+ exec
+ rm -rf /rpmbuild
+ mkdir -p /rpmbuild
+ su -c 'rpmbuild -ba /builddir/build/SPECS/lagan.spec --define "debug_package %{nil}" --undefine _annotated_build --define "_missing_doc_files_terminate_build %{nil}" --define "_emacs_sitestartdir /usr/share/emacs/site-lisp/site-start.d" --define "_emacs_sitelispdir /usr/share/emacs/site-lisp" --nocheck ' mockbuild
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.3trMEh
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf lagan20
+ /usr/bin/gzip -dc /builddir/build/SOURCES/lagan20.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd lagan20
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (lagan20-chris.patch):'
Patch #0 (lagan20-chris.patch):
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .chris --fuzz=0
patching file Readmes/README.FIRST
patching file Readmes/README.shuffle
patching file Readmes/README.chaos
patching file Readmes/README.lagan
patching file src/utils/scorealign.c
patching file src/utils/Glue.cpp
patching file src/utils/mrun.pl
patching file src/utils/mrunfile.pl
patching file src/utils/mrunpairs.pl
patching file src/utils/mviz.pl
patching file src/mlagan.c
patching file src/prolagan.c
patching file src/slagan-mfa.pl
patching file src/supermap.pl
patching file src/xmfa2mfa.pl
patching file utils/mrunpairs.pl
patching file utils/draft.pl
patching file utils/mrunfile.pl
patching file utils/mviz.pl
patching file utils/mrun.pl
patching file slagan.pl
patching file lagan.pl
patching file rechaos.pl
patching file slagan-mfa.pl
patching file supermap.pl
patching file xmfa2mfa.pl
patching file src/glocal/rightinfluence.cpp
patching file src/glocal/score.cpp
+ sed -i 's/^CC .*$/CC = gcc $(RPM_OPT_FLAGS)/;
s/^CPP .*$/CPP = g++ $(RPM_OPT_FLAGS)/' Makefile
+ sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c src/utils/bin2bl.c src/utils/bin2mf.c src/utils/cextract.c src/utils/contigorder.c src/utils/cstat.c src/utils/fa2xfa.c src/utils/getbounds.c src/utils/getcontigpos.c src/utils/getlength.c src/utils/getoverlap.c src/utils/overlay.c src/utils/rc.c src/utils/scorealign.c src/utils/scorecontigs.c src/utils/seqmerge.c
+ sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/utils/Glue.cpp src/utils/dotplot.cpp
+ sed -i 's|$ENV{LAGAN_DIR}|"/usr/lib64/lagan"|g' anal_gloc.pl lagan.pl rechaos.pl slagan-mfa.pl slagan.pl supermap.pl xmfa2mfa.pl src/anal_gloc.pl src/lagan.pl src/rechaos.pl src/slagan-mfa.pl src/slagan.pl src/supermap.pl src/xmfa2mfa.pl utils/cmerge2.pl utils/draft.pl utils/flipchaos.pl utils/mextract.pl utils/mf2bin.pl utils/mpretty.pl utils/mproject.pl utils/mrun.pl utils/mrunfile.pl utils/mrunpairs.pl utils/msplit.pl utils/mviz.pl src/utils/cmerge2.pl src/utils/draft.pl src/utils/mextract.pl src/utils/mf2bin.pl src/utils/mpretty.pl src/utils/mproject.pl src/utils/mrun.pl src/utils/mrunfile.pl src/utils/mrunpairs.pl src/utils/mviz.pl
+ sed -i 's|$LAGAN_DIR|/usr/lib64/lagan|g' Readmes/README.shuffle src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c
+ sed -i s/getline/GetLine/g src/anchors.c
+ rm prolagan
+ chmod -x src/glocal/Makefile src/glocal/default.score src/glocal/glocal src/glocal/glocal.cpp src/glocal/glocal.h src/glocal/io.cpp src/glocal/io.h src/glocal/leftinfluence.cpp src/glocal/leftinfluence.h src/glocal/rightinfluence.cpp src/glocal/rightinfluence.cpp.chris src/glocal/rightinfluence.h src/glocal/score.cpp src/glocal/score.cpp.chris src/glocal/score.h src/glocal/structs.h src/glocal/test.score
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mFzz4x
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ make -j4 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 ' 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 '
(cd src; make)
make[1]: Entering directory '/builddir/build/BUILD/lagan20/src'
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../anchors anchors.c skiplist.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../order order.c diagmatrix.c filebuffer.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
anchors.c: In function 'hptrcomp':
anchors.c:49:7: warning: unused variable 'jt' [-Wunused-variable]
int jt = ((hptr*)p2)->isstart;
^~
anchors.c: In function 'doOutput':
anchors.c:171:17: warning: unused variable 'bestscore' [-Wunused-variable]
int chl=0, i, bestscore=-1;
^~~~~~~~~
anchors.c:171:14: warning: unused variable 'i' [-Wunused-variable]
int chl=0, i, bestscore=-1;
^
anchors.c:168:7: warning: variable 'len' set but not used [-Wunused-but-set-variable]
int len;
^~~
order.c: In function 'readAncFile':
order.c:237:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ((tt->seq1start >= s1start && tt->seq1end <= s1end || s1start == 0 && s1end == 0) &&
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
order.c:238:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(tt->seq2start >= s2start && tt->seq2end <= s2end || s2start == 0 && s2end == 0)){
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
order.c: In function 'mkBarrel':
order.c:274:7: warning: unused variable 'incr' [-Wunused-variable]
int incr;
^~~~
order.c: In function 'doAlign':
order.c:409:5: warning: implicit declaration of function 'printMFAAlign'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration]
printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
^~~~~~~~~~~~~
printBinAlign
order.c:411:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printTextAlign'? [-Wimplicit-function-declaration]
printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
^~~~~~~~~~~~~~
printTextAlign
anchors.c: In function 'GetLine':
anchors.c:232:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(temp, 1024, infile);
^~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function 'getChain':
order.c:486:7: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^~~~
order.c: In function 'saveNeck':
order.c:561:6: warning: unused variable 'second' [-Wunused-variable]
*second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
^~~~~~
order.c:560:9: warning: unused variable 'first' [-Wunused-variable]
alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
^~~~~
order.c: In function 'joinAligns':
order.c:586:10: warning: unused variable 'n' [-Wunused-variable]
align *n = a->nextalign, *t;
^
order.c: In function 'printBinAlign':
mlagan.c: In function 'hptrcomp':
order.c:718:18: warning: array subscript has type 'char' [-Wchar-subscripts]
left = lets[seq1[s1++]];
^
mlagan.c:38:7: warning: unused variable 'jt' [-Wunused-variable]
int jt = ((hptr*)p2)->isstart;
^~
order.c:720:19: warning: array subscript has type 'char' [-Wchar-subscripts]
right = lets[seq2[s2++]];
^
mlagan.c: In function 'readfile':
mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function 'printMFAAlign':
order.c:773:27: warning: unused variable 'nlets' [-Wunused-variable]
int nm=0, nga=0, ngb=0, nlets=0;
^~~~~
order.c:773:7: warning: unused variable 'nm' [-Wunused-variable]
int nm=0, nga=0, ngb=0, nlets=0;
^~
order.c: In function 'printXMFAAlign':
order.c:805:27: warning: unused variable 'nlets' [-Wunused-variable]
int nm=0, nga=0, ngb=0, nlets=0;
^~~~~
mlagan.c: In function 'getAnchsFromFile':
mlagan.c:161:29: warning: unused variable 'first' [-Wunused-variable]
hll *myres = 0, *tt = 0, *first = 0;
^~~~~
order.c:805:7: warning: unused variable 'nm' [-Wunused-variable]
int nm=0, nga=0, ngb=0, nlets=0;
^~
fchaos.c: In function 'removeDups':
fchaos.c:302:24: warning: unused variable 'temp' [-Wunused-variable]
hll *i, *j, *jprev, *temp;
^~~~
mlagan.c: In function 'generateAnchors':
mlagan.c:213:8: warning: unused variable 'flip' [-Wunused-variable]
char flip = 0;
^~~~
mlagan.c:211:10: warning: unused variable 'temp' [-Wunused-variable]
align* temp;
^~~~
fchaos.c: In function 'readfile':
fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
^~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function 'remakeHLL':
mlagan.c:310:10: warning: unused variable 'bestscore' [-Wunused-variable]
int i, bestscore=-1;
^~~~~~~~~
mlagan.c:310:7: warning: unused variable 'i' [-Wunused-variable]
int i, bestscore=-1;
^
mlagan.c:309:20: warning: unused variable 't3' [-Wunused-variable]
hll *temp, *t2, *t3;
^~
mlagan.c:309:15: warning: unused variable 't2' [-Wunused-variable]
hll *temp, *t2, *t3;
^~
mlagan.c:307:7: warning: unused variable 'len' [-Wunused-variable]
int len;
^~~
fchaos.c: In function 'chain':
fchaos.c:401:16: warning: unused variable 'd2' [-Wunused-variable]
int i, d1=0, d2=0;
^~
fchaos.c:401:10: warning: unused variable 'd1' [-Wunused-variable]
int i, d1=0, d2=0;
^~
fchaos.c:401:7: warning: unused variable 'i' [-Wunused-variable]
int i, d1=0, d2=0;
^
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function 'iterativeImprovement':
mlagan.c:485:10: warning: unused variable 'readd' [-Wunused-variable]
align *readd, *old, *new;
^~~~~
mlagan.c:483:12: warning: unused variable 'oldscore' [-Wunused-variable]
int i=0, oldscore, cutoff;
^~~~~~~~
fchaos.c: In function 'findPrev':
fchaos.c:440:7: warning: unused variable 'doneset' [-Wunused-variable]
int doneset = 0;
^~~~~~~
mlagan.c: In function 'treeToRPN':
mlagan.c:528:16: warning: unused variable 'j' [-Wunused-variable]
int i=0; int j, k;
^
fchaos.c: In function 'doAlgo':
fchaos.c:543:24: warning: unused variable 'bestdbaseloc' [-Wunused-variable]
int bestqueryloc=-1, bestdbaseloc=-1, numhits;
^~~~~~~~~~~~
fchaos.c:543:7: warning: unused variable 'bestqueryloc' [-Wunused-variable]
int bestqueryloc=-1, bestdbaseloc=-1, numhits;
^~~~~~~~~~~~
fchaos.c:542:9: warning: unused variable 'bestscore' [-Wunused-variable]
float bestscore=-1, baseval;
^~~~~~~~~
fchaos.c: In function 'main':
mlagan.c: In function 'main':
mlagan.c:1067:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration]
printXMFAAlign(outfile, final);
^~~~~~~~~~~~~~
printFASTAAlign
fchaos.c:885:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
fchaos.c: In function 'saveScore':
fchaos.c:970:7: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^~~~
mlagan.c:942:8: warning: unused variable 'command' [-Wunused-variable]
char command[256];
^~~~~~~
mlagan.c:941:24: warning: unused variable 'y' [-Wunused-variable]
int i = 1, j = 1, x, y;
^
mlagan.c:941:21: warning: unused variable 'x' [-Wunused-variable]
int i = 1, j = 1, x, y;
^
mlagan.c:939:14: warning: unused variable 'seqfile' [-Wunused-variable]
FileBuffer seqfile;
^~~~~~~
order.c: In function 'printBinAlign':
order.c:725:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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);
^~~~~~~~~~~~~~~~~~~~~~~
order.c: In function 'printTextAlign':
order.c:769:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
order.c: In function 'printMFAAlign':
order.c:801:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
order.c: In function 'printXMFAAlign':
order.c:833:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
fchaos.c: In function 'savenfreeLList':
fchaos.c:1137:9: warning: variable 'j' set but not used [-Wunused-but-set-variable]
int i,j;
^
mlagan.c: In function 'treeToRPN':
mlagan.c:565:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
anchors.c: In function 'findBestChain':
anchors.c:164:10: warning: 'bestptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (hll*)bestptr->myelem;
^~~~~~~~~~~~~~~~~~~~~
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);
~^ ~~~~~~~~~~~
%p
skiplist.c: In function 'makeSkLst':
skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
skiplist.c: In function 'SLinsert':
skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
sle* prev = SLfind(trgt, index), *tbe;
^~~
mlagan.c: In function 'buildTree':
mlagan.c:623:53: warning: 'mlj' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp = (char*) malloc ((namelens[mli] + namelens[mlj] +4)* sizeof(char));
~~~~~~~~^~~~~
mlagan.c:623:37: warning: 'mli' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp = (char*) malloc ((namelens[mli] + namelens[mlj] +4)* sizeof(char));
~~~~~~~~^~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
prolagan.c: In function 'hptrcomp':
prolagan.c:41:7: warning: unused variable 'jt' [-Wunused-variable]
int jt = ((hptr*)p2)->isstart;
^~
prolagan.c: In function 'readfile':
prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function 'appendAlignProfile':
prolagan.c:163:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
prolagan.c: In function 'readProfile':
prolagan.c:198:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while ( myseq = FileRead( with_gaps,0,0,VER_MLAGAN )) {
^~~~~
prolagan.c: In function 'getAnchsFromFile':
prolagan.c:246:29: warning: unused variable 'first' [-Wunused-variable]
hll *myres = 0, *tt = 0, *first = 0;
^~~~~
prolagan.c: In function 'generateAnchors':
prolagan.c:298:8: warning: unused variable 'flip' [-Wunused-variable]
char flip = 0;
^~~~
prolagan.c:296:10: warning: unused variable 'temp' [-Wunused-variable]
align* temp;
^~~~
prolagan.c: In function 'remakeHLL':
prolagan.c:395:10: warning: unused variable 'bestscore' [-Wunused-variable]
int i, bestscore=-1;
^~~~~~~~~
prolagan.c:395:7: warning: unused variable 'i' [-Wunused-variable]
int i, bestscore=-1;
^
prolagan.c:394:20: warning: unused variable 't3' [-Wunused-variable]
hll *temp, *t2, *t3;
^~
prolagan.c:394:15: warning: unused variable 't2' [-Wunused-variable]
hll *temp, *t2, *t3;
^~
prolagan.c:392:7: warning: unused variable 'len' [-Wunused-variable]
int len;
^~~
prolagan.c: In function 'processAnchors':
prolagan.c:539:36: warning: unused variable 'uni' [-Wunused-variable]
align *first, *second, *result, *uni;
^~~
prolagan.c: In function 'iterativeImprovement':
prolagan.c:587:10: warning: unused variable 'readd' [-Wunused-variable]
align *readd, *old, *new;
^~~~~
prolagan.c:585:12: warning: unused variable 'oldscore' [-Wunused-variable]
int i=0, oldscore, cutoff;
^~~~~~~~
prolagan.c: In function 'treeToRPN':
prolagan.c:630:16: warning: unused variable 'j' [-Wunused-variable]
int i=0; int j, k;
^
diagmatrix.c: In function 'DMsetPtr':
diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
char res;
^~~
diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
int dn = x+y-1, loc;
^~~
prolagan.c: In function 'main':
prolagan.c:1087:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration]
printXMFAAlign(outfile, final);
^~~~~~~~~~~~~~
printFASTAAlign
prolagan.c:966:8: warning: unused variable 'table' [-Wunused-variable]
hll* table[MAX_SEQ][MAX_SEQ];
^~~~~
prolagan.c:960:8: warning: unused variable 'command' [-Wunused-variable]
char command[256];
^~~~~~~
prolagan.c:954:14: warning: unused variable 'seqfile' [-Wunused-variable]
FileBuffer seqfile;
^~~~~~~
prolagan.c: In function 'readfile':
prolagan.c:79:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(temp, 255, input);
^~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function 'treeToRPN':
prolagan.c:667:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
fchaos.c: In function 'doTranslated':
fchaos.c:865:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
procPairs(currquery, currdbase);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function 'main':
fchaos.c:955:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
procPairs(currquery, currdbase);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c: In function 'getAnchsFromAlign':
multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable]
float peakfrac;
^~~~~~~~
multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable]
char ingap = 0, isfrst = 1;
^~~~~~
multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable]
int currscore=0, oldscore, peakscore;
^~~~~~~~~
multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable]
int currscore=0, oldscore, peakscore;
^~~~~~~~
multial.c: In function 'unifyAlign':
multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable]
int s1 = 0, s2 = 0, tgs, tgc;
^~~
multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable]
int s1 = 0, s2 = 0, tgs, tgc;
^~~
multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable]
int i,j,k, cbc, brcount;
^~~~~~~
multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable]
int i,j,k, cbc, brcount;
^~~
multial.c: In function 'getChain':
multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^~~~
multial.c: In function 'saveNeck':
multial.c:358:6: warning: unused variable 'second' [-Wunused-variable]
*second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
^~~~~~
multial.c:357:9: warning: unused variable 'first' [-Wunused-variable]
alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
^~~~~
multial.c: In function 'joinAligns':
multial.c:381:10: warning: unused variable 'n' [-Wunused-variable]
align *n = a->nextalign, *t;
^
multial.c: In function 'openGap':
multial.c:594:25: warning: unused variable 'i' [-Wunused-variable]
int alopen, pen, sav, i;
^
multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable]
int alopen, pen, sav, i;
^~~
multial.c: In function 'mkBarrel':
multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable]
int incr;
^~~~
multial.c: In function 'doNW':
multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable]
int numNecks =0, oldneck =0;
^~~~~~~
multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable]
char rh, ptr=0, isneck;
^~
multial.c:807:14: warning: unused variable 'b' [-Wunused-variable]
align* a, *b;
^
multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable]
int tt, prevgap;
^~~~~~~
multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable]
int tt, prevgap;
^~
multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable]
int gapend[3];
^~~~~~
multial.c: In function 'removeSeqByName':
multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
seq *removed;
^~~~~~~
multial.c: In function 'getSeqNum':
multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable]
seq *removed;
^~~~~~~
multial.c: In function 'remapHLLs':
multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
^
multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable]
int mybp, i, *searchint, stmybp, mylen, olen, osize;
^~~~
multial.c: In function 'hllJoin':
multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
multial.c: In function 'minHLL':
multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
multial.c: In function 'mergeHLLs':
multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, mscore;
^
multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable]
int i, j, mscore;
^
multial.c: In function 'printTextAlign':
multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: In function 'printFASTAAlign':
multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: In function 'printXMFAAlign':
multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: At top level:
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 'scoreLocal':
multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c: In function 'removeSeqByName':
multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printTextAlign':
multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printFASTAAlign':
multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printXMFAAlign':
multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrtrie.c: In function 'makeAlpha':
thrtrie.c:33:14: warning: array subscript has type 'char' [-Wchar-subscripts]
indeces[*alpha] = i;
^
thrtrie.c:35:18: warning: array subscript has type 'char' [-Wchar-subscripts]
else indeces [*alpha] = i++;
^
thrtrie.c: In function 'lookup':
thrtrie.c:42:17: warning: array subscript has type 'char' [-Wchar-subscripts]
return indeces[c];
^
thrtrie.c: In function 'insertString':
thrtrie.c:174:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, wordlen = root->height, letprev, letcurr;
^
In file included from thrtrie.c:13:0:
mempage.c: In function 'MPallfree':
mempage.c:48:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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) ?
^~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/bin2mf utils/bin2mf.c
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);
~^ ~~~~~~~~~~~
%p
skiplist.c: In function 'makeSkLst':
skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
skiplist.c: In function 'SLinsert':
skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
sle* prev = SLfind(trgt, index), *tbe;
^~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/bin2bl utils/bin2bl.c
multial.c: In function 'getAnchsFromAlign':
multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable]
float peakfrac;
^~~~~~~~
multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable]
char ingap = 0, isfrst = 1;
^~~~~~
multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable]
int currscore=0, oldscore, peakscore;
^~~~~~~~~
multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable]
int currscore=0, oldscore, peakscore;
^~~~~~~~
multial.c: In function 'unifyAlign':
multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable]
int s1 = 0, s2 = 0, tgs, tgc;
^~~
multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable]
int s1 = 0, s2 = 0, tgs, tgc;
^~~
multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable]
int i,j,k, cbc, brcount;
^~~~~~~
multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable]
int i,j,k, cbc, brcount;
^~~
multial.c: In function 'getChain':
multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^~~~
multial.c: In function 'saveNeck':
multial.c:358:6: warning: unused variable 'second' [-Wunused-variable]
*second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
^~~~~~
multial.c:357:9: warning: unused variable 'first' [-Wunused-variable]
alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
^~~~~
multial.c: In function 'joinAligns':
multial.c:381:10: warning: unused variable 'n' [-Wunused-variable]
align *n = a->nextalign, *t;
^
multial.c: In function 'openGap':
multial.c:594:25: warning: unused variable 'i' [-Wunused-variable]
int alopen, pen, sav, i;
^
multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable]
int alopen, pen, sav, i;
^~~
multial.c: In function 'mkBarrel':
multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable]
int incr;
^~~~
multial.c: In function 'doNW':
multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable]
int numNecks =0, oldneck =0;
^~~~~~~
multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable]
char rh, ptr=0, isneck;
^~
multial.c:807:14: warning: unused variable 'b' [-Wunused-variable]
align* a, *b;
^
multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable]
int tt, prevgap;
^~~~~~~
multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable]
int tt, prevgap;
^~
multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable]
int gapend[3];
^~~~~~
utils/bin2bl.c: In function 'main':
utils/bin2bl.c:52:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (argv[1][0] == '-')
^
utils/bin2bl.c:22:7: warning: unused variable 'width' [-Wunused-variable]
int width = 60;
^~~~~
multial.c: In function 'removeSeqByName':
multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
seq *removed;
^~~~~~~
multial.c: In function 'getSeqNum':
multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable]
seq *removed;
^~~~~~~
global.c: In function 'ismatch':
global.c:12:17: warning: array subscript has type 'char' [-Wchar-subscripts]
return indeces[a] == indeces[b];
^
global.c:12:31: warning: array subscript has type 'char' [-Wchar-subscripts]
return indeces[a] == indeces[b];
^
multial.c: In function 'remapHLLs':
multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
^
multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable]
int mybp, i, *searchint, stmybp, mylen, olen, osize;
^~~~
multial.c: In function 'hllJoin':
multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
multial.c: In function 'minHLL':
multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
global.c: In function 'global':
global.c:34:31: warning: unused variable 'score' [-Wunused-variable]
int mm = end2 - start2 + 1, score;
^~~~~
multial.c: In function 'mergeHLLs':
multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, mscore;
^
multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable]
int i, j, mscore;
^
multial.c: In function 'printTextAlign':
multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: In function 'printFASTAAlign':
multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: In function 'printXMFAAlign':
multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable]
int nlets=0;
^~~~~
multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable]
int s1=0, s2=0, c, k, i;
^~
multial.c: At top level:
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]) |
^~~~~~~~~~
global.c: In function 'printalign':
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]) |
^~~~~~~~~~
global.c:172:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'scoreLocal':
multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c: In function 'removeSeqByName':
multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printTextAlign':
multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printFASTAAlign':
multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
multial.c: In function 'printXMFAAlign':
multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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);
^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cextract.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ch == '>') ungetc (ch, file);
^
translate.c: In function 'toPeptide':
translate.c:9:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, sum=0, mask = 0;
^
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/cstat utils/cstat.c
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) ?
^~~~~~~
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: In function 'main':
utils/cstat.c:234:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
utils/cstat.c: In function 'cntlets':
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);
^~~~~~~~~~~~~~~~~~~~~~~
diagmatrix.c: In function 'DMsetPtr':
diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
char res;
^~~
diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
int dn = x+y-1, loc;
^~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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:26:16: warning: too many arguments for format [-Wformat-extra-args]
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");
~^
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/getbounds utils/getbounds.c
utils/contigorder.c: In function 'solveOrder':
utils/contigorder.c:176:30: warning: unused variable 'ptr' [-Wunused-variable]
int **best, *first, *last, ptr, newScore, **scoreOf;
^~~
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]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getbounds.c: In function 'main':
utils/getbounds.c:32:27: warning: unused variable 'ext' [-Wunused-variable]
int S1B, S1E, S2B, S2E, ext, len1, len2;
^~~
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/getlength utils/getlength.c
utils/contigorder.c: In function 'solveOrder':
utils/contigorder.c:249:63: warning: 'bestRange' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j = 0; k && j < numRanges; j++) if (last[j] < first[bestRange]){
^
utils/contigorder.c:251:22: warning: 'bestState' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (newScore == best[bestState][bestRange]){
^
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);
~^ ~~~~~~~~~~~
%p
skiplist.c: In function 'makeSkLst':
skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
skiplist.c: In function 'SLinsert':
skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
sle* prev = SLfind(trgt, index), *tbe;
^~~
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/getoverlap utils/getoverlap.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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);
^~~~~~~~~~~~~~~~~~~~~~~
diagmatrix.c: In function 'DMsetPtr':
diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
char res;
^~~
diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
int dn = x+y-1, loc;
^~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/seqmerge utils/seqmerge.c
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) ?
^~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/scorealign utils/scorealign.c -lm
utils/seqmerge.c: In function 'main':
utils/seqmerge.c:33:15: warning: suggest parentheses around comparison in operand of '^' [-Wparentheses]
if (written ^ 60 != 0) printf ("\n");
^
utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets (buffer, 1024, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/scorecontigs utils/scorecontigs.c -lm
utils/scorealign.c: In function 'getSequence':
utils/scorealign.c:262:8: warning: variable 'prevch' set but not used [-Wunused-but-set-variable]
char prevch = '~';
^~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/getcontigpos utils/getcontigpos.c
utils/scorealign.c: In function 'getSequences':
utils/scorealign.c:322:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (newseq = getSequence (file, &si, &ss, &se, &sd, &sc)){
^~~~~~
utils/scorealign.c:310:7: warning: unused variable 'i' [-Wunused-variable]
int i, si, ss, se;
^
utils/scorealign.c: In function 'processSequences':
utils/scorealign.c:353:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
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:411:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets (line, 1024, file);
^~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:419:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (file, "%1s", &(line[0]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:421:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (file, "%d", &k);
^~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:426:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (file, "%d%d", &gapopen, &gapcont);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 'analyze':
utils/scorecontigs.c:344:13: warning: unused variable 'k' [-Wunused-variable]
int i, j, k;
^
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);
^~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c: In function 'print':
utils/getcontigpos.c:66:46: warning: unused variable 'j' [-Wunused-variable]
int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
^
utils/getcontigpos.c:66:33: warning: unused variable 'written' [-Wunused-variable]
int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
^~~~~~~
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ch == '>') ungetc (ch, file);
^
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);
~^ ~~~~~~~~~~~
%p
skiplist.c: In function 'makeSkLst':
skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
skiplist.c: In function 'SLinsert':
skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
sle* prev = SLfind(trgt, index), *tbe;
^~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/fa2xfa utils/fa2xfa.c
utils/fa2xfa.c: In function 'print':
utils/fa2xfa.c:81:36: warning: unused variable 'j' [-Wunused-variable]
int i = 0, pos = 0, written = 0, j = 0;
^
utils/fa2xfa.c:81:14: warning: unused variable 'pos' [-Wunused-variable]
int i = 0, pos = 0, written = 0, j = 0;
^~~
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);
^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/fa2xfa.c:74:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ch == '>') ungetc (ch, file);
^
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) ?
^~~~~~~
g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/Glue utils/Glue.cpp
g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -o ../utils/dotplot utils/dotplot.cpp
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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:101:30: warning: unused variable 'tt' [-Wunused-variable]
char currchar, checkchar, *tt;
^~
utils/overlay.c: In function 'read_sequences':
utils/overlay.c:176:19: warning: unused variable 'breaker' [-Wunused-variable]
int i, j, kmer, breaker;
^~~~~~~
utils/overlay.c:176:13: warning: unused variable 'kmer' [-Wunused-variable]
int i, j, kmer, breaker;
^~~~
utils/overlay.c:176:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, kmer, breaker;
^
utils/overlay.c: In function 'main':
utils/overlay.c:232:16: warning: unused variable 'test' [-Wunused-variable]
float ttree, test;
^~~~
utils/overlay.c:232:9: warning: unused variable 'ttree' [-Wunused-variable]
float ttree, test;
^~~~~
utils/overlay.c:231:7: warning: unused variable 'moved' [-Wunused-variable]
int moved, i;
^~~~~
utils/overlay.c:230:8: warning: unused variable 'string_tree' [-Wunused-variable]
char string_tree[16537]; //noone will ever need more :)))
^~~~~~~~~~~
utils/overlay.c: In function 'read_align':
utils/overlay.c:109:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(temp, 255, input);
^~~~~~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp: In function 'int main(int, char**)':
utils/dotplot.cpp:6:27: warning: variable 'pa' set but not used [-Wunused-but-set-variable]
int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
^~
utils/dotplot.cpp:6:31: warning: variable 'pb' set but not used [-Wunused-but-set-variable]
int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
^~
utils/dotplot.cpp:37:11: 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:74:11: 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:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets (buffer, 105, file);
~~~~~~^~~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function 'void readScoreMatrix(char*)':
utils/Glue.cpp:33:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
lagan_dir = "/usr/lib64/lagan";
^~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function 'void calculateScoreMatrix(int)':
utils/Glue.cpp:60:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *alpha = "ATCG";
^~~~~~
utils/Glue.cpp:68:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
readScoreMatrix (NUCLEOTIDE_MATRIX_FILE);
^
utils/Glue.cpp: In function 'int countLets(SafeVector<char>&)':
utils/Glue.cpp:228:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (data[i] >= 'A' && data[i] <= 'Z' || data[i] >= 'a' && data[i] <= 'z')
utils/Glue.cpp: In function 'int main(int, char**)':
utils/Glue.cpp:372:19: warning: variable 'end1' set but not used [-Wunused-but-set-variable]
int begin1 = 1, end1 = 1;
^~~~
utils/Glue.cpp: In function 'void readScoreMatrix(char*)':
utils/Glue.cpp:40:9: 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:48:12: 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:50:14: 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:55:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf (file, "%d%d", &gapopen, &gapcont);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(cd glocal; make)
make[2]: Entering directory '/builddir/build/BUILD/lagan20/src/glocal'
g++ -Wno-deprecated -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I./ -c glocal.cpp
g++ -Wno-deprecated -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I./ -c io.cpp
g++ -Wno-deprecated -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I./ -c rightinfluence.cpp
g++ -Wno-deprecated -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I./ -c leftinfluence.cpp
In file included from ./rightinfluence.h:4:0,
from rightinfluence.cpp:1:
rightinfluence.cpp: In function 'void initRI(RI*, long long int)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
rightinfluence.cpp:9:22: note: in expansion of macro 'RELPOSSHIFT'
if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
^~~~~~~~~~~
rightinfluence.cpp: In function 'long long int RICommitEndPoint(RI*, Fragment*)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
rightinfluence.cpp:119:85: note: in expansion of macro 'RELPOSSHIFT'
int possibleCase = NEGATIVE << DOWNSTRANDSHIFT | NEGATIVE <<UPSTRANDSHIFT | LEFT << RELPOSSHIFT;
^~~~~~~~~~~
In file included from ./leftinfluence.h:4:0,
from leftinfluence.cpp:1:
leftinfluence.cpp: In function 'void InitLI(LI*, long long int)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
leftinfluence.cpp:135:22: note: in expansion of macro 'RELPOSSHIFT'
if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
^~~~~~~~~~~
In file included from ./score.h:4:0,
from glocal.cpp:1:
glocal.cpp: In function 'int main(int, char**)':
./structs.h:31:50: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define TOTALSHIFT UPSTRANDBITS + DOWNSTRANDBITS + RELPOSBITS
^
glocal.cpp:64:16: note: in expansion of macro 'TOTALSHIFT'
for (i=0;i<1<<TOTALSHIFT;i++) {
^~~~~~~~~~
glocal.cpp: In function 'long long int startPointHandler()':
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
glocal.cpp:131:86: note: in expansion of macro 'RELPOSSHIFT'
possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
^~~~~~~~~~~
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
glocal.cpp:142:87: note: in expansion of macro 'RELPOSSHIFT'
possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos << RELPOSSHIFT;
^~~~~~~~~~~
glocal.cpp:120:8: warning: variable 'current_score' set but not used [-Wunused-but-set-variable]
float current_score;
^~~~~~~~~~~~~
In file included from ./score.h:4:0,
from glocal.cpp:1:
glocal.cpp: In function 'long long int endPointHandler()':
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
glocal.cpp:224:88: note: in expansion of macro 'RELPOSSHIFT'
possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
^~~~~~~~~~~
leftinfluence.cpp: In function 'void printState(LI*)':
leftinfluence.cpp:619:16: warning: variable 'colCount' set but not used [-Wunused-but-set-variable]
long long int colCount, diagCount, ownerCount;
^~~~~~~~
leftinfluence.cpp:619:26: warning: variable 'diagCount' set but not used [-Wunused-but-set-variable]
long long int colCount, diagCount, ownerCount;
^~~~~~~~~
leftinfluence.cpp:619:37: warning: variable 'ownerCount' set but not used [-Wunused-but-set-variable]
long long int colCount, diagCount, ownerCount;
^~~~~~~~~~
io.cpp: In function 'long long int getline(FILE*, hll*)':
io.cpp:60:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(temp, 1024, infile);
~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -Wno-deprecated -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I./ -c score.cpp
In file included from score.cpp:1:0:
score.cpp: In function 'void createScoreFunctionObjects(char*)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
score.cpp:92:106: note: in expansion of macro 'RELPOSSHIFT'
cases[i]= charToCase(updir)<<UPSTRANDSHIFT | charToCase(downdir)<<DOWNSTRANDSHIFT |charToCase(relpos)<<RELPOSSHIFT;
^~~~~~~~~~~
score.cpp: In function 'float scoreAll(Fragment*, Fragment*, long long int)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
score.cpp:143:19: note: in expansion of macro 'RELPOSSHIFT'
if (ret_case >> RELPOSSHIFT != UNRELATED) {
^~~~~~~~~~~
score.cpp: In function 'float fragmentSetScore(Fragment*, Fragment*, LI*, RI*, long long int)':
./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
#define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
^
score.cpp:185:120: note: in expansion of macro 'RELPOSSHIFT'
tempScore = scoreAll(owner,current, current->strand << DOWNSTRANDSHIFT | owner->strand <<UPSTRANDSHIFT | UNRELATED<< RELPOSSHIFT);
^~~~~~~~~~~
g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm
make[2]: Leaving directory '/builddir/build/BUILD/lagan20/src/glocal'
make[1]: Leaving directory '/builddir/build/BUILD/lagan20/src'
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DnNlaX
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
++ dirname /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
+ cd lagan20
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
+ mkdir -p /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/bin /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ install -m755 chaos /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/bin
+ install -m755 mlagan /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/bin
+ install -m755 prolagan /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/bin
+ install -m755 lagan.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/bin/lagan
+ install -m755 slagan.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/bin/slagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 anal_gloc.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 anchors /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 glocal /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 order /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 rechaos.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 supermap.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 xmfa2mfa.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/bin2bl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/bin2mf /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cextract /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cmerge2.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/contigorder /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cstat /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/dotplot /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/draft.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/fa2xfa /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getbounds /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getcontigpos /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getlength /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getoverlap /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/Glue /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mextract.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mf2bin.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mpretty.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mproject.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrunfile.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrunpairs.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrun.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mviz.pl /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/rc /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/scorealign /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/scorecontigs /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/seqmerge /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/overlay /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan/utils
+ install -m644 blosum62.txt blosum62s.txt nucmatrix.txt test.score /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64//usr/lib64/lagan
+ rm -f Readmes/README.FIRST.chris Readmes/README.chaos.chris Readmes/README.lagan.chris Readmes/README.shuffle.chris
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip /usr/bin/strip
+ /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in ./usr/lib64/lagan/anal_gloc.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/rechaos.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mviz.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mproject.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mf2bin.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mrunpairs.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mrunfile.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mrun.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mpretty.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/cmerge2.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/draft.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/lib64/lagan/utils/mextract.pl from #!/usr/bin/env perl to #!/usr/bin/perl
mangling shebang in ./usr/bin/lagan from #!/usr/bin/env perl to #!/usr/bin/perl
Processing files: lagan-2.0-19.fc28.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.l7f24M
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ DOCDIR=/builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/share/doc/lagan
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/share/doc/lagan
+ cp -pr Readmes/LICENSE Readmes/README.FIRST Readmes/README.chaos Readmes/README.lagan Readmes/README.mlagan Readmes/README.shuffle Readmes/README.tools /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/share/doc/lagan
+ cp -pr sample.fasta sample.params /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64/usr/share/doc/lagan
+ exit 0
Provides: lagan = 2.0-19.fc28 lagan(riscv-64) = 2.0-19.fc28
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
Wrote: /builddir/build/SRPMS/lagan-2.0-19.fc28.src.rpm
Wrote: /builddir/build/RPMS/riscv64/lagan-2.0-19.fc28.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qp8A9b
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-19.fc28.riscv64
+ exit 0
+ touch /buildok
+ cleanup
+ set +e
+ sync
+ sleep 5
+ sync
+ poweroff
Terminated
++ cleanup
++ set +e
++ sync
++ sleep 5
+++ cleanup
+++ set +e
+++ sync
+++ sleep 5
+++ sync
+++ poweroff