Build log

samtools-0.1.12a:20110312-054737.log (text/plain), 15.87 KB, created by Diego Elio Pettenò (RETIRED) on 2011-03-12 14:32:36 UTC

 * Package:    sci-biology/samtools-0.1.12a
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        elibc_glibc kernel_linux test userland_GNU x86
 * FEATURES:   sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking samtools-0.1.12a.tar.bz2 to /var/tmp/portage/sci-biology/samtools-0.1.12a/work
>>> Source unpacked in /var/tmp/portage/sci-biology/samtools-0.1.12a/work
>>> Preparing source in /var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a ...
make -j14 dylib 
make[1]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
make[1]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
make[1]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
bam_import.c: In function ‘append_text’:
bam_import.c:179:13: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
bam_import.c:186:9: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
bam_import.c:186:9: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘size_t’
bam_import.c:186:9: warning: format ‘%ld’ expects type ‘long int’, but argument 5 has type ‘size_t’
bam_import.c:186:9: warning: format ‘%ld’ expects type ‘long int’, but argument 6 has type ‘size_t’
sam.c: In function ‘samopen’:
sam.c:92:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c: In function ‘download_from_remote’:
bam_index.c:430:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:319:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:326:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:339:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:342:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:346:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:350:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:360:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:364:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c: In function ‘bam_index_save’:
bam_index.c:251:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:254:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:255:15: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:263:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:264:16: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:270:34: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:271:22: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:276:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:282:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:283:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:284:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:291:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:292:16: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:297:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:300:16: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bam_index.c:305:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
razf.c: In function ‘razf_close’:
razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘razf_end_flush’:
razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘_razf_write’:
razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘save_zindex’:
razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
faidx.c: In function ‘download_and_open’:
faidx.c:251:15: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
razf.c: In function ‘razf_flush’:
razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:416:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:237:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function ‘bam_reheader’:
bam_reheader.c:28:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -g -Wall -O2  -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -shared -Wl,-soname,libbam.so -o libbam.so.1 bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o -lc -lz
make[1]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
make -j14 
make[1]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
make[2]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
make[2]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/bcftools'
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
vcf.c: In function ‘vcf_write’:
vcf.c:118:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
vcf.c: In function ‘vcf_hdr_write’:
vcf.c:101:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
index.c: In function ‘download_from_remote’:
index.c:195:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/bcftools'
make[2]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/misc'
gcc -O2 -pipe -g -Wall -O2  -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o libbam.a -lm  -lcurses  -lz -Lbcftools -lbcf
make[1]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a'
make[1]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/bcftools'
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
main.c: In function ‘bcf_cat’:
main.c:33:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
gcc -O2 -pipe -g -Wall -O2  -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm  -lz -L. -lbcf
make[1]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/bcftools'
make[1]: Entering directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/misc'
gcc -c -O2 -pipe -g -Wall -O2  -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -O2 -pipe -g -Wall -O2  -c -I.. -o md5fa.o md5fa.c
gcc -O2 -pipe -g -Wall -O2  -o maq2sam-short maq2sam.c -lz
gcc -O2 -pipe -g -Wall -O2  -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -O2 -pipe -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -O2 -pipe -g -Wall -O2  -o md5sum-lite md5sum-lite.o
gcc -O2 -pipe -g -Wall -O2  -o md5fa md5.o md5fa.o -lz
gcc -O2 -pipe -g -Wall -O2  -o wgsim wgsim.o -lm
make[1]: Leaving directory `/var/tmp/portage/sci-biology/samtools-0.1.12a/work/samtools-0.1.12a/misc'
>>> Source compiled.
>>> Test phase [none]: sci-biology/samtools-0.1.12a

>>> Install samtools-0.1.12a into /var/tmp/portage/sci-biology/samtools-0.1.12a/image/ category sci-biology
>>> Completed installing samtools-0.1.12a into /var/tmp/portage/sci-biology/samtools-0.1.12a/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/lib/libbam.so.1
   usr/bin/samtools
   usr/bin/md5sum-lite
   usr/bin/md5fa
   usr/bin/wgsim
   usr/bin/maq2sam-short
   usr/bin/maq2sam-long

 * QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/lib/libbam.so.1
 * /usr/bin/samtools
 * /usr/bin/md5sum-lite
 * /usr/bin/md5fa
 * /usr/bin/wgsim
 * /usr/bin/maq2sam-short
 * /usr/bin/maq2sam-long