* Package: sci-biology/lagan-2.0-r2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking lagan20.tar.gz to /var/tmp/portage/sci-biology/lagan-2.0-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/lagan-2.0-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20 ... * Applying lagan-2.0-flags.patch ... [ ok ] * Applying lagan-2.0-gcc4.3.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20 ... make -j1 CC=x86_64-pc-linux-gnu-gcc CXX=x86_64-pc-linux-gnu-g++ 'CXXFLAGS=-march=native -O2 -pipe' 'CFLAGS=-march=native -O2 -pipe' make -C src make[1]: Entering directory '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20/src' x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../anchors anchors.c skiplist.c anchors.c: In function ‘my_getline’: anchors.c:232:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 1024, infile); ^~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] printf(" %d %x\n", tbp->index, tbp->myelem); ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG fchaos.c: In function ‘readfile’: fchaos.c:344:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function ‘readSubstMatrix’: fchaos.c:622:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gappenstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gappenext); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] printf(" %d %x\n", tbp->index, tbp->myelem); ^ In file included from /usr/include/string.h:630:0, from filebuffer.c:3: filebuffer.c: In function ‘FileRead’: filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../order order.c diagmatrix.c filebuffer.c order.c: In function ‘doAlign’: order.c:409:5: warning: implicit declaration of function ‘printMFAAlign’ [-Wimplicit-function-declaration] printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^~~~~~~~~~~~~ order.c:411:5: warning: implicit declaration of function ‘printXMFAAlign’ [-Wimplicit-function-declaration] printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^~~~~~~~~~~~~~ order.c: In function ‘readfile’: order.c:61:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘readSubstMatrix’: order.c:145:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:149:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gapstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:150:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gapcont); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:630:0, from filebuffer.c:3: filebuffer.c: In function ‘FileRead’: filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG mlagan.c: In function ‘main’: mlagan.c:1071:5: warning: implicit declaration of function ‘printXMFAAlign’ [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); ^~~~~~~~~~~~~~ mlagan.c: In function ‘readfile’: mlagan.c:79:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: ‘gapcache’ is static but used in inline function ‘openGap’ which is not static sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | ^~~~~~~~ multial.c:586:10: warning: ‘gapcache’ is static but used in inline function ‘contGap’ which is not static return gapcache[(v(other->cnts[CNTS_GS][ow])) | ^~~~~~~~ multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static return matchcache[v(other->cnts[0][ow]) | ^~~~~~~~~~ multial.c:556:5: warning: ‘gapcache’ is static but used in inline function ‘matchscore’ which is not static gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | ^~~~~~~~ multial.c:552:5: warning: ‘matchcache’ is static but used in inline function ‘matchscore’ which is not static matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | ^~~~~~~~~~ multial.c: In function ‘readSubstMatrix’: multial.c:478:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &k); ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gapstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &gapcont); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] printf(" %d %x\n", tbp->index, tbp->myelem); ^ In file included from /usr/include/string.h:630:0, from filebuffer.c:3: filebuffer.c: In function ‘FileRead’: filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/bin2mf utils/bin2mf.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/bin2bl utils/bin2bl.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/cextract utils/cextract.c utils/cextract.c: In function ‘getLength’: utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function ‘readfile’: utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/cstat utils/cstat.c utils/cstat.c: In function ‘cntlets’: utils/cstat.c:51:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^~~~~~~ utils/cstat.c:52:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] currchar = toupper(currchar); ^~~~~~~ utils/cstat.c:44:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function ‘readseq’: utils/cstat.c:67:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/contigorder utils/contigorder.c utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] fprintf (stderr, "contigorder: Error opening file: %s\n"); ^ utils/contigorder.c:26:18: warning: unknown conversion type character ‘&’ in format [-Wformat=] fscanf (file, "%&d", &dummy); ^ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] fprintf (stderr, "contigorder: Error opening file: %s\n"); ^ utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "numContigs = %d\n", numContigs); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "seqLen = %d\n", seqLen); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%&d", &dummy); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "numContigs = %*d\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "seqLen = %*d\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &((*score)[i][j])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/getbounds utils/getbounds.c utils/getbounds.c: In function ‘getLength’: utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/getlength utils/getlength.c utils/getlength.c: In function ‘main’: utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, BUF_SIZE, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/getoverlap utils/getoverlap.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/rc utils/rc.c utils/rc.c: In function ‘main’: utils/rc.c:39:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, stdin); ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/seqmerge utils/seqmerge.c utils/seqmerge.c: In function ‘main’: utils/seqmerge.c:19:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/scorealign utils/scorealign.c -lm utils/scorealign.c: In function ‘getSequence’: utils/scorealign.c:266:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function ‘readScoreMatrix’: utils/scorealign.c:415:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%1s", &(line[0])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &k); ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d%d", &gapopen, &gapcont); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/scorecontigs utils/scorecontigs.c -lm utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:63:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^~~~~~~ utils/scorecontigs.c:64:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] currchar = toupper(currchar); ^~~~~~~ utils/scorecontigs.c:65:27: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration] if (!lettersonly || isalpha (currchar)){ ^~~~~~~ utils/scorecontigs.c: In function ‘main’: utils/scorecontigs.c:384:38: warning: format ‘%s’ expects argument of type ‘char *’, but argument 6 has type ‘char (*)[1024]’ [-Wformat=] if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ ^ utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:55:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 1024, input); ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function ‘readseq’: utils/scorecontigs.c:81:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (temp, 1024, input); ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/getcontigpos utils/getcontigpos.c utils/getcontigpos.c: In function ‘getLength’: utils/getcontigpos.c:16:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function ‘readfile’: utils/getcontigpos.c:41:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/fa2xfa utils/fa2xfa.c utils/fa2xfa.c: In function ‘getLength’: utils/fa2xfa.c:30:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function ‘readfile’: utils/fa2xfa.c:55:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 1024, file); ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/Glue utils/Glue.cpp utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’: utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] char *alpha = "ATCG"; ^~~~~~ utils/Glue.cpp:72:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); ^ utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’: utils/Glue.cpp:44:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, 1024, file); ^ utils/Glue.cpp:52:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%1s", &(line[0])); ^ utils/Glue.cpp:54:30: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d", &k); ^ utils/Glue.cpp:59:44: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (file, "%d%d", &gapopen, &gapcont); ^ x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/dotplot utils/dotplot.cpp utils/dotplot.cpp: In function ‘int main(int, char**)’: utils/dotplot.cpp:37:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 105, file); ^ utils/dotplot.cpp:74:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 105, file); ^ utils/dotplot.cpp:97:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buffer, 105, file); ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ../utils/overlay utils/overlay.c utils/overlay.c: In function ‘read_align’: utils/overlay.c:119:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^~~~~~~ utils/overlay.c:120:19: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] checkchar = toupper(currchar); ^~~~~~~ utils/overlay.c:109:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 255, input); ^~~~~~~~~~~~~~~~~~~~~~~ make -C glocal make[2]: Entering directory '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20/src/glocal' x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -I./ -c glocal.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -I./ -c io.cpp io.cpp: In function ‘long long int my_getline(FILE*, hll*)’: io.cpp:60:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(temp, 1024, infile); ^ x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -I./ -c rightinfluence.cpp rightinfluence.cpp: In function ‘void initRI(RI*, long long int)’: rightinfluence.cpp:21:2: error: reference to ‘end’ is ambiguous end.score = -2; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:22:22: error: reference to ‘end’ is ambiguous origin.totalScore = end.totalScore = 0; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:25:2: error: reference to ‘end’ is ambiguous end.seq1End = 0; end.seq2End = 0; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:25:19: error: reference to ‘end’ is ambiguous end.seq1End = 0; end.seq2End = 0; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:26:2: error: reference to ‘end’ is ambiguous end.seq1Start = 0; end.seq2Start = 0; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:26:21: error: reference to ‘end’ is ambiguous end.seq1Start = 0; end.seq2Start = 0; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ rightinfluence.cpp:31:34: error: reference to ‘end’ is ambiguous RightInfluence->act[+INF] = &end; ^~~ rightinfluence.cpp:3:18: note: candidates are: Fragment end Fragment origin, end; ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:66:0, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:107:37: note: template const _Tp* std::end(const std::valarray<_Tp>&) template const _Tp* end(const valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:106:31: note: template _Tp* std::end(std::valarray<_Tp>&) template _Tp* end(valarray<_Tp>&); ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:97:5: note: template constexpr _Tp* std::end(_Tp (&)[_Nm]) end(_Tp (&__arr)[_Nm]) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:78:5: note: template decltype (__cont.end()) std::end(const _Container&) end(const _Container& __cont) -> decltype(__cont.end()) ^~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/range_access.h:68:5: note: template decltype (__cont.end()) std::end(_Container&) end(_Container& __cont) -> decltype(__cont.end()) ^~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:63:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/vector:64, from ./structs.h:6, from ./rightinfluence.h:4, from rightinfluence.cpp:1: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/initializer_list:99:5: note: template constexpr const _Tp* std::end(std::initializer_list<_Tp>) end(initializer_list<_Tp> __ils) noexcept ^~~ make[2]: *** [Makefile:13: rightinfluence.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20/src/glocal' make[1]: *** [Makefile:7: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20/src' make: *** [Makefile:2: all] Error 2 emake failed >>> Source compiled. >>> Test phase [not enabled]: sci-biology/lagan-2.0-r2 >>> Install lagan-2.0-r2 into /var/tmp/portage/sci-biology/lagan-2.0-r2/image/ category sci-biology !!! doexe: glocal does not exist doexe failed * ERROR: sci-biology/lagan-2.0-r2::gentoo failed (install phase): * (no error message) * * Call stack: * ebuild.sh, line 115: Called src_install * environment, line 2002: Called die * The specific snippet of code: * doexe *.pl anchors chaos glocal order prolagan || die; * * If you need support, post the output of `emerge --info '=sci-biology/lagan-2.0-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/lagan-2.0-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:lagan-2.0-r2:20160917-185915.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/lagan-2.0-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/lagan-2.0-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20' * S: '/var/tmp/portage/sci-biology/lagan-2.0-r2/work/lagan20' * QA Notice: file does not exist: * * doexe: glocal does not exist