Mock Version: 1.4.14
Mock Version: 1.4.14
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f31-build-115595-34500/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c0898>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1548979200
Wrote: /builddir/build/SRPMS/lagan-2.0-25.fc31.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f31-build-115595-34500/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c0898>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1548979200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.l7V1fs
+ 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 $(RPM_OPT_FLAGS)/;
BUILDSTDERR:         s/^CPP .*$/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
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BzldMu
+ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' '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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
(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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
BUILDSTDERR: order.c: In function 'readAncFile':
BUILDSTDERR: order.c:237:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
BUILDSTDERR:   237 |     if ((tt->seq1start >= s1start && tt->seq1end <= s1end || s1start == 0 && s1end == 0) &&
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: order.c:238:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
BUILDSTDERR:   238 |  (tt->seq2start >= s2start && tt->seq2end <= s2end || s2start == 0 && s2end == 0)){
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: order.c: In function 'mkBarrel':
BUILDSTDERR: order.c:274:7: warning: unused variable 'incr' [-Wunused-variable]
BUILDSTDERR:   274 |   int incr;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: order.c: In function 'doAlign':
BUILDSTDERR: order.c:409:5: warning: implicit declaration of function 'printMFAAlign'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration]
BUILDSTDERR:   409 |     printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
BUILDSTDERR:       |     ^~~~~~~~~~~~~
BUILDSTDERR:       |     printBinAlign
BUILDSTDERR: order.c:411:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printTextAlign'? [-Wimplicit-function-declaration]
BUILDSTDERR:   411 |     printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~
BUILDSTDERR:       |     printTextAlign
BUILDSTDERR: anchors.c: In function 'hptrcomp':
BUILDSTDERR: anchors.c:49:7: warning: unused variable 'jt' [-Wunused-variable]
BUILDSTDERR:    49 |   int jt = ((hptr*)p2)->isstart;
BUILDSTDERR:       |       ^~
BUILDSTDERR: order.c: In function 'getChain':
BUILDSTDERR: order.c:486:7: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   486 |   int temp;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: order.c: In function 'saveNeck':
BUILDSTDERR: order.c:561:6: warning: unused variable 'second' [-Wunused-variable]
BUILDSTDERR:   561 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
BUILDSTDERR:       |      ^~~~~~
BUILDSTDERR: order.c:560:9: warning: unused variable 'first' [-Wunused-variable]
BUILDSTDERR:   560 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: order.c: In function 'joinAligns':
BUILDSTDERR: order.c:586:10: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:   586 |   align *n = a->nextalign, *t;
BUILDSTDERR:       |          ^
BUILDSTDERR: anchors.c: In function 'doOutput':
BUILDSTDERR: anchors.c:171:17: warning: unused variable 'bestscore' [-Wunused-variable]
BUILDSTDERR:   171 |   int chl=0, i, bestscore=-1;
BUILDSTDERR:       |                 ^~~~~~~~~
BUILDSTDERR: anchors.c:171:14: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   171 |   int chl=0, i, bestscore=-1;
BUILDSTDERR:       |              ^
BUILDSTDERR: anchors.c:168:7: warning: variable 'len' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   168 |   int len;
BUILDSTDERR:       |       ^~~
BUILDSTDERR: order.c: In function 'printBinAlign':
BUILDSTDERR: order.c:718:23: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:   718 |       left = lets[seq1[s1++]];
BUILDSTDERR:       |                   ~~~~^~~~~~
BUILDSTDERR: order.c:720:24: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:   720 |       right = lets[seq2[s2++]];
BUILDSTDERR:       |                    ~~~~^~~~~~
BUILDSTDERR: order.c: In function 'printMFAAlign':
BUILDSTDERR: order.c:773:27: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:   773 |   int nm=0, nga=0, ngb=0, nlets=0;
BUILDSTDERR:       |                           ^~~~~
BUILDSTDERR: order.c:773:7: warning: unused variable 'nm' [-Wunused-variable]
BUILDSTDERR:   773 |   int nm=0, nga=0, ngb=0, nlets=0;
BUILDSTDERR:       |       ^~
BUILDSTDERR: order.c: In function 'printXMFAAlign':
BUILDSTDERR: order.c:805:27: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:   805 |   int nm=0, nga=0, ngb=0, nlets=0;
BUILDSTDERR:       |                           ^~~~~
BUILDSTDERR: order.c:805:7: warning: unused variable 'nm' [-Wunused-variable]
BUILDSTDERR:   805 |   int nm=0, nga=0, ngb=0, nlets=0;
BUILDSTDERR:       |       ^~
BUILDSTDERR: order.c: In function 'readfile':
BUILDSTDERR: order.c:61:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    61 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: order.c: In function 'readSubstMatrix':
BUILDSTDERR: order.c:145:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   145 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: order.c:149:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   149 |   fscanf (file, "%d", &gapstart);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: order.c:150:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   150 |   fscanf (file, "%d", &gapcont);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: anchors.c: In function 'GetLine':
BUILDSTDERR: anchors.c:232:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   232 |   fgets(temp, 1024, infile);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: mlagan.c: In function 'hptrcomp':
BUILDSTDERR: mlagan.c:38:7: warning: unused variable 'jt' [-Wunused-variable]
BUILDSTDERR:    38 |   int jt = ((hptr*)p2)->isstart;
BUILDSTDERR:       |       ^~
BUILDSTDERR: mlagan.c: In function 'readfile':
BUILDSTDERR: mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
BUILDSTDERR:    93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
BUILDSTDERR:       |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: mlagan.c: In function 'getAnchsFromFile':
BUILDSTDERR: mlagan.c:161:29: warning: unused variable 'first' [-Wunused-variable]
BUILDSTDERR:   161 |   hll *myres = 0, *tt = 0, *first = 0;
BUILDSTDERR:       |                             ^~~~~
BUILDSTDERR: mlagan.c: In function 'generateAnchors':
BUILDSTDERR: mlagan.c:213:8: warning: unused variable 'flip' [-Wunused-variable]
BUILDSTDERR:   213 |   char flip = 0;
BUILDSTDERR:       |        ^~~~
BUILDSTDERR: mlagan.c:211:10: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   211 |   align* temp;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: mlagan.c: In function 'remakeHLL':
BUILDSTDERR: mlagan.c:310:10: warning: unused variable 'bestscore' [-Wunused-variable]
BUILDSTDERR:   310 |   int i, bestscore=-1;
BUILDSTDERR:       |          ^~~~~~~~~
BUILDSTDERR: mlagan.c:310:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   310 |   int i, bestscore=-1;
BUILDSTDERR:       |       ^
BUILDSTDERR: mlagan.c:309:20: warning: unused variable 't3' [-Wunused-variable]
BUILDSTDERR:   309 |   hll *temp, *t2, *t3;
BUILDSTDERR:       |                    ^~
BUILDSTDERR: mlagan.c:309:15: warning: unused variable 't2' [-Wunused-variable]
BUILDSTDERR:   309 |   hll *temp, *t2, *t3;
BUILDSTDERR:       |               ^~
BUILDSTDERR: mlagan.c:307:7: warning: unused variable 'len' [-Wunused-variable]
BUILDSTDERR:   307 |   int len;
BUILDSTDERR:       |       ^~~
BUILDSTDERR: order.c: In function 'printBinAlign':
BUILDSTDERR: order.c:725:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   725 | }
BUILDSTDERR:       | ^
BUILDSTDERR: order.c: In function 'printTextAlign':
BUILDSTDERR: order.c:769:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   769 | }
BUILDSTDERR:       | ^
BUILDSTDERR: order.c: In function 'printMFAAlign':
BUILDSTDERR: order.c:801:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   801 | }
BUILDSTDERR:       | ^
BUILDSTDERR: mlagan.c: In function 'iterativeImprovement':
BUILDSTDERR: mlagan.c:485:10: warning: unused variable 'readd' [-Wunused-variable]
BUILDSTDERR:   485 |   align *readd, *old, *new;
BUILDSTDERR:       |          ^~~~~
BUILDSTDERR: mlagan.c:483:12: warning: unused variable 'oldscore' [-Wunused-variable]
BUILDSTDERR:   483 |   int i=0, oldscore, cutoff;
BUILDSTDERR:       |            ^~~~~~~~
BUILDSTDERR: order.c: In function 'printXMFAAlign':
BUILDSTDERR: fchaos.c: In function 'removeDups':
BUILDSTDERR: fchaos.c:302:24: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   302 |   hll *i, *j, *jprev, *temp;
BUILDSTDERR:       |                        ^~~~
BUILDSTDERR: order.c:833:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   833 | }
BUILDSTDERR:       | ^
BUILDSTDERR: mlagan.c: In function 'treeToRPN':
BUILDSTDERR: mlagan.c:528:16: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   528 |   int i=0; int j, k;
BUILDSTDERR:       |                ^
BUILDSTDERR: fchaos.c: In function 'readfile':
BUILDSTDERR: fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args]
BUILDSTDERR:   357 |  fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
BUILDSTDERR:       |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c: In function 'chain':
BUILDSTDERR: fchaos.c:401:16: warning: unused variable 'd2' [-Wunused-variable]
BUILDSTDERR:   401 |   int i, d1=0, d2=0;
BUILDSTDERR:       |                ^~
BUILDSTDERR: fchaos.c:401:10: warning: unused variable 'd1' [-Wunused-variable]
BUILDSTDERR:   401 |   int i, d1=0, d2=0;
BUILDSTDERR:       |          ^~
BUILDSTDERR: fchaos.c:401:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   401 |   int i, d1=0, d2=0;
BUILDSTDERR:       |       ^
BUILDSTDERR: fchaos.c: In function 'findPrev':
BUILDSTDERR: fchaos.c:440:7: warning: unused variable 'doneset' [-Wunused-variable]
BUILDSTDERR:   440 |   int doneset = 0;
BUILDSTDERR:       |       ^~~~~~~
BUILDSTDERR: fchaos.c: In function 'doAlgo':
BUILDSTDERR: fchaos.c:543:24: warning: unused variable 'bestdbaseloc' [-Wunused-variable]
BUILDSTDERR:   543 |   int bestqueryloc=-1, bestdbaseloc=-1, numhits;
BUILDSTDERR:       |                        ^~~~~~~~~~~~
BUILDSTDERR: fchaos.c:543:7: warning: unused variable 'bestqueryloc' [-Wunused-variable]
BUILDSTDERR:   543 |   int bestqueryloc=-1, bestdbaseloc=-1, numhits;
BUILDSTDERR:       |       ^~~~~~~~~~~~
BUILDSTDERR: fchaos.c:542:9: warning: unused variable 'bestscore' [-Wunused-variable]
BUILDSTDERR:   542 |   float bestscore=-1, baseval;
BUILDSTDERR:       |         ^~~~~~~~~
BUILDSTDERR: mlagan.c: In function 'main':
BUILDSTDERR: mlagan.c:1067:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration]
BUILDSTDERR:  1067 |     printXMFAAlign(outfile, final);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~
BUILDSTDERR:       |     printFASTAAlign
BUILDSTDERR: mlagan.c:942:8: warning: unused variable 'command' [-Wunused-variable]
BUILDSTDERR:   942 |   char command[256];
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: mlagan.c:941:24: warning: unused variable 'y' [-Wunused-variable]
BUILDSTDERR:   941 |   int i = 1, j = 1, x, y;
BUILDSTDERR:       |                        ^
BUILDSTDERR: mlagan.c:941:21: warning: unused variable 'x' [-Wunused-variable]
BUILDSTDERR:   941 |   int i = 1, j = 1, x, y;
BUILDSTDERR:       |                     ^
BUILDSTDERR: mlagan.c:939:14: warning: unused variable 'seqfile' [-Wunused-variable]
BUILDSTDERR:   939 |   FileBuffer seqfile;
BUILDSTDERR:       |              ^~~~~~~
BUILDSTDERR: fchaos.c: In function 'main':
BUILDSTDERR: fchaos.c:885:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   885 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: fchaos.c: In function 'saveScore':
BUILDSTDERR: fchaos.c:970:7: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   970 |   int temp;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: mlagan.c: In function 'readfile':
BUILDSTDERR: mlagan.c:79:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    79 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c: In function 'savenfreeLList':
BUILDSTDERR: fchaos.c:1137:9: warning: variable 'j' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1137 |   int i,j;
BUILDSTDERR:       |         ^
BUILDSTDERR: mlagan.c: In function 'treeToRPN':
BUILDSTDERR: mlagan.c:565:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   565 | }
BUILDSTDERR:       | ^
BUILDSTDERR: fchaos.c: In function 'readfile':
BUILDSTDERR: fchaos.c:344:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   344 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c: In function 'readSubstMatrix':
BUILDSTDERR: fchaos.c:622:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   622 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c:627:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   627 |   fscanf (file, "%d", &gappenstart);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c:628:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   628 |   fscanf (file, "%d", &gappenext);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: anchors.c: In function 'findBestChain':
BUILDSTDERR: anchors.c:164:10: warning: 'bestptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   164 |   return (hll*)bestptr->myelem;
BUILDSTDERR:       |          ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: skiplist.c: In function 'printSLE':
BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
BUILDSTDERR:    12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
BUILDSTDERR:       |                  ~^                 ~~~~~~~~~~~
BUILDSTDERR:       |                   |                    |
BUILDSTDERR:       |                   unsigned int         void *
BUILDSTDERR:       |                  %p
BUILDSTDERR: skiplist.c: In function 'makeSkLst':
BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:    33 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: skiplist.c: In function 'SLinsert':
BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
BUILDSTDERR:   100 |   sle* prev = SLfind(trgt, index), *tbe;
BUILDSTDERR:       |                                     ^~~
BUILDSTDERR: mlagan.c: In function 'buildTree':
BUILDSTDERR: mlagan.c:597:12: warning: 'mlj' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   597 |   int mli, mlj;
BUILDSTDERR:       |            ^~~
BUILDSTDERR: mlagan.c:597:7: warning: 'mli' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   597 |   int mli, mlj;
BUILDSTDERR:       |       ^~~
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
BUILDSTDERR: prolagan.c: In function 'hptrcomp':
BUILDSTDERR: prolagan.c:41:7: warning: unused variable 'jt' [-Wunused-variable]
BUILDSTDERR:    41 |   int jt = ((hptr*)p2)->isstart;
BUILDSTDERR:       |       ^~
BUILDSTDERR: prolagan.c: In function 'readfile':
BUILDSTDERR: prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
BUILDSTDERR:    93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
BUILDSTDERR:       |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: prolagan.c: In function 'appendAlignProfile':
BUILDSTDERR: prolagan.c:163:9: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   163 |   int i,j,k;
BUILDSTDERR:       |         ^
BUILDSTDERR: prolagan.c: In function 'readProfile':
BUILDSTDERR: prolagan.c:198:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
BUILDSTDERR:   198 |   while ( myseq = FileRead( with_gaps,0,0,VER_MLAGAN )) {
BUILDSTDERR:       |           ^~~~~
BUILDSTDERR: prolagan.c: In function 'getAnchsFromFile':
BUILDSTDERR: prolagan.c:246:29: warning: unused variable 'first' [-Wunused-variable]
BUILDSTDERR:   246 |   hll *myres = 0, *tt = 0, *first = 0;
BUILDSTDERR:       |                             ^~~~~
BUILDSTDERR: prolagan.c: In function 'generateAnchors':
BUILDSTDERR: prolagan.c:298:8: warning: unused variable 'flip' [-Wunused-variable]
BUILDSTDERR:   298 |   char flip = 0;
BUILDSTDERR:       |        ^~~~
BUILDSTDERR: prolagan.c:296:10: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   296 |   align* temp;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: prolagan.c: In function 'remakeHLL':
BUILDSTDERR: prolagan.c:395:10: warning: unused variable 'bestscore' [-Wunused-variable]
BUILDSTDERR:   395 |   int i, bestscore=-1;
BUILDSTDERR:       |          ^~~~~~~~~
BUILDSTDERR: prolagan.c:395:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   395 |   int i, bestscore=-1;
BUILDSTDERR:       |       ^
BUILDSTDERR: prolagan.c:394:20: warning: unused variable 't3' [-Wunused-variable]
BUILDSTDERR:   394 |   hll *temp, *t2, *t3;
BUILDSTDERR:       |                    ^~
BUILDSTDERR: prolagan.c:394:15: warning: unused variable 't2' [-Wunused-variable]
BUILDSTDERR:   394 |   hll *temp, *t2, *t3;
BUILDSTDERR:       |               ^~
BUILDSTDERR: prolagan.c:392:7: warning: unused variable 'len' [-Wunused-variable]
BUILDSTDERR:   392 |   int len;
BUILDSTDERR:       |       ^~~
BUILDSTDERR: prolagan.c: In function 'processAnchors':
BUILDSTDERR: prolagan.c:539:36: warning: unused variable 'uni' [-Wunused-variable]
BUILDSTDERR:   539 |   align *first, *second, *result, *uni;
BUILDSTDERR:       |                                    ^~~
BUILDSTDERR: prolagan.c: In function 'iterativeImprovement':
BUILDSTDERR: prolagan.c:587:10: warning: unused variable 'readd' [-Wunused-variable]
BUILDSTDERR:   587 |   align *readd, *old, *new;
BUILDSTDERR:       |          ^~~~~
BUILDSTDERR: prolagan.c:585:12: warning: unused variable 'oldscore' [-Wunused-variable]
BUILDSTDERR:   585 |   int i=0, oldscore, cutoff;
BUILDSTDERR:       |            ^~~~~~~~
BUILDSTDERR: prolagan.c: In function 'treeToRPN':
BUILDSTDERR: prolagan.c:630:16: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   630 |   int i=0; int j, k;
BUILDSTDERR:       |                ^
BUILDSTDERR: prolagan.c: In function 'main':
BUILDSTDERR: prolagan.c:1087:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration]
BUILDSTDERR:  1087 |     printXMFAAlign(outfile, final);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~
BUILDSTDERR:       |     printFASTAAlign
BUILDSTDERR: prolagan.c:966:8: warning: unused variable 'table' [-Wunused-variable]
BUILDSTDERR:   966 |   hll* table[MAX_SEQ][MAX_SEQ];
BUILDSTDERR:       |        ^~~~~
BUILDSTDERR: prolagan.c:960:8: warning: unused variable 'command' [-Wunused-variable]
BUILDSTDERR:   960 |   char command[256];
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: prolagan.c:954:14: warning: unused variable 'seqfile' [-Wunused-variable]
BUILDSTDERR:   954 |   FileBuffer seqfile;
BUILDSTDERR:       |              ^~~~~~~
BUILDSTDERR: prolagan.c: In function 'readfile':
BUILDSTDERR: prolagan.c:79:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    79 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: prolagan.c: In function 'treeToRPN':
BUILDSTDERR: prolagan.c:667:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   667 | }
BUILDSTDERR:       | ^
BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr':
BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
BUILDSTDERR:   155 |   char res;
BUILDSTDERR:       |        ^~~
BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
BUILDSTDERR:   154 |   int dn = x+y-1, loc;
BUILDSTDERR:       |                   ^~~
BUILDSTDERR: fchaos.c: In function 'doTranslated':
BUILDSTDERR: fchaos.c:865:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   865 |       procPairs(currquery, currdbase);
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: fchaos.c: In function 'main':
BUILDSTDERR: fchaos.c:955:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   955 |       procPairs(currquery, currdbase);
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c: In function 'getAnchsFromAlign':
BUILDSTDERR: multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable]
BUILDSTDERR:   104 |   float peakfrac;
BUILDSTDERR:       |         ^~~~~~~~
BUILDSTDERR: multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable]
BUILDSTDERR:   103 |   char ingap = 0, isfrst = 1;
BUILDSTDERR:       |                   ^~~~~~
BUILDSTDERR: multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable]
BUILDSTDERR:    99 |   int currscore=0, oldscore, peakscore;
BUILDSTDERR:       |                              ^~~~~~~~~
BUILDSTDERR: multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable]
BUILDSTDERR:    99 |   int currscore=0, oldscore, peakscore;
BUILDSTDERR:       |                    ^~~~~~~~
BUILDSTDERR: multial.c: In function 'unifyAlign':
BUILDSTDERR: multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable]
BUILDSTDERR:   188 |   int s1 = 0, s2 = 0, tgs, tgc;
BUILDSTDERR:       |                            ^~~
BUILDSTDERR: multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable]
BUILDSTDERR:   188 |   int s1 = 0, s2 = 0, tgs, tgc;
BUILDSTDERR:       |                       ^~~
BUILDSTDERR: multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable]
BUILDSTDERR:   187 |   int i,j,k, cbc, brcount;
BUILDSTDERR:       |                   ^~~~~~~
BUILDSTDERR: multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable]
BUILDSTDERR:   187 |   int i,j,k, cbc, brcount;
BUILDSTDERR:       |              ^~~
BUILDSTDERR: multial.c: In function 'getChain':
BUILDSTDERR: multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   247 |   int temp;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: multial.c: In function 'saveNeck':
BUILDSTDERR: multial.c:358:6: warning: unused variable 'second' [-Wunused-variable]
BUILDSTDERR:   358 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
BUILDSTDERR:       |      ^~~~~~
BUILDSTDERR: multial.c:357:9: warning: unused variable 'first' [-Wunused-variable]
BUILDSTDERR:   357 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: multial.c: In function 'joinAligns':
BUILDSTDERR: multial.c:381:10: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:   381 |   align *n = a->nextalign, *t;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c: In function 'openGap':
BUILDSTDERR: multial.c:594:25: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   594 |   int alopen, pen, sav, i;
BUILDSTDERR:       |                         ^
BUILDSTDERR: multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable]
BUILDSTDERR:   594 |   int alopen, pen, sav, i;
BUILDSTDERR:       |               ^~~
BUILDSTDERR: multial.c: In function 'mkBarrel':
BUILDSTDERR: multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable]
BUILDSTDERR:   615 |   int incr;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: multial.c: In function 'doNW':
BUILDSTDERR: multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   811 |   int numNecks =0, oldneck =0;
BUILDSTDERR:       |                    ^~~~~~~
BUILDSTDERR: multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable]
BUILDSTDERR:   808 |   char rh, ptr=0, isneck;
BUILDSTDERR:       |        ^~
BUILDSTDERR: multial.c:807:14: warning: unused variable 'b' [-Wunused-variable]
BUILDSTDERR:   807 |   align* a, *b;
BUILDSTDERR:       |              ^
BUILDSTDERR: multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable]
BUILDSTDERR:   805 |   int tt, prevgap;
BUILDSTDERR:       |           ^~~~~~~
BUILDSTDERR: multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable]
BUILDSTDERR:   805 |   int tt, prevgap;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable]
BUILDSTDERR:   804 |   int gapend[3];
BUILDSTDERR:       |       ^~~~~~
BUILDSTDERR: multial.c: In function 'removeSeqByName':
BUILDSTDERR: multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1062 |   seq *removed;
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: multial.c: In function 'getSeqNum':
BUILDSTDERR: multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable]
BUILDSTDERR:  1073 |   seq *removed;
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: multial.c: In function 'remapHLLs':
BUILDSTDERR: multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
BUILDSTDERR:  1262 |  if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
BUILDSTDERR:       |                 ^
BUILDSTDERR: multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable]
BUILDSTDERR:  1104 |   int mybp, i, *searchint, stmybp, mylen, olen, osize;
BUILDSTDERR:       |                                           ^~~~
BUILDSTDERR: multial.c: In function 'hllJoin':
BUILDSTDERR: multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1352 |   int i, j;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:  1352 |   int i, j;
BUILDSTDERR:       |       ^
BUILDSTDERR: multial.c: In function 'minHLL':
BUILDSTDERR: multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1368 |   int i, j;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c: In function 'mergeHLLs':
BUILDSTDERR: multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1408 |   int i, j, mscore;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:  1408 |   int i, j, mscore;
BUILDSTDERR:       |       ^
BUILDSTDERR: multial.c: In function 'printTextAlign':
BUILDSTDERR: multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1466 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1465 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1465 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: In function 'printFASTAAlign':
BUILDSTDERR: multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1525 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1524 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1524 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: In function 'printXMFAAlign':
BUILDSTDERR: multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1553 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1552 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1552 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: At top level:
BUILDSTDERR: multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static
BUILDSTDERR:   603 |   sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) |
BUILDSTDERR:       |         ^~~~~~~~
BUILDSTDERR: multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static
BUILDSTDERR:   586 |   return gapcache[(v(other->cnts[CNTS_GS][ow])) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static
BUILDSTDERR:   581 |   return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static
BUILDSTDERR:   576 |   return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static
BUILDSTDERR:   570 |   return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static
BUILDSTDERR:   563 |   return matchcache[v(other->cnts[0][ow]) |
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static
BUILDSTDERR:   556 |     gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) |
BUILDSTDERR:       |     ^~~~~~~~
BUILDSTDERR: multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static
BUILDSTDERR:   552 |     matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
BUILDSTDERR:       |     ^~~~~~~~~~
BUILDSTDERR: multial.c: In function 'scoreLocal':
BUILDSTDERR: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:    84 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'readSubstMatrix':
BUILDSTDERR: multial.c:478:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   478 |       fscanf (file, "%d", &k);
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c:486:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   486 |   fscanf (file, "%d", &gapstart);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c:487:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   487 |   fscanf (file, "%d", &gapcont);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c: In function 'removeSeqByName':
BUILDSTDERR: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1068 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printTextAlign':
BUILDSTDERR: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1521 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printFASTAAlign':
BUILDSTDERR: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1549 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printXMFAAlign':
BUILDSTDERR: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1579 | }
BUILDSTDERR:       | ^
BUILDSTDERR: thrtrie.c: In function 'makeAlpha':
BUILDSTDERR: thrtrie.c:33:15: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:    33 |       indeces[*alpha] = i;
BUILDSTDERR:       |               ^~~~~~
BUILDSTDERR: thrtrie.c:35:19: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:    35 |     else indeces [*alpha] = i++;
BUILDSTDERR:       |                   ^~~~~~
BUILDSTDERR: thrtrie.c: In function 'lookup':
BUILDSTDERR: thrtrie.c:42:17: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:    42 |   return indeces[c];
BUILDSTDERR:       |                 ^
BUILDSTDERR: thrtrie.c: In function 'insertString':
BUILDSTDERR: thrtrie.c:174:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   174 |   int i, j, wordlen = root->height, letprev, letcurr;
BUILDSTDERR:       |          ^
BUILDSTDERR: In file included from thrtrie.c:13:
BUILDSTDERR: mempage.c: In function 'MPallfree':
BUILDSTDERR: mempage.c:48:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:    48 | }
BUILDSTDERR:       | ^
BUILDSTDERR: filebuffer.c: In function 'FileRead':
BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
BUILDSTDERR:   123 |     temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
BUILDSTDERR:       |                                  ^~~~~~~
BUILDSTDERR: skiplist.c: In function 'printSLE':
BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
BUILDSTDERR:    12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
BUILDSTDERR:       |                  ~^                 ~~~~~~~~~~~
BUILDSTDERR:       |                   |                    |
BUILDSTDERR:       |                   unsigned int         void *
BUILDSTDERR:       |                  %p
BUILDSTDERR: skiplist.c: In function 'makeSkLst':
BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:    33 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: skiplist.c: In function 'SLinsert':
BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
BUILDSTDERR:   100 |   sle* prev = SLfind(trgt, index), *tbe;
BUILDSTDERR:       |                                     ^~~
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2mf utils/bin2mf.c
BUILDSTDERR: multial.c: In function 'getAnchsFromAlign':
BUILDSTDERR: multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable]
BUILDSTDERR:   104 |   float peakfrac;
BUILDSTDERR:       |         ^~~~~~~~
BUILDSTDERR: multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable]
BUILDSTDERR:   103 |   char ingap = 0, isfrst = 1;
BUILDSTDERR:       |                   ^~~~~~
BUILDSTDERR: multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable]
BUILDSTDERR:    99 |   int currscore=0, oldscore, peakscore;
BUILDSTDERR:       |                              ^~~~~~~~~
BUILDSTDERR: multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable]
BUILDSTDERR:    99 |   int currscore=0, oldscore, peakscore;
BUILDSTDERR:       |                    ^~~~~~~~
BUILDSTDERR: multial.c: In function 'unifyAlign':
BUILDSTDERR: multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable]
BUILDSTDERR:   188 |   int s1 = 0, s2 = 0, tgs, tgc;
BUILDSTDERR:       |                            ^~~
BUILDSTDERR: multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable]
BUILDSTDERR:   188 |   int s1 = 0, s2 = 0, tgs, tgc;
BUILDSTDERR:       |                       ^~~
BUILDSTDERR: multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable]
BUILDSTDERR:   187 |   int i,j,k, cbc, brcount;
BUILDSTDERR:       |                   ^~~~~~~
BUILDSTDERR: multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable]
BUILDSTDERR:   187 |   int i,j,k, cbc, brcount;
BUILDSTDERR:       |              ^~~
BUILDSTDERR: multial.c: In function 'getChain':
BUILDSTDERR: multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   247 |   int temp;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: multial.c: In function 'saveNeck':
BUILDSTDERR: multial.c:358:6: warning: unused variable 'second' [-Wunused-variable]
BUILDSTDERR:   358 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
BUILDSTDERR:       |      ^~~~~~
BUILDSTDERR: multial.c:357:9: warning: unused variable 'first' [-Wunused-variable]
BUILDSTDERR:   357 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: multial.c: In function 'joinAligns':
BUILDSTDERR: multial.c:381:10: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:   381 |   align *n = a->nextalign, *t;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c: In function 'openGap':
BUILDSTDERR: multial.c:594:25: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   594 |   int alopen, pen, sav, i;
BUILDSTDERR:       |                         ^
BUILDSTDERR: multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable]
BUILDSTDERR:   594 |   int alopen, pen, sav, i;
BUILDSTDERR:       |               ^~~
BUILDSTDERR: multial.c: In function 'mkBarrel':
BUILDSTDERR: multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable]
BUILDSTDERR:   615 |   int incr;
BUILDSTDERR:       |       ^~~~
BUILDSTDERR: multial.c: In function 'doNW':
BUILDSTDERR: multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   811 |   int numNecks =0, oldneck =0;
BUILDSTDERR:       |                    ^~~~~~~
BUILDSTDERR: multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable]
BUILDSTDERR:   808 |   char rh, ptr=0, isneck;
BUILDSTDERR:       |        ^~
BUILDSTDERR: multial.c:807:14: warning: unused variable 'b' [-Wunused-variable]
BUILDSTDERR:   807 |   align* a, *b;
BUILDSTDERR:       |              ^
BUILDSTDERR: multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable]
BUILDSTDERR:   805 |   int tt, prevgap;
BUILDSTDERR:       |           ^~~~~~~
BUILDSTDERR: multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable]
BUILDSTDERR:   805 |   int tt, prevgap;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable]
BUILDSTDERR:   804 |   int gapend[3];
BUILDSTDERR:       |       ^~~~~~
BUILDSTDERR: multial.c: In function 'removeSeqByName':
BUILDSTDERR: multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1062 |   seq *removed;
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: multial.c: In function 'getSeqNum':
BUILDSTDERR: multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable]
BUILDSTDERR:  1073 |   seq *removed;
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: multial.c: In function 'remapHLLs':
BUILDSTDERR: multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
BUILDSTDERR:  1262 |  if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
BUILDSTDERR:       |                 ^
BUILDSTDERR: multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable]
BUILDSTDERR:  1104 |   int mybp, i, *searchint, stmybp, mylen, olen, osize;
BUILDSTDERR:       |                                           ^~~~
BUILDSTDERR: multial.c: In function 'hllJoin':
BUILDSTDERR: multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1352 |   int i, j;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:  1352 |   int i, j;
BUILDSTDERR:       |       ^
BUILDSTDERR: multial.c: In function 'minHLL':
BUILDSTDERR: multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1368 |   int i, j;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c: In function 'mergeHLLs':
BUILDSTDERR: multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:  1408 |   int i, j, mscore;
BUILDSTDERR:       |          ^
BUILDSTDERR: multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:  1408 |   int i, j, mscore;
BUILDSTDERR:       |       ^
BUILDSTDERR: multial.c: In function 'printTextAlign':
BUILDSTDERR: multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1466 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1465 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1465 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: In function 'printFASTAAlign':
BUILDSTDERR: multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1525 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1524 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1524 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: In function 'printXMFAAlign':
BUILDSTDERR: multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable]
BUILDSTDERR:  1553 |   int nlets=0;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable]
BUILDSTDERR:  1552 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |             ^~
BUILDSTDERR: multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable]
BUILDSTDERR:  1552 |   int s1=0, s2=0, c, k, i;
BUILDSTDERR:       |       ^~
BUILDSTDERR: multial.c: At top level:
BUILDSTDERR: multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static
BUILDSTDERR:   603 |   sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) |
BUILDSTDERR:       |         ^~~~~~~~
BUILDSTDERR: multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static
BUILDSTDERR:   586 |   return gapcache[(v(other->cnts[CNTS_GS][ow])) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static
BUILDSTDERR:   581 |   return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static
BUILDSTDERR:   576 |   return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static
BUILDSTDERR:   570 |   return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
BUILDSTDERR:       |          ^~~~~~~~
BUILDSTDERR: multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static
BUILDSTDERR:   563 |   return matchcache[v(other->cnts[0][ow]) |
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static
BUILDSTDERR:   556 |     gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) |
BUILDSTDERR:       |     ^~~~~~~~
BUILDSTDERR: multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static
BUILDSTDERR:   552 |     matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
BUILDSTDERR:       |     ^~~~~~~~~~
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2bl utils/bin2bl.c
BUILDSTDERR: multial.c: In function 'scoreLocal':
BUILDSTDERR: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:    84 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'readSubstMatrix':
BUILDSTDERR: multial.c:478:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   478 |       fscanf (file, "%d", &k);
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c:486:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   486 |   fscanf (file, "%d", &gapstart);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c:487:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   487 |   fscanf (file, "%d", &gapcont);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: multial.c: In function 'removeSeqByName':
BUILDSTDERR: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1068 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printTextAlign':
BUILDSTDERR: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1521 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printFASTAAlign':
BUILDSTDERR: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1549 | }
BUILDSTDERR:       | ^
BUILDSTDERR: multial.c: In function 'printXMFAAlign':
BUILDSTDERR: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:  1579 | }
BUILDSTDERR:       | ^
BUILDSTDERR: utils/bin2bl.c: In function 'main':
BUILDSTDERR: utils/bin2bl.c:52:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
BUILDSTDERR:    52 |   if (argv[1][0] == '-')
BUILDSTDERR:       |      ^
BUILDSTDERR: utils/bin2bl.c:22:7: warning: unused variable 'width' [-Wunused-variable]
BUILDSTDERR:    22 |   int width = 60;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: global.c: In function 'ismatch':
BUILDSTDERR: global.c:12:17: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:    12 |   return indeces[a] == indeces[b];
BUILDSTDERR:       |                 ^
BUILDSTDERR: global.c:12:31: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:    12 |   return indeces[a] == indeces[b];
BUILDSTDERR:       |                               ^
BUILDSTDERR: global.c: In function 'global':
BUILDSTDERR: global.c:34:31: warning: unused variable 'score' [-Wunused-variable]
BUILDSTDERR:    34 |   int mm = end2 - start2 + 1, score;
BUILDSTDERR:       |                               ^~~~~
BUILDSTDERR: global.c: In function 'printalign':
BUILDSTDERR: global.c:172:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   172 | }
BUILDSTDERR:       | ^
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/cextract utils/cextract.c
BUILDSTDERR: utils/cextract.c: In function 'getLength':
BUILDSTDERR: utils/cextract.c:16:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    16 |   fgets (buffer, 1024, file);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/cextract.c: In function 'readfile':
BUILDSTDERR: utils/cextract.c:41:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    41 |     fgets (buffer, 1024, file);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: translate.c: In function 'toPeptide':
BUILDSTDERR: translate.c:9:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:     9 |   int i, j, sum=0, mask = 0;
BUILDSTDERR:       |          ^
BUILDSTDERR: utils/cextract.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    59 |     if (ch == '>') ungetc (ch, file);
BUILDSTDERR:       |        ^
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/cstat utils/cstat.c
BUILDSTDERR: filebuffer.c: In function 'FileRead':
BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
BUILDSTDERR:   123 |     temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
BUILDSTDERR:       |                                  ^~~~~~~
BUILDSTDERR: utils/cstat.c: In function 'cntlets':
BUILDSTDERR: utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration]
BUILDSTDERR:    51 |     if (!isspace(currchar)) {
BUILDSTDERR:       |          ^~~~~~~
BUILDSTDERR: utils/cstat.c:52:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
BUILDSTDERR:    52 |       currchar = toupper(currchar);
BUILDSTDERR:       |                  ^~~~~~~
BUILDSTDERR: utils/cstat.c: In function 'main':
BUILDSTDERR: utils/cstat.c:234:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   234 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: utils/cstat.c: In function 'cntlets':
BUILDSTDERR: utils/cstat.c:44:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    44 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/cstat.c: In function 'readseq':
BUILDSTDERR: utils/cstat.c:67:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    67 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /usr/bin/ld: /tmp/ccTn9NAo.o: in function `chain':
BUILDSTDERR: /builddir/build/BUILD/lagan20/src/fchaos.c:412: undefined reference to `findPrev'
BUILDSTDERR: collect2: error: ld returned 1 exit status
BUILDSTDERR: make[1]: *** [Makefile:14: ../chaos] Error 1
BUILDSTDERR: make[1]: *** Waiting for unfinished jobs....
BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr':
BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
BUILDSTDERR:   155 |   char res;
BUILDSTDERR:       |        ^~~
BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
BUILDSTDERR:   154 |   int dn = x+y-1, loc;
BUILDSTDERR:       |                   ^~~
BUILDSTDERR: skiplist.c: In function 'printSLE':
BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
BUILDSTDERR:    12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
BUILDSTDERR:       |                  ~^                 ~~~~~~~~~~~
BUILDSTDERR:       |                   |                    |
BUILDSTDERR:       |                   unsigned int         void *
BUILDSTDERR:       |                  %p
BUILDSTDERR: skiplist.c: In function 'makeSkLst':
BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:    33 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: skiplist.c: In function 'SLinsert':
BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
BUILDSTDERR:   100 |   sle* prev = SLfind(trgt, index), *tbe;
BUILDSTDERR:       |                                     ^~~
BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr':
BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable]
BUILDSTDERR:   155 |   char res;
BUILDSTDERR:       |        ^~~
BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable]
BUILDSTDERR:   154 |   int dn = x+y-1, loc;
BUILDSTDERR:       |                   ^~~
BUILDSTDERR: filebuffer.c: In function 'FileRead':
BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
BUILDSTDERR:   123 |     temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
BUILDSTDERR:       |                                  ^~~~~~~
BUILDSTDERR: skiplist.c: In function 'printSLE':
BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
BUILDSTDERR:    12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
BUILDSTDERR:       |                  ~^                 ~~~~~~~~~~~
BUILDSTDERR:       |                   |                    |
BUILDSTDERR:       |                   unsigned int         void *
BUILDSTDERR:       |                  %p
BUILDSTDERR: skiplist.c: In function 'makeSkLst':
BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:    33 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: skiplist.c: In function 'SLinsert':
BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable]
BUILDSTDERR:   100 |   sle* prev = SLfind(trgt, index), *tbe;
BUILDSTDERR:       |                                     ^~~
BUILDSTDERR: filebuffer.c: In function 'FileRead':
BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
BUILDSTDERR:   123 |     temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
BUILDSTDERR:       |                                  ^~~~~~~
make[1]: Leaving directory '/builddir/build/BUILD/lagan20/src'
BUILDSTDERR: make: *** [Makefile:2: all] Error 2
RPM build errors:
BUILDSTDERR: error: Bad exit status from /var/tmp/rpm-tmp.BzldMu (%build)
BUILDSTDERR:     Bad exit status from /var/tmp/rpm-tmp.BzldMu (%build)
Child return code was: 1
EXCEPTION: [Error()]
Traceback (most recent call last):
  File "/usr/lib/python3.7/site-packages/mockbuild/trace_decorator.py", line 96, in trace
    result = func(*args, **kw)
  File "/usr/lib/python3.7/site-packages/mockbuild/util.py", line 700, in do
    raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode)
mockbuild.exception.Error: Command failed: 
 # bash --login -c /usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec