build.log

build.log (text/plain), 12.79 KB, created by Martin Mokrejš on 2010-12-18 00:28:10 UTC

 [32;01m*[0m CPV:  sci-biology/qrna-2.0.3c
 [32;01m*[0m REPO: gentoo
 [32;01m*[0m USE:  amd64 elibc_glibc kernel_linux multilib userland_GNU
>>> Unpacking source...
>>> Unpacking qrna-2.0.3c.tar.bz2 to /var/tmp/portage/sci-biology/qrna-2.0.3c/work
 [32;01m*[0m Applying qrna-2.0.3c-glibc-2.10.patch ...
[A[119C  [34;01m[ [32;01mok[34;01m ][0m
>>> Source unpacked in /var/tmp/portage/sci-biology/qrna-2.0.3c/work
>>> Compiling source in /var/tmp/portage/sci-biology/qrna-2.0.3c/work/qrna-2.0.3c ...
make -j5 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c aligneval.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c alignio.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c cluster.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c dayhoff.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c file.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c getopt.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c interleaved.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c sqerror.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c gnuregex.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c sqio.c		
gnuregex.c: In function 're_match_2':
gnuregex.c:3752: warning: cast from pointer to integer of different size
gnuregex.c:3752: warning: cast from pointer to integer of different size
gnuregex.c:3758: warning: cast to pointer from integer of different size
gnuregex.c:3758: warning: cast to pointer from integer of different size
gnuregex.c:3905: warning: cast to pointer from integer of different size
gnuregex.c:3905: warning: cast to pointer from integer of different size
gnuregex.c:3958: warning: cast to pointer from integer of different size
gnuregex.c:3958: warning: cast to pointer from integer of different size
gnuregex.c:4064: warning: cast from pointer to integer of different size
gnuregex.c:4064: warning: cast from pointer to integer of different size
gnuregex.c:4097: warning: cast to pointer from integer of different size
gnuregex.c:4097: warning: cast to pointer from integer of different size
gnuregex.c:4110: warning: cast to pointer from integer of different size
gnuregex.c:4110: warning: cast to pointer from integer of different size
gnuregex.c:4278: warning: cast from pointer to integer of different size
gnuregex.c:4278: warning: cast from pointer to integer of different size
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c iupac.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c msf.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c revcomp.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c rk.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c selex.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c seqencode.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c sre_ctype.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c sre_math.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c sre_string.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c stack.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c translate.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c types.c		
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona  -c weight.c		
ar rcv libsquid.a aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o interleaved.o sqerror.o gnuregex.o sqio.o iupac.o msf.o revcomp.o rk.o selex.o seqencode.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o
a - aligneval.o
a - alignio.o
a - cluster.o
a - dayhoff.o
a - file.o
a - getopt.o
a - interleaved.o
a - sqerror.o
a - gnuregex.o
a - sqio.o
a - iupac.o
a - msf.o
a - revcomp.o
a - rk.o
a - selex.o
a - seqencode.o
a - sre_ctype.o
a - sre_math.o
a - sre_string.o
a - stack.o
a - translate.o
a - types.o
a - weight.o
if test -x /bin/ranlib; then /bin/ranlib libsquid.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libsquid.a; else exit 0; fi
if test -x ranlib; then ranlib libsquid.a; else exit 0; fi
chmod 644 libsquid.a
make -j5 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/cfgio.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/cfgmodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/cfgparse.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/codcreatealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/coddp.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/coddpscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/codmodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/codon.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/codscorealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/er_math.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evd.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolcodmodel.c	
../src/evolcodmodel.c: In function 'EvolChangeCODProbsNaive':
../src/evolcodmodel.c:272: warning: unknown conversion type character 0xa in format
../src/evolcodmodel.c:273: warning: unknown conversion type character 0xa in format
../src/evolcodmodel.c:274: warning: unknown conversion type character 0xa in format
../src/evolcodmodel.c: In function 'EvolChangeCODProbsYuAltchul':
../src/evolcodmodel.c:420: warning: unknown conversion type character 0xa in format
../src/evolcodmodel.c:421: warning: unknown conversion type character 0xa in format
../src/evolcodmodel.c:422: warning: unknown conversion type character 0xa in format
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolemissions.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolmisc.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolothmodel.c	
../src/evolmisc.c: In function 'EvolCalculateNaiveTargetError':
../src/evolmisc.c:127: warning: unknown conversion type character 0xa in format
../src/evolmisc.c:128: warning: unknown conversion type character 0xa in format
../src/evolmisc.c: In function 'EvolCalculateMutProbsTargetError':
../src/evolmisc.c:177: warning: unknown conversion type character 0xa in format
../src/evolmisc.c: In function 'EvolCalculateMut5ProbsTargetError':
../src/evolmisc.c:235: warning: unknown conversion type character 0xa in format
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolnullmodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolqrnaversion.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolriboprob.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolrnadp.c	
../src/evolriboprob.c: In function 'EvolCalculateRIBOTargetError':
../src/evolriboprob.c:1191: warning: unknown conversion type character 0xa in format
../src/evolriboprob.c: In function 'EvolCalculateNaivePairTargetError':
../src/evolriboprob.c:1301: warning: unknown conversion type character 0xa in format
../src/evolriboprob.c:1302: warning: unknown conversion type character 0xa in format
../src/evolriboprob.c:1304: warning: unknown conversion type character 0xa in format
../src/evolriboprob.c:1305: warning: unknown conversion type character 0xa in format
../src/evolriboprob.c: In function 'EvolCalculateRIBO5TargetError':
../src/evolriboprob.c:1364: warning: unknown conversion type character 0xa in format
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolrnadpscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolrnamodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolrnascorealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolscorewithmodels.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolscorewithmodelscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/evolve.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/globals.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/hexamer.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/matrix.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/misc.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/nrnscfg.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/nullmodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/othcreatealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/othmodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/othdp.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/othdpscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/othscorealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/posterior.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/qrnaversion.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/riboprob.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnacreatealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnadp.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnadpscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnaio.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnamodel.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnaoutput.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnascorealign.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnascfg.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/rnascfgscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/scorewithmodels.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/scorewithmodelscanfast.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/seqio.c	
../src/seqio.c: In function 'StripDegeneracy':
../src/seqio.c:2768: warning: ignoring return value of 'realloc', declared with attribute warn_unused_result
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/trace.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/traceSCFG.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/tying.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/main.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/cfgbuild.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/eqrna.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/eqrna_sample.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid -c ../src/shuffle.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid02 -c ../src/nstack.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid02 -c ../src/rnamat.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -DASSERT  -I../squid02 -c ../src/rnamat_main.c	
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=nocona -o rnamat_main -L../squid02 rnamat_main.o globals.o nstack.o rnamat.o  -lsquid -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible ../squid02/libsquid.a when searching for -lsquid
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lsquid
collect2: ld returned 1 exit status
make: *** [rnamat_main] Error 1
make: *** Waiting for unfinished jobs....
 [31;01m*[0m ERROR: sci-biology/qrna-2.0.3c failed:
 [31;01m*[0m   (no error message)
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  54:  Called src_compile
 [31;01m*[0m   environment, line 2354:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake || die
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/qrna-2.0.3c',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/qrna-2.0.3c'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/qrna-2.0.3c/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/qrna-2.0.3c/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/qrna-2.0.3c/work/qrna-2.0.3c'