* 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... 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(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 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'/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 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/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatMatchList.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 RepeatMatch.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/RepeatMatch.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 Backbone.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Backbone.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 PairwiseMatchFinder.lo /tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/PairwiseMatchFinder.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/DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.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 -fPIC -DPIC -o .libs/twister.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/RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.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/gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.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/MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.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/RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.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/RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.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/Islands.cpp -fPIC -DPIC -o .libs/Islands.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/MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.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/MatchList.cpp -fPIC -DPIC -o .libs/MatchList.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/MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.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/IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.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/GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.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/PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.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/DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.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/MemHash.cpp -fPIC -DPIC -o .libs/MemHash.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/SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.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/Interval.cpp -fPIC -DPIC -o .libs/Interval.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/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 >; _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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter)' 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' 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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter&) 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' to '__gnu_cxx::__ops::_Iter_comp_iter&' 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 >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' __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 >**, std::vector >*, std::allocator >*> > >; _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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter)' 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' 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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter&) 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' to '__gnu_cxx::__ops::_Iter_comp_iter&' 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 >**, std::vector >*, std::allocator >*> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' __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 >; _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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter)' { 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' 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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter&) 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' to '__gnu_cxx::__ops::_Iter_comp_iter&' 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 >**, std::vector >*, std::allocator >*> > >; _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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter)' { 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' 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::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter&) 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' to '__gnu_cxx::__ops::_Iter_comp_iter&' 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'