* Package: sci-biology/tophat-2.1.1-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking tophat-2.1.1.tar.gz to /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1 ... * Applying tophat-2.1.1-unbundle-seqan-samtools.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: tophat-2.1.1/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1 ... * econf: updating tophat-2.1.1/config.sub with /usr/share/gnuconfig/config.sub * econf: updating tophat-2.1.1/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/tophat-2.1.1-r1 --htmldir=/usr/share/doc/tophat-2.1.1-r1/html --libdir=/usr/lib64 --disable-debug 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... GNU checking dependency style of x86_64-pc-linux-gnu-g++... none 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 x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking the archiver (x86_64-pc-linux-gnu-ar) interface... ar checking for gawk... (cached) gawk checking whether we are using the GNU C++ compiler... (cached) yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... (cached) yes checking dependency style of x86_64-pc-linux-gnu-g++... (cached) none checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none checking whether make sets $(MAKE)... (cached) yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking whether /usr/bin/python2.7 version is >= 2.4... yes checking for /usr/bin/python2.7 version... 2.7 checking for /usr/bin/python2.7 platform... linux2 checking for /usr/bin/python2.7 script directory... ${prefix}/lib64/python2.7/site-packages checking for /usr/bin/python2.7 extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... yes checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -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 stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none checking dependency style of x86_64-pc-linux-gnu-g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.1.1 Configuration Results -- C++ compiler: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include Linker flags: -L/usr/lib -Wl,-O1 -Wl,--as-needed BOOST libraries: -lboost_thread -lboost_system GCC version: x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0 p1.0) 6.2.0 Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1 ... make -j1 (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o GBase.o GBase.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o gdna.o gdna.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o GStr.o GStr.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o gff.o gff.cpp rm -f libgc.a x86_64-pc-linux-gnu-ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o x86_64-pc-linux-gnu-ranlib libgc.a x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o reads.o reads.cpp x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -c -o alphabet.o alphabet.c x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o bwt_map.o bwt_map.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o junctions.o junctions.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o insertions.o insertions.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o deletions.o deletions.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o fusions.o fusions.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o align_status.o align_status.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o fragments.o fragments.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o inserts.o inserts.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o qual.o qual.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o bam_merge_impl.o bam_merge_impl.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o utils.o utils.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o coverage.o coverage.cpp rm -f libtophat.a x86_64-pc-linux-gnu-ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o x86_64-pc-linux-gnu-ranlib libtophat.a x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o prep_reads.o prep_reads.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o prep_reads prep_reads.o libtophat.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o GTFToFasta.o GTFToFasta.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o FastaTools.o FastaTools.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o gtf_to_fasta GTFToFasta.o FastaTools.o libtophat.a libgc.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o fix_map_ordering.o fix_map_ordering.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o fix_map_ordering fix_map_ordering.o libtophat.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o bam2fastx.o bam2fastx.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o bam2fastx bam2fastx.o libgc.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o segment_juncs.o segment_juncs.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib -Wl,-O1 -Wl,--as-needed -o segment_juncs segment_juncs.o libtophat.a -lboost_thread -lboost_system -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o gtf_juncs.o gtf_juncs.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o gtf_juncs gtf_juncs.o libtophat.a libgc.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o juncs_db.o juncs_db.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o juncs_db juncs_db.o libtophat.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o long_spanning_reads.o long_spanning_reads.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib -Wl,-O1 -Wl,--as-needed -o long_spanning_reads long_spanning_reads.o libtophat.a -lboost_thread -lboost_system -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o bam_merge.o bam_merge.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o bam_merge bam_merge.o libtophat.a libgc.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o map2gtf.o map2gtf.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -L/usr/lib -Wl,-O1 -Wl,--as-needed -L/usr/lib -Wl,-O1 -Wl,--as-needed -o map2gtf map2gtf.o libtophat.a libgc.a -lbam-0.1-legacy -lz x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/bam-0.1-legacy/ -I/usr/include/seqan-1.4 -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable -DNDEBUG -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp tophat_reports.cpp: In function ‘void driver(const string&, std::istream&, const std::vector >&, const string&, const std::vector >&, const string&, FILE*, FILE*, FILE*, FILE*)’: tophat_reports.cpp:2708:128: error: no matching function for call to ‘make_pair(Junction, JunctionStats&)’ onStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/char_traits.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:40, from /usr/include/boost/thread/exceptions.hpp:20, from /usr/include/boost/thread/pthread/thread_data.hpp:10, from /usr/include/boost/thread/thread_only.hpp:17, from /usr/include/boost/thread/thread.hpp:12, from /usr/include/boost/thread.hpp:13, from tophat_reports.cpp:19: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: candidate: template constexpr std::pair::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed: tophat_reports.cpp:2708:128: note: cannot convert ‘junction_stat’ (type ‘JunctionStats’) to type ‘JunctionStats&&’ onStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ^ make[2]: *** [Makefile:829: tophat_reports.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/src' make[1]: *** [Makefile:383: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1' make: *** [Makefile:324: all] Error 2 * ERROR: sci-biology/tophat-2.1.1-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/tophat-2.1.1-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/tophat-2.1.1-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:tophat-2.1.1-r1:20160920-161727.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1' * S: '/var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1'