emerge log

sci-biology-samtools-1.2-20150223-065420.log (text/plain), 10.40 KB, created by Toralf Förster on 2015-02-23 13:05:45 UTC

 * Package:    sci-biology/samtools-1.2
 * 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
 * Applying samtools-1.2-buildsystem.patch ...
 [ ok ]
Use of my $_ is experimental at /usr/lib64/perl5/vendor_perl/5.20.2/OpenBSD/PkgConfig.pm line 94.
Use of my $_ is experimental at /usr/lib64/perl5/vendor_perl/5.20.2/OpenBSD/PkgConfig.pm line 94.
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_index.o bam_index.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_plcmd.o bam_plcmd.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o sam_view.o sam_view.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_cat.o bam_cat.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_md.o bam_md.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_reheader.o bam_reheader.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_sort.o bam_sort.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bedidx.o bedidx.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o kprobaln.o kprobaln.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_rmdup.o bam_rmdup.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_rmdupse.o bam_rmdupse.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_mate.o bam_mate.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_stat.o bam_stat.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.2"' > version.h
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bamtk.o bamtk.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam2bcf.o bam2bcf.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam2bcf_indel.o bam2bcf_indel.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o errmod.o errmod.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o sample.o sample.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o cut_target.o cut_target.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o phase.o phase.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam2depth.o bam2depth.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o padding.o padding.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bedcov.o bedcov.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bamshuf.o bamshuf.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o faidx.o faidx.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o stats.o stats.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o stats_isize.o stats_isize.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_flags.o bam_flags.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_split.o bam_split.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview.o bam_tview.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview_curses.o bam_tview_curses.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview_html.o bam_tview_html.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_lpileup.o bam_lpileup.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_aux.o bam_aux.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam.o bam.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_import.o bam_import.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o sam.o sam.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o sam_header.o sam_header.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_plbuf.o bam_plbuf.c
x86_64-pc-linux-gnu-ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -shared -Wl,--soname,libbam.so.1.0 -o libbam.so.1.0 bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o -L/usr/lib64 -lhts -lz
ln -sf libbam.so.1.0 libbam.so.0
ln -sf libbam.so.1.0 libbam.so
x86_64-pc-linux-gnu-gcc -pthread -Wl,-O1 -Wl,--as-needed  -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.so -L/usr/lib64 -lhts  -L/usr/lib64 -lncurses -lm -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/ace2sam.o misc/ace2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/ace2sam misc/ace2sam.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/maq2sam-long misc/maq2sam-long.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/maq2sam-short.o misc/maq2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/maq2sam-short misc/maq2sam-short.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/md5fa.o misc/md5fa.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/md5.o misc/md5.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/md5fa misc/md5fa.o misc/md5.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/md5sum-lite misc/md5sum-lite.o 
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/wgsim.o misc/wgsim.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/wgsim misc/wgsim.o  -lm -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o test/test.o test/test.c
make: *** No rule to make target '-L/usr/lib64', needed by 'test/merge/test_bam_translate'.  Stop.
 * ERROR: sci-biology/samtools-1.2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/samtools-1.2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/samtools-1.2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:samtools-1.2:20150223-065420.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/samtools-1.2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/samtools-1.2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/samtools-1.2/work/samtools-1.2'
 * S: '/var/tmp/portage/sci-biology/samtools-1.2/work/samtools-1.2'