* Package: sci-libs/libmems-1.6_p1-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking libmems-1.6_p1.tar.xz to /var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work >>> Source unpacked in /var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work >>> Preparing source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1 ... * Applying libmems-1.6_p1-build.patch ... [ ok ] * Applying libmems-1.6_p1-boost.patch ... [ ok ] * Applying libmems-1.6_p1-gcc-4.7.patch ... [ ok ] * Applying libmems-1.6_p1-broken-constness.patch ... [ ok ] * Applying libmems-1.6_p1-format-security.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: libmems-1.6_p1/ * Running elibtoolize in: libmems-1.6_p1/config/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.4.3 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1 ... * econf: updating libmems-1.6_p1/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating libmems-1.6_p1/config/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/libmems-1.6_p1-r1 --htmldir=/usr/share/doc/libmems-1.6_p1-r1/html --libdir=/usr/lib64 configure: loading site script /usr/share/config.site checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... 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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... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for x86_64-pc-linux-gnu-perl... no checking for perl... /usr/bin/perl checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking whether x86_64-pc-linux-gnu-gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libMems/Makefile config.status: creating libMems-1.6.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1 ... make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1' Making all in libMems make[2]: Entering directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1/libMems' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o RepeatHash.lo RepeatHash.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o libtool: 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-I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o MatchList.lo MatchList.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o Aligner.lo Aligner.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Aligner.cpp:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/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.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o Islands.lo Islands.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Islands.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/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.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Islands.cpp -o Islands.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o MaskedMemHash.lo MaskedMemHash.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o GappedAlignment.lo GappedAlignment.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o MuscleInterface.lo MuscleInterface.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o In file included from 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:46, from /usr/include/boost/dynamic_bitset.hpp:15, from ../libMems/AbstractMatch.h:21, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: /usr/include/assert.h:85:0: note: this is the location of the previous definition # define assert(expr) \ libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o PhyloTree.lo PhyloTree.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o RepeatMatchList.lo RepeatMatchList.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o Backbone.lo Backbone.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/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.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c -o ProgressiveAligner.lo ProgressiveAligner.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -march=native -O2 -pipe -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/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 \ ^~~~~~~ ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::constructLcbTrackingMatches(node_id_t, std::vector&, std::vector >&)’: ProgressiveAligner.cpp:1603:74: error: no matching function for call to ‘std::vector*, std::vector >*, mems::AbstractMatch*> >::push_back(std::tuple, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*>)’ cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64:0, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:914:7: note: candidate: void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>; _Alloc = std::allocator*, std::vector >*, mems::AbstractMatch*> >; std::vector<_Tp, _Alloc>::value_type = boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>] push_back(const value_type& __x) ^~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:914:7: note: no known conversion for argument 1 from ‘std::tuple, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*>’ to ‘const value_type& {aka const boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>&}’ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:932:7: note: candidate: void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>; _Alloc = std::allocator*, std::vector >*, mems::AbstractMatch*> >; std::vector<_Tp, _Alloc>::value_type = boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>] push_back(value_type&& __x) ^~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:932:7: note: no known conversion for argument 1 from ‘std::tuple, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*>’ to ‘std::vector*, std::vector >*, mems::AbstractMatch*> >::value_type&& {aka boost::tuples::tuple*, std::vector >*, mems::AbstractMatch*>&&}’ make[2]: *** [Makefile:759: ProgressiveAligner.lo] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1/libMems' make[1]: *** [Makefile:540: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1' make: *** [Makefile:448: all] Error 2 * ERROR: sci-libs/libmems-1.6_p1-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-libs/libmems-1.6_p1-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/libmems-1.6_p1-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:libmems-1.6_p1-r1:20160922-140537.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1' * S: '/var/tmp/portage/sci-libs/libmems-1.6_p1-r1/work/libmems-1.6_p1'