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Gentoo's Bugzilla – Attachment 300197 Details for
Bug 401227
sci-biology/tophat-1.3.2: /usr/lib/libbam.so: undefined reference to `log'
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build.log
build.log (text/plain), 20.72 KB, created by
Martin Mokrejš
on 2012-01-28 20:20:57 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Martin Mokrejš
Created:
2012-01-28 20:20:57 UTC
Size:
20.72 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-biology/tophat-1.3.2 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: weaver@gentoo.org sci-biology@gentoo.org >[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 <cole@cs.umd.edu> 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 âvoid BWA_decode(const std::string&, const std::string&, const std::string&, std::string&)â: >reads.cpp:512:54: warning: array subscript has type âcharâ >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 âvirtual bool SplicedBowtieHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)â: >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 âvirtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)â: >bwt_map.cpp:1144:37: warning: array subscript has type âcharâ >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 âvoid writeFasta(FILE*, const char*, const char*, const char*, int, int)â: >GBase.cpp:707:52: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, 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 âvoid print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const FragmentAlignmentGrade&, FragmentType, FILE*, GBamWriter&)â: >tophat_reports.cpp:373:10: warning: unused variable âgot_readâ >tophat_reports.cpp: In function âvoid print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const HitsForRead&, const InsertAlignmentGrade&, FILE*, FILE*, GBamWriter&)â: >tophat_reports.cpp:451:10: warning: unused variable âgot_left_readâ >tophat_reports.cpp:460:10: warning: unused variable âgot_right_readâ >tophat_reports.cpp: In function âvoid driver(GBamWriter&, std::string&, FILE*, std::string&, FILE*, FILE*, FILE*, FILE*)â: >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'
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bug 401227
: 300197