sci-biology:mrfast-2.6.0.1:20201120-061056.log

sci-biology:mrfast-2.6.0.1:20201120-061056.log (text/plain), 9.93 KB, created by Toralf Förster on 2020-11-20 15:54:32 UTC

 * Package:    sci-biology/mrfast-2.6.0.1
 * Repository: science
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking mrfast-2.6.0.1.tar.gz to /var/tmp/portage/sci-biology/mrfast-2.6.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/mrfast-2.6.0.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/mrfast-2.6.0.1/work/mrfast-2.6.0.1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/mrfast-2.6.0.1/work/mrfast-2.6.0.1 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/mrfast-2.6.0.1/work/mrfast-2.6.0.1 ...
make -j1 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  baseFAST.c -o baseFAST.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  CommandLineParser.c -o CommandLineParser.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  Common.c -o Common.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  HashTable.c -o HashTable.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  MrFAST.c -o MrFAST.o 
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setFullMappingInfo’ at MrFAST.c:6225:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setFullMappingInfo’:
MrFAST.c:6225:50: note: length computed here
 6225 |   strncpy(bestHitMappingInfo[readNumber].md, md, strlen(md) + 1);
      |                                                  ^~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setFullMappingInfo’ at MrFAST.c:6236:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setFullMappingInfo’:
MrFAST.c:6236:56: note: length computed here
 6236 |   strncpy(bestHitMappingInfo[readNumber].chr, refName, strlen(refName) + 1);
      |                                                        ^~~~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setFullMappingInfo’ at MrFAST.c:6237:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setFullMappingInfo’:
MrFAST.c:6237:56: note: length computed here
 6237 |   strncpy(bestHitMappingInfo[readNumber].cigar, cigar, strlen(cigar) + 1);
      |                                                        ^~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setPairFullMappingInfo’ at MrFAST.c:6260:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setPairFullMappingInfo’:
MrFAST.c:6260:58: note: length computed here
 6260 |   strncpy(bestHitMappingInfo[readNumber * 2].md, mi1.md, strlen(mi1.md) + 1);
      |                                                          ^~~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setPairFullMappingInfo’ at MrFAST.c:6261:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setPairFullMappingInfo’:
MrFAST.c:6262:4: note: length computed here
 6262 |    strlen(mi1.cigar) + 1);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setPairFullMappingInfo’ at MrFAST.c:6281:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setPairFullMappingInfo’:
MrFAST.c:6282:4: note: length computed here
 6282 |    strlen(mi2.md) + 1);
      |    ^~~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from MrFAST.c:48:
In function ‘strncpy’,
    inlined from ‘setPairFullMappingInfo’ at MrFAST.c:6283:3:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MrFAST.c: In function ‘setPairFullMappingInfo’:
MrFAST.c:6284:4: note: length computed here
 6284 |    strlen(mi2.cigar) + 1);
      |    ^~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  Output.c -o Output.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  Reads.c -o Reads.o 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c  RefGenome.c -o RefGenome.o 
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 baseFAST.o CommandLineParser.o Common.o HashTable.o MrFAST.o Output.o Reads.o RefGenome.o -o mrfast -lz -lm  
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: HashTable.o:(.bss+0x50): multiple definition of `generateHashTable'; baseFAST.o:(.bss+0x20): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: HashTable.o:(.bss+0x48): multiple definition of `loadHashTable'; baseFAST.o:(.bss+0x18): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: HashTable.o:(.bss+0x40): multiple definition of `finalizeLoadingHashTable'; baseFAST.o:(.bss+0x10): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: HashTable.o:(.bss+0x38): multiple definition of `getCandidates'; baseFAST.o:(.bss+0x8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f80): multiple definition of `getCandidates'; baseFAST.o:(.bss+0x8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f48): multiple definition of `mappingOutput'; CommandLineParser.o:(.data.rel.local+0x390): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f70): multiple definition of `output'; baseFAST.o:(.bss+0x28): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f78): multiple definition of `finalizeOutput'; baseFAST.o:(.bss+0x30): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f88): multiple definition of `finalizeLoadingHashTable'; baseFAST.o:(.bss+0x10): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f90): multiple definition of `loadHashTable'; baseFAST.o:(.bss+0x18): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MrFAST.o:(.bss+0x27570f98): multiple definition of `generateHashTable'; baseFAST.o:(.bss+0x20): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Output.o:(.bss+0x49418): multiple definition of `finalizeOutput'; baseFAST.o:(.bss+0x30): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Output.o:(.bss+0x49410): multiple definition of `output'; baseFAST.o:(.bss+0x28): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:13: mrfast] Error 1
 * ERROR: sci-biology/mrfast-2.6.0.1::science failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/mrfast-2.6.0.1::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/mrfast-2.6.0.1::science'`.
 * The complete build log is located at '/var/log/portage/sci-biology:mrfast-2.6.0.1:20201120-061056.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mrfast-2.6.0.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mrfast-2.6.0.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/mrfast-2.6.0.1/work/mrfast-2.6.0.1'
 * S: '/var/tmp/portage/sci-biology/mrfast-2.6.0.1/work/mrfast-2.6.0.1'