]': >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:77: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LabeledMem*, std::vector<mems::LabeledMem> >; _Compare = mems::LabeledMemComparator]' >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:489:47: required from here >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:127:46: error: no matching function for call to '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>)' > { return _Iter_comp_iter<_Compare>(__comp); } > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:127:46: note: candidates are: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::_Iter_comp_iter(_Compare) [with _Compare = mems::LabeledMemComparator] > _Iter_comp_iter(_Compare __comp) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>' to 'mems::LabeledMemComparator' >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: __gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>&) > struct _Iter_comp_iter > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>&' >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h: In instantiation of '__gnu_cxx::__ops::_Iter_comp_iter<_Compare> __gnu_cxx::__ops::__iter_comp_iter(_Compare) [with _Compare = mems::MatchLeftEndComparator]': >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/stl_algo.h:4716:77: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >**, std::vector<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, std::allocator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >; _Compare = mems::MatchLeftEndComparator]' >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:979:40: required from here >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:127:46: error: no matching function for call to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>)' > { return _Iter_comp_iter<_Compare>(__comp); } > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:127:46: note: candidates are: >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::_Iter_comp_iter(_Compare) [with _Compare = mems::MatchLeftEndComparator] > _Iter_comp_iter(_Compare __comp) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:114:7: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to 'mems::MatchLeftEndComparator' >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: __gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&) > struct _Iter_comp_iter > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/bits/predefined_ops.h:110:12: note: no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&' >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/alinuxaio.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/aPOSIXaio.c >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/alibc.c >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/awin32aio.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO': >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.c:115:21: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type > rval = aio_suspend(request_array, 1, &zero_wait); > ^ >In file included from /usr/include/features.h:366:0, > from /usr/include/sys/types.h:25, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/asyncio.h:24, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.h:8, > from /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.c:5: >/usr/include/aio.h:199:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' > extern int __REDIRECT_NTH (aio_suspend, > ^ >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/alibc.c -o alibc.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/buffer.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o util.lo `test -f 'dmSML/util.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/util.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/sorting.c >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o >/bin/bash ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/'`dmSML/dmsort.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/util.c -fPIC -DPIC -o .libs/util.o >Makefile:748: recipe for target 'Aligner.lo' failed >make[2]: *** [Aligner.lo] Error 1 >make[2]: *** Waiting for unfinished jobs.... >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/util.c: In function 'removeFile': >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/util.c:126:24: warning: assignment discards 'const' qualifier from pointer target type > rm_cmd = Fmt( "/bin/rm -fv %s", filename ); > ^ >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/util.c:128:24: warning: assignment discards 'const' qualifier from pointer target type > rm_cmd = Fmt( "/bin/rm -f %s", filename ); > ^ >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/util.c -o util.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/buffer.c -o buffer.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/sorting.c -o sorting.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/dmsort.c: In function 'InitdmSML': >/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/dmsort.c:828:4: warning: format not a string literal and no format arguments [-Wformat-security] > fprintf( stderr, buf ); > ^ >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/MemHash.cpp -o MemHash.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/FileSML.cpp -o FileSML.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.cpp -o Islands.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Backbone.cpp -o Backbone.o >/dev/null 2>&1 >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 >make[2]: Leaving directory '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build/libMems' >Makefile:529: recipe for target 'all-recursive' failed >make[1]: *** [all-recursive] Error 1 >make[1]: Leaving directory '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build' >Makefile:436: recipe for target 'all' failed >make: *** [all] Error 2 > * ERROR: sci-libs/libmems-1.6_p1::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-libs/libmems-1.6_p1::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-libs/libmems-1.6_p1::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-libs:libmems-1.6_p1:20141111-234036.log'. > * The ebuild environment file is located at '/tmp/portage/sci-libs/libmems-1.6_p1/temp/environment'. > * Working directory: '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build' > * S: '/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1'
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bug 529770
: 390018