Build log

bfast-0.6.4c:20100518-171833.log (text/plain), 38.67 KB, created by Diego Elio Pettenò (RETIRED) on 2010-05-18 18:34:01 UTC

 * CPV:  sci-biology/bfast-0.6.4c
 * REPO: gentoo
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking bfast-0.6.4c.tar.gz to /var/tmp/portage/sci-biology/bfast-0.6.4c/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bfast-0.6.4c/work
>>> Preparing source in /var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c' ...
 * Running aclocal ...
  [ ok ]
 * Running autoconf ...
  [ ok ]
 * Running autoheader ...
  [ ok ]
 * Running automake --add-missing --copy ...
  [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c ...
 * econf: updating bfast-0.6.4c/config/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating bfast-0.6.4c/config/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib
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... i686-pc-linux-gnu
checking for i686-pc-linux-gnu-gcc... i686-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 i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking how to run the C preprocessor... i686-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 of the parent directories): .git
checking for BZ2_bzRead in -lbz2... yes
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 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... 4
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 bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.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 /var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c ...
make -j14 
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
Making all in bfast
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedEnd.o -MD -MP -MF .deps/AlignedEnd.Tpo -c -o AlignedEnd.o AlignedEnd.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedEntry.o -MD -MP -MF .deps/AlignedEntry.Tpo -c -o AlignedEntry.o AlignedEntry.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedRead.o -MD -MP -MF .deps/AlignedRead.Tpo -c -o AlignedRead.o AlignedRead.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedReadConvert.o -MD -MP -MF .deps/AlignedReadConvert.Tpo -c -o AlignedReadConvert.o AlignedReadConvert.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BError.o -MD -MP -MF .deps/BError.Tpo -c -o BError.o BError.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BLib.o -MD -MP -MF .deps/BLib.Tpo -c -o BLib.o BLib.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGBinary.o -MD -MP -MF .deps/RGBinary.Tpo -c -o RGBinary.o RGBinary.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndex.o -MD -MP -MF .deps/RGIndex.Tpo -c -o RGIndex.o RGIndex.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndexAccuracy.o -MD -MP -MF .deps/RGIndexAccuracy.Tpo -c -o RGIndexAccuracy.o RGIndexAccuracy.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndexExons.o -MD -MP -MF .deps/RGIndexExons.Tpo -c -o RGIndexExons.o RGIndexExons.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndexLayout.o -MD -MP -MF .deps/RGIndexLayout.Tpo -c -o RGIndexLayout.o RGIndexLayout.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGMatch.o -MD -MP -MF .deps/RGMatch.Tpo -c -o RGMatch.o RGMatch.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGMatches.o -MD -MP -MF .deps/RGMatches.Tpo -c -o RGMatches.o RGMatches.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGRanges.o -MD -MP -MF .deps/RGRanges.Tpo -c -o RGRanges.o RGRanges.c
mv -f .deps/RGIndexLayout.Tpo .deps/RGIndexLayout.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGReads.o -MD -MP -MF .deps/RGReads.Tpo -c -o RGReads.o RGReads.c
mv -f .deps/BError.Tpo .deps/BError.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT ScoringMatrix.o -MD -MP -MF .deps/ScoringMatrix.Tpo -c -o ScoringMatrix.o ScoringMatrix.c
mv -f .deps/RGIndexExons.Tpo .deps/RGIndexExons.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT Align.o -MD -MP -MF .deps/Align.Tpo -c -o Align.o Align.c
mv -f .deps/AlignedEntry.Tpo .deps/AlignedEntry.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignNTSpace.o -MD -MP -MF .deps/AlignNTSpace.Tpo -c -o AlignNTSpace.o AlignNTSpace.c
mv -f .deps/ScoringMatrix.Tpo .deps/ScoringMatrix.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignColorSpace.o -MD -MP -MF .deps/AlignColorSpace.Tpo -c -o AlignColorSpace.o AlignColorSpace.c
mv -f .deps/RGRanges.Tpo .deps/RGRanges.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignMatrix.o -MD -MP -MF .deps/AlignMatrix.Tpo -c -o AlignMatrix.o AlignMatrix.c
mv -f .deps/AlignedRead.Tpo .deps/AlignedRead.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT MatchesReadInputFiles.o -MD -MP -MF .deps/MatchesReadInputFiles.Tpo -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c
AlignColorSpace.c: In function ‘AlignColorSpaceGappedConstrained’:
AlignColorSpace.c:358:40: warning: operation on ‘(*(matrix->cells + ((unsigned int)i + 1u) * 4u) + ((unsigned int)j + 1u) * 180u)->s.score[k]’ may be undefined
mv -f .deps/AlignedEnd.Tpo .deps/AlignedEnd.Po
mv -f .deps/AlignMatrix.Tpo .deps/AlignMatrix.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RunMatch.o -MD -MP -MF .deps/RunMatch.Tpo -c -o RunMatch.o RunMatch.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RunLocalAlign.o -MD -MP -MF .deps/RunLocalAlign.Tpo -c -o RunLocalAlign.o RunLocalAlign.c
mv -f .deps/RGBinary.Tpo .deps/RGBinary.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RunPostProcess.o -MD -MP -MF .deps/RunPostProcess.Tpo -c -o RunPostProcess.o RunPostProcess.c
mv -f .deps/RGReads.Tpo .deps/RGReads.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RunAlign.o -MD -MP -MF .deps/RunAlign.Tpo -c -o RunAlign.o RunAlign.c
mv -f .deps/RGMatches.Tpo .deps/RGMatches.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastFasta2BRG.o -MD -MP -MF .deps/BfastFasta2BRG.Tpo -c -o BfastFasta2BRG.o BfastFasta2BRG.c
mv -f .deps/RunAlign.Tpo .deps/RunAlign.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastIndex.o -MD -MP -MF .deps/BfastIndex.Tpo -c -o BfastIndex.o BfastIndex.c
mv -f .deps/AlignedReadConvert.Tpo .deps/AlignedReadConvert.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastMatch.o -MD -MP -MF .deps/BfastMatch.Tpo -c -o BfastMatch.o BfastMatch.c
mv -f .deps/Align.Tpo .deps/Align.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastLocalAlign.o -MD -MP -MF .deps/BfastLocalAlign.Tpo -c -o BfastLocalAlign.o BfastLocalAlign.c
mv -f .deps/RunLocalAlign.Tpo .deps/RunLocalAlign.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastPostProcess.o -MD -MP -MF .deps/BfastPostProcess.Tpo -c -o BfastPostProcess.o BfastPostProcess.c
mv -f .deps/AlignNTSpace.Tpo .deps/AlignNTSpace.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastBAFConvert.o -MD -MP -MF .deps/BfastBAFConvert.Tpo -c -o BfastBAFConvert.o BfastBAFConvert.c
mv -f .deps/RGIndexAccuracy.Tpo .deps/RGIndexAccuracy.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastHeader.o -MD -MP -MF .deps/BfastHeader.Tpo -c -o BfastHeader.o BfastHeader.c
mv -f .deps/BfastFasta2BRG.Tpo .deps/BfastFasta2BRG.Po
mv -f .deps/RGMatch.Tpo .deps/RGMatch.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastBMFConvert.o -MD -MP -MF .deps/BfastBMFConvert.Tpo -c -o BfastBMFConvert.o BfastBMFConvert.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastBRG2Fasta.o -MD -MP -MF .deps/BfastBRG2Fasta.Tpo -c -o BfastBRG2Fasta.o BfastBRG2Fasta.c
mv -f .deps/MatchesReadInputFiles.Tpo .deps/MatchesReadInputFiles.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BfastAlign.o -MD -MP -MF .deps/BfastAlign.Tpo -c -o BfastAlign.o BfastAlign.c
mv -f .deps/BfastHeader.Tpo .deps/BfastHeader.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT aflib.o -MD -MP -MF .deps/aflib.Tpo -c -o aflib.o aflib.c
mv -f .deps/BfastIndex.Tpo .deps/BfastIndex.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT Main.o -MD -MP -MF .deps/Main.Tpo -c -o Main.o Main.c
mv -f .deps/BfastBMFConvert.Tpo .deps/BfastBMFConvert.Po
mv -f .deps/BfastMatch.Tpo .deps/BfastMatch.Po
mv -f .deps/BfastLocalAlign.Tpo .deps/BfastLocalAlign.Po
mv -f .deps/BfastBAFConvert.Tpo .deps/BfastBAFConvert.Po
mv -f .deps/BfastBRG2Fasta.Tpo .deps/BfastBRG2Fasta.Po
mv -f .deps/BLib.Tpo .deps/BLib.Po
mv -f .deps/RunMatch.Tpo .deps/RunMatch.Po
mv -f .deps/BfastPostProcess.Tpo .deps/BfastPostProcess.Po
mv -f .deps/BfastAlign.Tpo .deps/BfastAlign.Po
mv -f .deps/Main.Tpo .deps/Main.Po
mv -f .deps/AlignColorSpace.Tpo .deps/AlignColorSpace.Po
mv -f .deps/RunPostProcess.Tpo .deps/RunPostProcess.Po
mv -f .deps/aflib.Tpo .deps/aflib.Po
mv -f .deps/RGIndex.Tpo .deps/RGIndex.Po
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -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  -lz -lm -lbz2 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
Making all in butil
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BError.o -MD -MP -MF .deps/BError.Tpo -c -o BError.o `test -f '../bfast/BError.c' || echo './'`../bfast/BError.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndex.o -MD -MP -MF .deps/RGIndex.Tpo -c -o RGIndex.o `test -f '../bfast/RGIndex.c' || echo './'`../bfast/RGIndex.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BLib.o -MD -MP -MF .deps/BLib.Tpo -c -o BLib.o `test -f '../bfast/BLib.c' || echo './'`../bfast/BLib.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGBinary.o -MD -MP -MF .deps/RGBinary.Tpo -c -o RGBinary.o `test -f '../bfast/RGBinary.c' || echo './'`../bfast/RGBinary.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGRanges.o -MD -MP -MF .deps/RGRanges.Tpo -c -o RGRanges.o `test -f '../bfast/RGRanges.c' || echo './'`../bfast/RGRanges.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGMatch.o -MD -MP -MF .deps/RGMatch.Tpo -c -o RGMatch.o `test -f '../bfast/RGMatch.c' || echo './'`../bfast/RGMatch.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedRead.o -MD -MP -MF .deps/AlignedRead.Tpo -c -o AlignedRead.o `test -f '../bfast/AlignedRead.c' || echo './'`../bfast/AlignedRead.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedReadConvert.o -MD -MP -MF .deps/AlignedReadConvert.Tpo -c -o AlignedReadConvert.o `test -f '../bfast/AlignedReadConvert.c' || echo './'`../bfast/AlignedReadConvert.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedEnd.o -MD -MP -MF .deps/AlignedEnd.Tpo -c -o AlignedEnd.o `test -f '../bfast/AlignedEnd.c' || echo './'`../bfast/AlignedEnd.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignedEntry.o -MD -MP -MF .deps/AlignedEntry.Tpo -c -o AlignedEntry.o `test -f '../bfast/AlignedEntry.c' || echo './'`../bfast/AlignedEntry.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT balignmentscoredistribution.o -MD -MP -MF .deps/balignmentscoredistribution.Tpo -c -o balignmentscoredistribution.o balignmentscoredistribution.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT SimRead.o -MD -MP -MF .deps/SimRead.Tpo -c -o SimRead.o SimRead.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndexExons.o -MD -MP -MF .deps/RGIndexExons.Tpo -c -o RGIndexExons.o `test -f '../bfast/RGIndexExons.c' || echo './'`../bfast/RGIndexExons.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGMatches.o -MD -MP -MF .deps/RGMatches.Tpo -c -o RGMatches.o `test -f '../bfast/RGMatches.c' || echo './'`../bfast/RGMatches.c
mv -f .deps/BError.Tpo .deps/BError.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndexAccuracy.o -MD -MP -MF .deps/RGIndexAccuracy.Tpo -c -o RGIndexAccuracy.o `test -f '../bfast/RGIndexAccuracy.c' || echo './'`../bfast/RGIndexAccuracy.c
mv -f .deps/RGIndexExons.Tpo .deps/RGIndexExons.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RunLocalAlign.o -MD -MP -MF .deps/RunLocalAlign.Tpo -c -o RunLocalAlign.o `test -f '../bfast/RunLocalAlign.c' || echo './'`../bfast/RunLocalAlign.c
mv -f .deps/balignmentscoredistribution.Tpo .deps/balignmentscoredistribution.Po
mv -f .deps/RGRanges.Tpo .deps/RGRanges.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT ScoringMatrix.o -MD -MP -MF .deps/ScoringMatrix.Tpo -c -o ScoringMatrix.o `test -f '../bfast/ScoringMatrix.c' || echo './'`../bfast/ScoringMatrix.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT Align.o -MD -MP -MF .deps/Align.Tpo -c -o Align.o `test -f '../bfast/Align.c' || echo './'`../bfast/Align.c
mv -f .deps/AlignedEntry.Tpo .deps/AlignedEntry.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignColorSpace.o -MD -MP -MF .deps/AlignColorSpace.Tpo -c -o AlignColorSpace.o `test -f '../bfast/AlignColorSpace.c' || echo './'`../bfast/AlignColorSpace.c
mv -f .deps/AlignedRead.Tpo .deps/AlignedRead.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignNTSpace.o -MD -MP -MF .deps/AlignNTSpace.Tpo -c -o AlignNTSpace.o `test -f '../bfast/AlignNTSpace.c' || echo './'`../bfast/AlignNTSpace.c
mv -f .deps/AlignedEnd.Tpo .deps/AlignedEnd.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT AlignMatrix.o -MD -MP -MF .deps/AlignMatrix.Tpo -c -o AlignMatrix.o `test -f '../bfast/AlignMatrix.c' || echo './'`../bfast/AlignMatrix.c
../bfast/AlignColorSpace.c: In function ‘AlignColorSpaceGappedConstrained’:
../bfast/AlignColorSpace.c:358:40: warning: operation on ‘(*(matrix->cells + ((unsigned int)i + 1u) * 4u) + ((unsigned int)j + 1u) * 180u)->s.score[k]’ may be undefined
mv -f .deps/SimRead.Tpo .deps/SimRead.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT balignsim.o -MD -MP -MF .deps/balignsim.Tpo -c -o balignsim.o balignsim.c
mv -f .deps/ScoringMatrix.Tpo .deps/ScoringMatrix.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT bevalsim.o -MD -MP -MF .deps/bevalsim.Tpo -c -o bevalsim.o bevalsim.c
mv -f .deps/AlignMatrix.Tpo .deps/AlignMatrix.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT bgeneratereads.o -MD -MP -MF .deps/bgeneratereads.Tpo -c -o bgeneratereads.o bgeneratereads.c
mv -f .deps/RGBinary.Tpo .deps/RGBinary.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGReads.o -MD -MP -MF .deps/RGReads.Tpo -c -o RGReads.o `test -f '../bfast/RGReads.c' || echo './'`../bfast/RGReads.c
mv -f .deps/RunLocalAlign.Tpo .deps/RunLocalAlign.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT bindexdist.o -MD -MP -MF .deps/bindexdist.Tpo -c -o bindexdist.o bindexdist.c
mv -f .deps/bgeneratereads.Tpo .deps/bgeneratereads.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT bindexhist.o -MD -MP -MF .deps/bindexhist.Tpo -c -o bindexhist.o bindexhist.c
mv -f .deps/Align.Tpo .deps/Align.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT brepeat.o -MD -MP -MF .deps/brepeat.Tpo -c -o brepeat.o brepeat.c
mv -f .deps/BLib.Tpo .deps/BLib.Po
mv -f .deps/AlignedReadConvert.Tpo .deps/AlignedReadConvert.Po
mv -f .deps/RGMatches.Tpo .deps/RGMatches.Po
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT btestindexes.o -MD -MP -MF .deps/btestindexes.Tpo -c -o btestindexes.o btestindexes.c
mv -f .deps/RGMatch.Tpo .deps/RGMatch.Po
mv -f .deps/AlignNTSpace.Tpo .deps/AlignNTSpace.Po
mv -f .deps/balignsim.Tpo .deps/balignsim.Po
mv -f .deps/brepeat.Tpo .deps/brepeat.Po
mv -f .deps/btestindexes.Tpo .deps/btestindexes.Po
mv -f .deps/RGIndexAccuracy.Tpo .deps/RGIndexAccuracy.Po
mv -f .deps/bindexhist.Tpo .deps/bindexhist.Po
mv -f .deps/bevalsim.Tpo .deps/bevalsim.Po
mv -f .deps/bindexdist.Tpo .deps/bindexdist.Po
mv -f .deps/AlignColorSpace.Tpo .deps/AlignColorSpace.Po
mv -f .deps/RGReads.Tpo .deps/RGReads.Po
mv -f .deps/RGIndex.Tpo .deps/RGIndex.Po
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o balignmentscoredistribution BError.o RGIndex.o BLib.o RGBinary.o RGRanges.o RGMatch.o AlignedRead.o AlignedReadConvert.o AlignedEnd.o AlignedEntry.o balignmentscoredistribution.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o balignsim SimRead.o BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGMatch.o RGMatches.o RGRanges.o AlignedRead.o AlignedEnd.o RGIndexAccuracy.o AlignedEntry.o RunLocalAlign.o ScoringMatrix.o Align.o AlignColorSpace.o AlignNTSpace.o AlignMatrix.o balignsim.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o bevalsim BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGRanges.o RGMatches.o RGMatch.o AlignedRead.o AlignedEnd.o AlignedEntry.o bevalsim.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o bgeneratereads BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGMatch.o RGRanges.o SimRead.o bgeneratereads.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o bindexdist BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGMatch.o RGRanges.o RGReads.o bindexdist.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o bindexhist BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGMatch.o RGRanges.o RGReads.o bindexhist.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o brepeat BError.o RGIndexExons.o RGIndex.o BLib.o RGBinary.o RGMatch.o RGRanges.o brepeat.o  -lz -lm -lbz2 
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o btestindexes RGMatch.o RGRanges.o RGBinary.o RGIndex.o RGIndexAccuracy.o BError.o BLib.o btestindexes.o  -lz -lm -lbz2 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
Making all in scripts
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BError.o -MD -MP -MF .deps/BError.Tpo -c -o BError.o `test -f '../bfast/BError.c' || echo './'`../bfast/BError.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGIndex.o -MD -MP -MF .deps/RGIndex.Tpo -c -o RGIndex.o `test -f '../bfast/RGIndex.c' || echo './'`../bfast/RGIndex.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT BLib.o -MD -MP -MF .deps/BLib.Tpo -c -o BLib.o `test -f '../bfast/BLib.c' || echo './'`../bfast/BLib.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGBinary.o -MD -MP -MF .deps/RGBinary.Tpo -c -o RGBinary.o `test -f '../bfast/RGBinary.c' || echo './'`../bfast/RGBinary.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGRanges.o -MD -MP -MF .deps/RGRanges.Tpo -c -o RGRanges.o `test -f '../bfast/RGRanges.c' || echo './'`../bfast/RGRanges.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT RGMatch.o -MD -MP -MF .deps/RGMatch.Tpo -c -o RGMatch.o `test -f '../bfast/RGMatch.c' || echo './'`../bfast/RGMatch.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT aflib.o -MD -MP -MF .deps/aflib.Tpo -c -o aflib.o `test -f '../bfast/aflib.c' || echo './'`../bfast/aflib.c
i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64 -MT solid2fastq.o -MD -MP -MF .deps/solid2fastq.Tpo -c -o solid2fastq.o solid2fastq.c
mv -f .deps/BError.Tpo .deps/BError.Po
mv -f .deps/aflib.Tpo .deps/aflib.Po
mv -f .deps/RGRanges.Tpo .deps/RGRanges.Po
mv -f .deps/solid2fastq.Tpo .deps/solid2fastq.Po
mv -f .deps/RGBinary.Tpo .deps/RGBinary.Po
mv -f .deps/RGMatch.Tpo .deps/RGMatch.Po
mv -f .deps/BLib.Tpo .deps/BLib.Po
mv -f .deps/RGIndex.Tpo .deps/RGIndex.Po
i686-pc-linux-gnu-gcc  -O2 -pipe -Wall -g -O2 -pthread  -D_FILE_OFFSET_BITS=64  -Wl,-O1 -o solid2fastq BError.o RGIndex.o BLib.o RGBinary.o RGRanges.o RGMatch.o aflib.o solid2fastq.o  -lz -lm -lbz2 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
Making all in tests
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
>>> Source compiled.
make -j14 check 
Making check in bfast
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
Making check in butil
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
Making check in scripts
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
Making check in tests
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make  check-TESTS
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
./test.initialize.sh: line 3: .: test.definitions.sh: file not found
      Initializing data for tests.
mkdir: missing operand
Try `mkdir --help' for more information.
cp: omitting directory `/bin'
cp: omitting directory `/boot'
cp: omitting directory `/dev'
cp: omitting directory `/etc'
cp: `/etc.backup.0000' and `/./etc.backup.0000' are the same file
cp: `/etc.backup.0001' and `/./etc.backup.0001' are the same file
cp: `/gtk.immodules' and `/./gtk.immodules' are the same file
cp: omitting directory `/home'
cp: omitting directory `/lib'
cp: omitting directory `/libufconfig.so'
cp: omitting directory `/lost+found'
cp: omitting directory `/media'
cp: omitting directory `/mnt'
cp: omitting directory `/nonexistent'
cp: omitting directory `/opt'
cp: omitting directory `/proc'
cp: omitting directory `/root'
cp: omitting directory `/sbin'
cp: omitting directory `/service'
cp: omitting directory `/sys'
cp: omitting directory `/tmp'
cp: omitting directory `/usr'
cp: omitting directory `/var'
cp: omitting directory `/vz'
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.
md5sum -c /tests.md5
md5sum: /tests.md5: No such file or directory
FAIL: test.diff.sh
./test.cleanup.sh: line 3: .: test.definitions.sh: file not found
      Cleaning up files.
ls: cannot open directory /lost+found: Permission denied
      Files cleaned up.
PASS: test.cleanup.sh
=================================================
7 of 8 tests failed
Please report to [e-mail]
=================================================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make: *** [check-recursive] Error 1
 * ERROR: sci-biology/bfast-0.6.4c failed:
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  54:  Called src_test
 *   environment, line 2961:  Called die
 * The specific snippet of code:
 *       emake check || die
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/bfast-0.6.4c',
 * the complete build log and the output of 'emerge -pqv =sci-biology/bfast-0.6.4c'.
 * The complete build log is located at '/var/log/portage/build/sci-biology/bfast-0.6.4c:20100518-171833.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bfast-0.6.4c/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'

>>> Install bfast-0.6.4c into /var/tmp/portage/sci-biology/bfast-0.6.4c/image/ category sci-biology
make -j14 -j1 prefix=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr datadir=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share infodir=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/info localstatedir=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/var/lib mandir=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/man sysconfdir=/var/tmp/portage/sci-biology/bfast-0.6.4c/image/etc -j14 -j1 install 
Making install in bfast
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin"
  /usr/bin/install -c 'bfast' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bfast'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/bfast'
Making install in butil
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin"
  /usr/bin/install -c 'balignmentscoredistribution' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/balignmentscoredistribution'
  /usr/bin/install -c 'balignsim' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/balignsim'
  /usr/bin/install -c 'bevalsim' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bevalsim'
  /usr/bin/install -c 'bgeneratereads' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bgeneratereads'
  /usr/bin/install -c 'bindexdist' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bindexdist'
  /usr/bin/install -c 'bindexhist' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bindexhist'
  /usr/bin/install -c 'brepeat' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/brepeat'
  /usr/bin/install -c 'btestindexes' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/btestindexes'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/butil'
Making install in scripts
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin"
  /usr/bin/install -c 'solid2fastq' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/solid2fastq'
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin"
 /usr/bin/install -c 'bfast.resubmit.pl' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bfast.resubmit.pl'
 /usr/bin/install -c 'bfast.submit.pl' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/bfast.submit.pl'
 /usr/bin/install -c 'solid2fastq.pl' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/solid2fastq.pl'
 /usr/bin/install -c 'ill2fastq.pl' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin/ill2fastq.pl'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/scripts'
Making install in tests
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/bin"
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c/tests'
make[1]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
make[2]: Entering directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/doc/bfast" || /bin/mkdir -p "/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/doc/bfast"
 /usr/bin/install -c -m 644 'LICENSE' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/doc/bfast/LICENSE'
 /usr/bin/install -c -m 644 'manual/bfast-book.pdf' '/var/tmp/portage/sci-biology/bfast-0.6.4c/image/usr/share/doc/bfast/bfast-book.pdf'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bfast-0.6.4c/work/bfast-0.6.4c'
>>> Completed installing bfast-0.6.4c into /var/tmp/portage/sci-biology/bfast-0.6.4c/image/

 * Tinderbox QA Warning! Misplaced documentation
/usr/share/doc/bfast
 * Tinderbox QA Warning (end)! Misplaced documentation
 * QA Notice: command not found:
 * 
 * 	./test.fasta2brg.sh: line 42: bfast: command not found
 * 	./test.index.sh: line 51: bfast: command not found
 * 	./test.match.sh: line 44: bfast: command not found
 * 	./test.localalign.sh: line 42: bfast: command not found
 * 	./test.postprocess.sh: line 42: bfast: command not found
strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/brepeat
   usr/bin/balignmentscoredistribution
   usr/bin/bgeneratereads
   usr/bin/btestindexes
   usr/bin/bevalsim
   usr/bin/balignsim
   usr/bin/solid2fastq
   usr/bin/bfast
   usr/bin/bindexdist
   usr/bin/bindexhist