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Gentoo's Bugzilla – Attachment 287633 Details for
Bug 384367
sci-biology/bfast-0.6.5a fails tests
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build.log
bfast-0.6.5a:20110924-231005.log (text/plain), 35.75 KB, created by
Agostino Sarubbo
on 2011-09-24 23:15:35 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2011-09-24 23:15:35 UTC
Size:
35.75 KB
patch
obsolete
> * Package: sci-biology/bfast-0.6.5a > * Repository: gentoo > * Maintainer: weaver@gentoo.org sci-biology@gentoo.org > * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU > * FEATURES: sandbox test userpriv usersandbox >>>> Unpacking source... >>>> Unpacking bfast-0.6.5a.tar.gz to /tmp/portage/sci-biology/bfast-0.6.5a/work >>>> Source unpacked in /tmp/portage/sci-biology/bfast-0.6.5a/work >>>> Preparing source in /tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a ... > * Running eautoreconf in '/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a' ... > * Running aclocal ... > [ ok ] > * Running autoconf ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a ... > * econf: updating bfast-0.6.5a/config/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating bfast-0.6.5a/config/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 --libdir=/usr/lib64 >checking for a BSD-compatible install... /usr/bin/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 build system type... x86_64-pc-linux-gnu >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >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-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 >checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -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 minix/config.h usability... no >checking minix/config.h presence... no >checking for minix/config.h... no >checking whether it is safe to define __EXTENSIONS__... yes >fatal: Not a git repository (or any parent up to mount parent ) >Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). >checking bzlib.h usability... yes >checking bzlib.h presence... yes >checking for bzlib.h... 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 an ANSI C-conforming const... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible malloc... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible realloc... yes >checking for pow in -lm... yes >checking for gzread in -lz... yes >checking for floor... yes >checking for pow... yes >checking for sqrt... yes >checking for strchr... yes >checking for strdup... yes >checking for strpbrk... yes >checking for strstr... yes >checking for strtok_r... yes >checking for _LARGEFILE_SOURCE value needed for large files... no >checking for int8_t... yes >checking for int32_t... yes >checking for int64_t... yes >checking for uint8_t... yes >checking for uint32_t... yes >checking for uint64_t... yes >checking size of short int... 2 >checking size of int... 4 >checking size of long int... 8 >checking for ANSI C header files... (cached) yes >checking limits.h usability... yes >checking limits.h presence... yes >checking for limits.h... yes >checking for stdint.h... (cached) yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking sys/time.h usability... yes >checking sys/time.h presence... yes >checking for sys/time.h... yes >checking for unistd.h... (cached) yes >checking float.h usability... yes >checking float.h presence... yes >checking for float.h... yes >checking zlib.h usability... yes >checking zlib.h presence... yes >checking for zlib.h... yes >checking fcntl.h usability... yes >checking fcntl.h presence... yes >checking for fcntl.h... yes >checking for inline... inline >configure: creating ./config.status >config.status: creating Makefile >config.status: creating bfast/Makefile >config.status: creating butil/Makefile >config.status: creating scripts/Makefile >config.status: creating tests/Makefile >config.status: creating config.h >config.status: executing depfiles commands >>>> Source configured. >>>> Compiling source in /tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a ... >make -j4 V=1 >make all-recursive >make[1]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a' >Making all in bfast >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/bfast' >depbase=`echo AlignedEnd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignedEnd.o -MD -MP -MF $depbase.Tpo -c -o AlignedEnd.o AlignedEnd.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo AlignedEntry.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignedEntry.o -MD -MP -MF $depbase.Tpo -c -o AlignedEntry.o AlignedEntry.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo AlignedRead.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignedRead.o -MD -MP -MF $depbase.Tpo -c -o AlignedRead.o AlignedRead.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo AlignedReadConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignedReadConvert.o -MD -MP -MF $depbase.Tpo -c -o AlignedReadConvert.o AlignedReadConvert.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BError.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BError.o -MD -MP -MF $depbase.Tpo -c -o BError.o BError.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF $depbase.Tpo -c -o BLib.o BLib.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGBinary.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGBinary.o -MD -MP -MF $depbase.Tpo -c -o RGBinary.o RGBinary.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGIndex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGIndex.o -MD -MP -MF $depbase.Tpo -c -o RGIndex.o RGIndex.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGIndexAccuracy.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGIndexAccuracy.o -MD -MP -MF $depbase.Tpo -c -o RGIndexAccuracy.o RGIndexAccuracy.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGIndexExons.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGIndexExons.o -MD -MP -MF $depbase.Tpo -c -o RGIndexExons.o RGIndexExons.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGIndexLayout.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGIndexLayout.o -MD -MP -MF $depbase.Tpo -c -o RGIndexLayout.o RGIndexLayout.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGMatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGMatch.o -MD -MP -MF $depbase.Tpo -c -o RGMatch.o RGMatch.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGMatches.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGMatches.o -MD -MP -MF $depbase.Tpo -c -o RGMatches.o RGMatches.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGRanges.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGRanges.o -MD -MP -MF $depbase.Tpo -c -o RGRanges.o RGRanges.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RGReads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RGReads.o -MD -MP -MF $depbase.Tpo -c -o RGReads.o RGReads.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ScoringMatrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ScoringMatrix.o -MD -MP -MF $depbase.Tpo -c -o ScoringMatrix.o ScoringMatrix.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo Align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT Align.o -MD -MP -MF $depbase.Tpo -c -o Align.o Align.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo AlignNTSpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignNTSpace.o -MD -MP -MF $depbase.Tpo -c -o AlignNTSpace.o AlignNTSpace.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo AlignColorSpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignColorSpace.o -MD -MP -MF $depbase.Tpo -c -o AlignColorSpace.o AlignColorSpace.c &&\ >mv -f $depbase.Tpo $depbase.Po >AlignColorSpace.c: In function âAlignColorSpaceGappedConstrainedâ: >AlignColorSpace.c:358:40: warning: operation on â(*(matrix->cells + ((long unsigned int)(long unsigned int)i + 1u) * 8u) + ((long unsigned int)(long unsigned int)j + 1u) * 180u)->s.score[k]â may be undefined >depbase=`echo AlignMatrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT AlignMatrix.o -MD -MP -MF $depbase.Tpo -c -o AlignMatrix.o AlignMatrix.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo MatchesReadInputFiles.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT MatchesReadInputFiles.o -MD -MP -MF $depbase.Tpo -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RunMatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RunMatch.o -MD -MP -MF $depbase.Tpo -c -o RunMatch.o RunMatch.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RunLocalAlign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RunLocalAlign.o -MD -MP -MF $depbase.Tpo -c -o RunLocalAlign.o RunLocalAlign.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RunPostProcess.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RunPostProcess.o -MD -MP -MF $depbase.Tpo -c -o RunPostProcess.o RunPostProcess.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo RunAlign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT RunAlign.o -MD -MP -MF $depbase.Tpo -c -o RunAlign.o RunAlign.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastFasta2BRG.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastFasta2BRG.o -MD -MP -MF $depbase.Tpo -c -o BfastFasta2BRG.o BfastFasta2BRG.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastIndex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastIndex.o -MD -MP -MF $depbase.Tpo -c -o BfastIndex.o BfastIndex.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastMatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastMatch.o -MD -MP -MF $depbase.Tpo -c -o BfastMatch.o BfastMatch.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastLocalAlign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastLocalAlign.o -MD -MP -MF $depbase.Tpo -c -o BfastLocalAlign.o BfastLocalAlign.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastPostProcess.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastPostProcess.o -MD -MP -MF $depbase.Tpo -c -o BfastPostProcess.o BfastPostProcess.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastBAFConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastBAFConvert.o -MD -MP -MF $depbase.Tpo -c -o BfastBAFConvert.o BfastBAFConvert.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastHeader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastHeader.o -MD -MP -MF $depbase.Tpo -c -o BfastHeader.o BfastHeader.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastBMFConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastBMFConvert.o -MD -MP -MF $depbase.Tpo -c -o BfastBMFConvert.o BfastBMFConvert.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastBRG2Fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastBRG2Fasta.o -MD -MP -MF $depbase.Tpo -c -o BfastBRG2Fasta.o BfastBRG2Fasta.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo BfastAlign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT BfastAlign.o -MD -MP -MF $depbase.Tpo -c -o BfastAlign.o BfastAlign.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo aflib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT aflib.o -MD -MP -MF $depbase.Tpo -c -o aflib.o aflib.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo Main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT Main.o -MD -MP -MF $depbase.Tpo -c -o Main.o Main.c &&\ >mv -f $depbase.Tpo $depbase.Po >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lm -lbz2 -lz >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/bfast' >Making all in butil >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/butil' >depbase=`echo balignmentscoredistribution.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT balignmentscoredistribution.o -MD -MP -MF $depbase.Tpo -c -o balignmentscoredistribution.o balignmentscoredistribution.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo SimRead.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT SimRead.o -MD -MP -MF $depbase.Tpo -c -o SimRead.o SimRead.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo balignsim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT balignsim.o -MD -MP -MF $depbase.Tpo -c -o balignsim.o balignsim.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo bevalsim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT bevalsim.o -MD -MP -MF $depbase.Tpo -c -o bevalsim.o bevalsim.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo bgeneratereads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT bgeneratereads.o -MD -MP -MF $depbase.Tpo -c -o bgeneratereads.o bgeneratereads.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGReads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGReads.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGReads.o ../bfast/RGReads.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo bindexdist.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT bindexdist.o -MD -MP -MF $depbase.Tpo -c -o bindexdist.o bindexdist.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo bindexhist.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT bindexhist.o -MD -MP -MF $depbase.Tpo -c -o bindexhist.o bindexhist.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/MatchesReadInputFiles.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/MatchesReadInputFiles.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/MatchesReadInputFiles.o ../bfast/MatchesReadInputFiles.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/aflib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/aflib.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/aflib.o ../bfast/aflib.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo bmfmerge.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT bmfmerge.o -MD -MP -MF $depbase.Tpo -c -o bmfmerge.o bmfmerge.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo brepeat.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT brepeat.o -MD -MP -MF $depbase.Tpo -c -o brepeat.o brepeat.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo btestindexes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT btestindexes.o -MD -MP -MF $depbase.Tpo -c -o btestindexes.o btestindexes.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/BError.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/BError.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/BError.o ../bfast/BError.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGIndex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGIndex.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGIndex.o ../bfast/RGIndex.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/BLib.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/BLib.o ../bfast/BLib.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGBinary.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGBinary.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGBinary.o ../bfast/RGBinary.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGRanges.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGRanges.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGRanges.o ../bfast/RGRanges.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGMatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGMatch.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGMatch.o ../bfast/RGMatch.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignedRead.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignedRead.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignedRead.o ../bfast/AlignedRead.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignedReadConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignedReadConvert.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignedReadConvert.o ../bfast/AlignedReadConvert.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignedEnd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignedEnd.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignedEnd.o ../bfast/AlignedEnd.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignedEntry.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignedEntry.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignedEntry.o ../bfast/AlignedEntry.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGIndexExons.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGIndexExons.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGIndexExons.o ../bfast/RGIndexExons.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGMatches.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGMatches.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGMatches.o ../bfast/RGMatches.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RGIndexAccuracy.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RGIndexAccuracy.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RGIndexAccuracy.o ../bfast/RGIndexAccuracy.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/RunLocalAlign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/RunLocalAlign.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/RunLocalAlign.o ../bfast/RunLocalAlign.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/ScoringMatrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/ScoringMatrix.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/ScoringMatrix.o ../bfast/ScoringMatrix.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/Align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/Align.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/Align.o ../bfast/Align.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignColorSpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignColorSpace.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignColorSpace.o ../bfast/AlignColorSpace.c &&\ >mv -f $depbase.Tpo $depbase.Po >../bfast/AlignColorSpace.c: In function âAlignColorSpaceGappedConstrainedâ: >../bfast/AlignColorSpace.c:358:40: warning: operation on â(*(matrix->cells + ((long unsigned int)(long unsigned int)i + 1u) * 8u) + ((long unsigned int)(long unsigned int)j + 1u) * 180u)->s.score[k]â may be undefined >depbase=`echo ../bfast/AlignNTSpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignNTSpace.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignNTSpace.o ../bfast/AlignNTSpace.c &&\ >mv -f $depbase.Tpo $depbase.Po >depbase=`echo ../bfast/AlignMatrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT ../bfast/AlignMatrix.o -MD -MP -MF $depbase.Tpo -c -o ../bfast/AlignMatrix.o ../bfast/AlignMatrix.c &&\ >mv -f $depbase.Tpo $depbase.Po >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bevalsim ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatches.o ../bfast/RGMatch.o ../bfast/AlignedRead.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o bevalsim.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bgeneratereads ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o SimRead.o bgeneratereads.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bindexdist ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGReads.o bindexdist.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bindexhist ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGReads.o bindexhist.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bmfmerge ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGReads.o ../bfast/RGMatch.o ../bfast/RGMatches.o ../bfast/MatchesReadInputFiles.o ../bfast/aflib.o bmfmerge.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o brepeat ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o brepeat.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o btestindexes ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGBinary.o ../bfast/RGIndex.o ../bfast/RGIndexAccuracy.o ../bfast/BError.o ../bfast/BLib.o btestindexes.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o balignmentscoredistribution ../bfast/BError.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatch.o ../bfast/AlignedRead.o ../bfast/AlignedReadConvert.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o balignmentscoredistribution.o -lm -lbz2 -lz >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o balignsim SimRead.o ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGMatches.o ../bfast/RGRanges.o ../bfast/AlignedRead.o ../bfast/AlignedEnd.o ../bfast/RGIndexAccuracy.o ../bfast/AlignedEntry.o ../bfast/RunLocalAlign.o ../bfast/ScoringMatrix.o ../bfast/Align.o ../bfast/AlignColorSpace.o ../bfast/AlignNTSpace.o ../bfast/AlignMatrix.o balignsim.o -lm -lbz2 -lz >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/butil' >Making all in scripts >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/scripts' >depbase=`echo solid2fastq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=native -O2 -g0 -Wall -g -O2 -pthread -MT solid2fastq.o -MD -MP -MF $depbase.Tpo -c -o solid2fastq.o solid2fastq.c &&\ >mv -f $depbase.Tpo $depbase.Po >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o solid2fastq ../bfast/BError.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatch.o ../bfast/aflib.o solid2fastq.o -lm -lbz2 -lz >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/scripts' >Making all in tests >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >make[2]: Nessuna operazione da eseguire per «all». >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a' >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a' >make[1]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a' >>>> Source compiled. >make -j4 V=1 check >Making check in bfast >make[1]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/bfast' >x86_64-pc-linux-gnu-gcc -march=native -O2 -g0 -Wall -g -O2 -pthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lm -lbz2 -lz >make[1]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/bfast' >Making check in butil >make[1]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/butil' >make[1]: Nessuna operazione da eseguire per «check». >make[1]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/butil' >Making check in scripts >make[1]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/scripts' >make[1]: Nessuna operazione da eseguire per «check». >make[1]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/scripts' >Making check in tests >make[1]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >make check-TESTS >make[2]: Entering directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >./test.initialize.sh: line 3: .: test.definitions.sh: file not found > Initializing data for tests. >mkdir: operando mancante >Usare «mkdir --help» per ulteriori informazioni. >cp: directory "/bin" omessa >cp: directory "/boot" omessa >cp: directory "/dev" omessa >cp: directory "/etc" omessa >cp: directory "/home" omessa >cp: directory "/lib" omessa >cp: directory "/lib32" omessa >cp: directory "/lib64" omessa >cp: directory "/lost+found" omessa >cp: directory "/media" omessa >cp: directory "/mnt" omessa >cp: directory "/opt" omessa >cp: directory "/proc" omessa >cp: directory "/root" omessa >cp: directory "/sbin" omessa >cp: directory "/service" omessa >cp: directory "/sys" omessa >cp: directory "/tmp" omessa >cp: directory "/usr" omessa >cp: directory "/var" omessa >FAIL: test.initialize.sh >./test.fasta2brg.sh: line 3: .: test.definitions.sh: file not found > Building a reference genome. > Testing -A 0 CC=0 >bfast fasta2brg -f .fa -A 0 >./test.fasta2brg.sh: line 42: bfast: command not found >FAIL: test.fasta2brg.sh >./test.index.sh: line 2: .: test.definitions.sh: file not found > Building an index. > Testing -A 0 CC=0 >RETURN CODE=0 >bfast index -f .fa -A 0 -m 111101111011101111 -w 8 -d 2 -i 1 -n -T >./test.index.sh: line 51: bfast: command not found >FAIL: test.index.sh >./test.match.sh: line 3: .: test.definitions.sh: file not found > Finding matches. > Testing -A 0 CC=0 >bfast match -f .fa -r reads..fastq -A 0 -n -T > bfast.matches.file..bmf >./test.match.sh: line 44: bfast: command not found >FAIL: test.match.sh >./test.localalign.sh: line 3: .: test.definitions.sh: file not found > Running local alignment. > Testing -A 0 CC=0 >bfast localalign -f .fa -m bfast.matches.file..bmf -A 0 -n -o 15 > bfast.aligned.file..baf >./test.localalign.sh: line 42: bfast: command not found >FAIL: test.localalign.sh >./test.postprocess.sh: line 3: .: test.definitions.sh: file not found > Running postprocessing. > Testing -A 0 CC=0 >bfast postprocess -f .fa -i bfast.aligned.file..baf -a 3 -n > bfast.reported.file..sam >./test.postprocess.sh: line 42: bfast: command not found >FAIL: test.postprocess.sh >./test.diff.sh: line 3: .: test.definitions.sh: file not found > Double-checking output files. >FAIL: test.diff.sh >./test.cleanup.sh: line 3: .: test.definitions.sh: file not found > Cleaning up files. >ls: impossibile aprire la directory /lost+found: Permission denied >ls: impossibile aprire la directory /root: Permission denied > Files cleaned up. >PASS: test.cleanup.sh >================================================= >7 of 8 tests failed >Please report to bfast-help@lists.sourceforge.net >================================================= >make[2]: *** [check-TESTS] Errore 1 >make[2]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >make[1]: *** [check-am] Errore 2 >make[1]: Leaving directory `/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a/tests' >make: *** [check-recursive] Errore 1 >emake failed > * ERROR: sci-biology/bfast-0.6.5a failed (test phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 56: Called src_test > * environment, line 2842: Called die > * The specific snippet of code: > * emake check || die > * > * If you need support, post the output of 'emerge --info =sci-biology/bfast-0.6.5a', > * the complete build log and the output of 'emerge -pqv =sci-biology/bfast-0.6.5a'. > * The complete build log is located at '/home/ago/log/build/sci-biology/bfast-0.6.5a:20110924-231005.log'. > * The ebuild environment file is located at '/tmp/portage/sci-biology/bfast-0.6.5a/temp/environment'. > * S: '/tmp/portage/sci-biology/bfast-0.6.5a/work/bfast-0.6.5a'
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