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Gentoo's Bugzilla – Attachment 446268 Details for
Bug 594148
sci-biology/lagan-2.0-r2 : rightinfluence.cpp:21:2: error: reference to ‘end’ is ambiguous
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sci-biology:lagan-2.0-r2:20160917-185915.log
sci-biology:lagan-2.0-r2:20160917-185915.log (text/plain), 37.96 KB, created by
Toralf Förster
on 2016-09-17 22:25:35 UTC
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Description:
sci-biology:lagan-2.0-r2:20160917-185915.log
Filename:
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Creator:
Toralf Förster
Created:
2016-09-17 22:25:35 UTC
Size:
37.96 KB
patch
obsolete
> * 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 âmy_getlineâ: >anchors.c:232:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 1024, infile); > ^~~~~~~~~~~~~~~~~~~~~~~~~ >skiplist.c: In function âprintSLEâ: >skiplist.c:12:19: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âvoid *â [-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 âreadfileâ: >fchaos.c:344:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 255, input); > ^~~~~~~~~~~~~~~~~~~~~~~ >fchaos.c: In function âreadSubstMatrixâ: >fchaos.c:622:7: warning: ignoring return value of âfscanfâ, 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 âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &gappenstart); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fchaos.c:628:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &gappenext); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >skiplist.c: In function âprintSLEâ: >skiplist.c:12:19: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âvoid *â [-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 âFileReadâ: >filebuffer.c:123:34: warning: implicit declaration of function âtoupperâ [-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 âdoAlignâ: >order.c:409:5: warning: implicit declaration of function âprintMFAAlignâ [-Wimplicit-function-declaration] > printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); > ^~~~~~~~~~~~~ >order.c:411:5: warning: implicit declaration of function âprintXMFAAlignâ [-Wimplicit-function-declaration] > printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); > ^~~~~~~~~~~~~~ >order.c: In function âreadfileâ: >order.c:61:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 255, input); > ^~~~~~~~~~~~~~~~~~~~~~~ >order.c: In function âreadSubstMatrixâ: >order.c:145:7: warning: ignoring return value of âfscanfâ, 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 âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &gapstart); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >order.c:150:3: warning: ignoring return value of âfscanfâ, 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 âFileReadâ: >filebuffer.c:123:34: warning: implicit declaration of function âtoupperâ [-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 âmainâ: >mlagan.c:1071:5: warning: implicit declaration of function âprintXMFAAlignâ [-Wimplicit-function-declaration] > printXMFAAlign(outfile, final); > ^~~~~~~~~~~~~~ >mlagan.c: In function âreadfileâ: >mlagan.c:79:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 255, input); > ^~~~~~~~~~~~~~~~~~~~~~~ >multial.c:603:9: warning: âgapcacheâ is static but used in inline function âopenGapâ 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: âgapcacheâ is static but used in inline function âcontGapâ which is not static > return gapcache[(v(other->cnts[CNTS_GS][ow])) | > ^~~~~~~~ >multial.c:581:10: warning: âgapcacheâ is static but used in inline function âendGap2â 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: âgapcacheâ is static but used in inline function âendGap1â 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: âgapcacheâ is static but used in inline function âendGap0â which is not static > return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | > ^~~~~~~~ >multial.c:563:10: warning: âmatchcacheâ is static but used in inline function âscoreOppâ which is not static > return matchcache[v(other->cnts[0][ow]) | > ^~~~~~~~~~ >multial.c:556:5: warning: âgapcacheâ is static but used in inline function âmatchscoreâ which is not static > gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | > ^~~~~~~~ >multial.c:552:5: warning: âmatchcacheâ is static but used in inline function âmatchscoreâ which is not static > matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | > ^~~~~~~~~~ >multial.c: In function âreadSubstMatrixâ: >multial.c:478:7: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &k); > ^~~~~~~~~~~~~~~~~~~~~~~ >multial.c:486:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &gapstart); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >multial.c:487:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &gapcont); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >skiplist.c: In function âprintSLEâ: >skiplist.c:12:19: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âvoid *â [-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 âFileReadâ: >filebuffer.c:123:34: warning: implicit declaration of function âtoupperâ [-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 âgetLengthâ: >utils/cextract.c:16:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets (buffer, 1024, file); > ^~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/cextract.c: In function âreadfileâ: >utils/cextract.c:41:5: warning: ignoring return value of âfgetsâ, 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 âcntletsâ: >utils/cstat.c:51:10: warning: implicit declaration of function âisspaceâ [-Wimplicit-function-declaration] > if (!isspace(currchar)) { > ^~~~~~~ >utils/cstat.c:52:18: warning: implicit declaration of function âtoupperâ [-Wimplicit-function-declaration] > currchar = toupper(currchar); > ^~~~~~~ >utils/cstat.c:44:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 255, input); > ^~~~~~~~~~~~~~~~~~~~~~~ >utils/cstat.c: In function âreadseqâ: >utils/cstat.c:67:3: warning: ignoring return value of âfgetsâ, 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 âgetFileInfoâ: >utils/contigorder.c:15:57: warning: format â%sâ expects a matching âchar *â argument [-Wformat=] > fprintf (stderr, "contigorder: Error opening file: %s\n"); > ^ >utils/contigorder.c:26:18: warning: unknown conversion type character â&â in format [-Wformat=] > fscanf (file, "%&d", &dummy); > ^ >utils/contigorder.c: In function âgetScoresâ: >utils/contigorder.c:52:57: warning: format â%sâ expects a matching âchar *â argument [-Wformat=] > fprintf (stderr, "contigorder: Error opening file: %s\n"); > ^ >utils/contigorder.c: In function âgetFileInfoâ: >utils/contigorder.c:19:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "numContigs = %d\n", numContigs); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/contigorder.c:20:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "seqLen = %d\n", seqLen); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/contigorder.c:26:2: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%&d", &dummy); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/contigorder.c: In function âgetScoresâ: >utils/contigorder.c:56:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "numContigs = %*d\n"); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/contigorder.c:57:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "seqLen = %*d\n"); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/contigorder.c:63:2: warning: ignoring return value of âfscanfâ, 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 âgetLengthâ: >utils/getbounds.c:18:3: warning: ignoring return value of âfgetsâ, 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 âmainâ: >utils/getlength.c:20:3: warning: ignoring return value of âfgetsâ, 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 âmainâ: >utils/rc.c:39:3: warning: ignoring return value of âfgetsâ, 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 âmainâ: >utils/seqmerge.c:19:5: warning: ignoring return value of âfgetsâ, 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 âgetSequenceâ: >utils/scorealign.c:266:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets (line, 1024, file); > ^~~~~~~~~~~~~~~~~~~~~~~~ >utils/scorealign.c: In function âreadScoreMatrixâ: >utils/scorealign.c:415:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets (line, 1024, file); > ^~~~~~~~~~~~~~~~~~~~~~~~ >utils/scorealign.c:423:5: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%1s", &(line[0])); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/scorealign.c:425:7: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &k); > ^~~~~~~~~~~~~~~~~~~~~~~ >utils/scorealign.c:430:3: warning: ignoring return value of âfscanfâ, 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 âcntletsâ: >utils/scorecontigs.c:63:10: warning: implicit declaration of function âisspaceâ [-Wimplicit-function-declaration] > if (!isspace(currchar)) { > ^~~~~~~ >utils/scorecontigs.c:64:18: warning: implicit declaration of function âtoupperâ [-Wimplicit-function-declaration] > currchar = toupper(currchar); > ^~~~~~~ >utils/scorecontigs.c:65:27: warning: implicit declaration of function âisalphaâ [-Wimplicit-function-declaration] > if (!lettersonly || isalpha (currchar)){ > ^~~~~~~ >utils/scorecontigs.c: In function âmainâ: >utils/scorecontigs.c:384:38: warning: format â%sâ expects argument of type âchar *â, but argument 6 has type âchar (*)[1024]â [-Wformat=] > if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ > ^ >utils/scorecontigs.c: In function âcntletsâ: >utils/scorecontigs.c:55:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(temp, 1024, input); > ^~~~~~~~~~~~~~~~~~~~~~~~ >utils/scorecontigs.c: In function âreadseqâ: >utils/scorecontigs.c:81:3: warning: ignoring return value of âfgetsâ, 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 âgetLengthâ: >utils/getcontigpos.c:16:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets (buffer, 1024, file); > ^~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/getcontigpos.c: In function âreadfileâ: >utils/getcontigpos.c:41:5: warning: ignoring return value of âfgetsâ, 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 âgetLengthâ: >utils/fa2xfa.c:30:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets (buffer, 1024, file); > ^~~~~~~~~~~~~~~~~~~~~~~~~~ >utils/fa2xfa.c: In function âreadfileâ: >utils/fa2xfa.c:55:5: warning: ignoring return value of âfgetsâ, 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 âvoid calculateScoreMatrix(int)â: >utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] > char *alpha = "ATCG"; > ^~~~~~ >utils/Glue.cpp:72:44: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] > readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); > ^ >utils/Glue.cpp: In function âvoid readScoreMatrix(char*)â: >utils/Glue.cpp:44:27: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets (line, 1024, file); > ^ >utils/Glue.cpp:52:37: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%1s", &(line[0])); > ^ >utils/Glue.cpp:54:30: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (file, "%d", &k); > ^ >utils/Glue.cpp:59:44: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint main(int, char**)â: >utils/dotplot.cpp:37:30: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets (buffer, 105, file); > ^ >utils/dotplot.cpp:74:30: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets (buffer, 105, file); > ^ >utils/dotplot.cpp:97:30: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âread_alignâ: >utils/overlay.c:119:10: warning: implicit declaration of function âisspaceâ [-Wimplicit-function-declaration] > if (!isspace(currchar)) { > ^~~~~~~ >utils/overlay.c:120:19: warning: implicit declaration of function âtoupperâ [-Wimplicit-function-declaration] > checkchar = toupper(currchar); > ^~~~~~~ >utils/overlay.c:109:3: warning: ignoring return value of âfgetsâ, 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 âlong long int my_getline(FILE*, hll*)â: >io.cpp:60:27: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âvoid initRI(RI*, long long int)â: >rightinfluence.cpp:21:2: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:22:22: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:25:2: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:25:19: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:26:2: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:26:21: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> constexpr const _Tp* std::end(std::initializer_list<_Tp>) > end(initializer_list<_Tp> __ils) noexcept > ^~~ >rightinfluence.cpp:31:34: error: reference to âendâ 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<class _Tp> const _Tp* std::end(const std::valarray<_Tp>&) > template<typename _Tp> 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<class _Tp> _Tp* std::end(std::valarray<_Tp>&) > template<typename _Tp> _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<class _Tp, long unsigned int _Nm> 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<class _Container> 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<class _Container> 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<class _Tp> 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
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