* Package: sci-biology/mrfast-2.6.0.1 * Repository: science * Maintainer: sci-biology@gentoo.org * 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'