sci-biology:tophat-2.1.1-r1:20160920-161727.log

sci-biology:tophat-2.1.1-r1:20160920-161727.log (text/plain), 21.52 KB, created by Toralf Förster on 2016-09-20 19:48:52 UTC

 * Package:    sci-biology/tophat-2.1.1-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 <[e-mail]>.

>>> 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<std::__cxx11::basic_string<char> >&, const string&, const std::vector<std::__cxx11::basic_string<char> >&, 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<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__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'