build.log

build.log (text/plain), 20.72 KB, created by Martin Mokrejš on 2012-01-28 20:20:57 UTC

[32;01m * [39;49;00mPackage:    sci-biology/tophat-1.3.2
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        amd64 bam elibc_glibc kernel_linux multilib userland_GNU
[32;01m * [39;49;00mFEATURES:   nostrip sandbox splitdebug
>>> Unpacking source...
>>> Unpacking tophat-1.3.2.tar.gz to /var/tmp/portage/sci-biology/tophat-1.3.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/tophat-1.3.2/work
>>> Preparing source in /var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2 ...
 * econf: updating tophat-1.3.2/build-aux/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating tophat-1.3.2/build-aux/config.sub with /usr/share/gnuconfig/config.sub
./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 --libdir=/usr/lib64 --disable-dependency-tracking --with-bam
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
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 ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for perl... /usr/bin/perl
checking for bash... /bin/bash
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib64/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages
checking for bamlib... yes
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for egrep... 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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
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 stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
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 _LARGE_FILES 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 if gcc accepts -m64... yes
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
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands

-- tophat 1.3.2 Configuration Results --
  C compiler:          x86_64-pc-linux-gnu-gcc -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG
  C++ compiler:        x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include
  GCC version:         x86_64-pc-linux-gnu-gcc (Gentoo 4.5.3-r2 p1.0, pie-0.4.7) 4.5.3
  Host System type:    x86_64-pc-linux-gnu
  Install prefix:      /usr
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <[e-mail]> with questions and bug reports.

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2 ...
make -j5 -j1 
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2'
Making all in src
make[2]: Entering directory `/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2/src'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o reads.o reads.cpp
reads.cpp: In function ‘void BWA_decode(const std::string&, const std::string&, const std::string&, std::string&)’:
reads.cpp:512:54: warning: array subscript has type ‘char’
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include  -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -c alphabet.c
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o bwt_map.o bwt_map.cpp
bwt_map.cpp: In member function ‘virtual bool SplicedBowtieHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)’:
bwt_map.cpp:588:39: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:638:39: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:644:40: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp: In member function ‘virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)’:
bwt_map.cpp:1144:37: warning: array subscript has type ‘char’
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o common.o common.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o junctions.o junctions.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o insertions.o insertions.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o deletions.o deletions.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o align_status.o align_status.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o fragments.o fragments.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o tokenize.o tokenize.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o inserts.o inserts.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o qual.o qual.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 align_status.o fragments.o tokenize.o inserts.o qual.o 
x86_64-pc-linux-gnu-ranlib libtophat.a
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o GBase.o GBase.cpp
GBase.cpp: In function ‘void writeFasta(FILE*, const char*, const char*, const char*, int, int)’:
GBase.cpp:707:52: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o codons.o codons.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o gdna.o gdna.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o GStr.o GStr.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -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..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o prep_reads.o prep_reads.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o prep_reads -L/usr/lib prep_reads.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o tophat_reports.o tophat_reports.cpp
tophat_reports.cpp: In function ‘void print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const FragmentAlignmentGrade&, FragmentType, FILE*, GBamWriter&)’:
tophat_reports.cpp:373:10: warning: unused variable ‘got_read’
tophat_reports.cpp: In function ‘void print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const HitsForRead&, const InsertAlignmentGrade&, FILE*, FILE*, GBamWriter&)’:
tophat_reports.cpp:451:10: warning: unused variable ‘got_left_read’
tophat_reports.cpp:460:10: warning: unused variable ‘got_right_read’
tophat_reports.cpp: In function ‘void driver(GBamWriter&, std::string&, FILE*, std::string&, FILE*, FILE*, FILE*, FILE*)’:
tophat_reports.cpp:846:42: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:877:42: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:911:52: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:933:51: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:960:51: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:960:99: warning: comparison between signed and unsigned integer expressions
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o tophat_reports -L/usr/lib tophat_reports.o ../src/libtophat.a  -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o juncs_db.o juncs_db.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o juncs_db -L/usr/lib juncs_db.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o gtf_juncs.o gtf_juncs.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o gtf_juncs -L/usr/lib gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o extract_reads.o extract_reads.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o extract_reads -L/usr/lib extract_reads.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o segment_juncs.o segment_juncs.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o segment_juncs -L/usr/lib segment_juncs.o ../src/libtophat.a  -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o closures.o closures.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o closure_juncs -L/usr/lib closures.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o long_spanning_reads.o long_spanning_reads.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o long_spanning_reads -L/usr/lib long_spanning_reads.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o fix_map_ordering.o fix_map_ordering.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o fix_map_ordering -L/usr/lib fix_map_ordering.o ../src/libtophat.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o bam_merge.o bam_merge.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o bam_merge -L/usr/lib bam_merge.o ../src/libgc.a -lbam -lz -lz 
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -c -o bam2fastx.o bam2fastx.cpp
x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include  -Wl,-O1 -Wl,--as-needed -L/usr/lib -o bam2fastx -L/usr/lib bam2fastx.o ../src/libgc.a -lbam -lz -lz 
/usr/lib/libbam.so: undefined reference to `log'
/usr/lib/libbam.so: undefined reference to `pow'
/usr/lib/libbam.so: undefined reference to `sqrt'
collect2: ld returned 1 exit status
make[2]: *** [bam2fastx] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2'
make: *** [all] Error 2
 [31;01m*[0m ERROR: sci-biology/tophat-1.3.2 failed (compile phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/tophat-1.3.2',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/tophat-1.3.2'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/tophat-1.3.2/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/tophat-1.3.2/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2'