Mock Version: 1.4.16
Mock Version: 1.4.16
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f32-build-17483886-1260801/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff888ff1d0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --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': 'C.UTF-8'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1568073600
Wrote: /builddir/build/SRPMS/lagan-2.0-27.fc32.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f32-build-17483886-1260801/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff888ff1d0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --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': 'C.UTF-8'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1568073600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ol4kUS
+ 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 .
Patch #0 (lagan20-chris.patch):
+ echo '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
+ sed -i 's/^inline /inline __attribute__ ((always_inline)) /' src/fchaos.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/filebuffer.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/scorecontigs.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/overlay.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/cstat.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.FCZeoR
+ 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 -m64 -mcpu=power8 -mtune=power8 -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 -m64 -mcpu=power8 -mtune=power8 -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 -m64 -mcpu=power8 -mtune=power8 -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 -m64 -mcpu=power8 -mtune=power8 -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 -m64 -mcpu=power8 -mtune=power8 -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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: 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 '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: 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: 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: 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: 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: 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: order.c: In function 'printBinAlign':
BUILDSTDERR: order.c:725:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   725 | }
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 '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: order.c: In function 'printXMFAAlign':
BUILDSTDERR: order.c:833:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   833 | }
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: 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: 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: 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: 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 'removeDups':
BUILDSTDERR: fchaos.c:302:24: warning: unused variable 'temp' [-Wunused-variable]
BUILDSTDERR:   302 |   hll *i, *j, *jprev, *temp;
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: 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: 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: 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: 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: 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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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:       |       ^~~
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: 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: 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:       | ^
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2mf utils/bin2mf.c
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2bl utils/bin2bl.c
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: 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: 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 -m64 -mcpu=power8 -mtune=power8 -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: utils/cextract.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    59 |     if (ch == '>') ungetc (ch, 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:       |          ^
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/cstat utils/cstat.c
BUILDSTDERR: utils/cstat.c: In function 'main':
BUILDSTDERR: utils/cstat.c:235:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   235 |   int i;
BUILDSTDERR:       |       ^
BUILDSTDERR: utils/cstat.c: In function 'cntlets':
BUILDSTDERR: utils/cstat.c:45:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    45 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/cstat.c: In function 'readseq':
BUILDSTDERR: utils/cstat.c:68:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    68 |   fgets(temp, 255, input);
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/contigorder utils/contigorder.c
BUILDSTDERR: utils/contigorder.c: In function 'getFileInfo':
BUILDSTDERR: utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
BUILDSTDERR:    15 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
BUILDSTDERR:       |                                                        ~^
BUILDSTDERR:       |                                                         |
BUILDSTDERR:       |                                                         char *
BUILDSTDERR: utils/contigorder.c:26:18: warning: unknown conversion type character '&' in format [-Wformat=]
BUILDSTDERR:    26 |  fscanf (file, "%&d", &dummy);
BUILDSTDERR:       |                  ^
BUILDSTDERR: utils/contigorder.c:26:16: warning: too many arguments for format [-Wformat-extra-args]
BUILDSTDERR:    26 |  fscanf (file, "%&d", &dummy);
BUILDSTDERR:       |                ^~~~~
BUILDSTDERR: utils/contigorder.c: In function 'getScores':
BUILDSTDERR: utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
BUILDSTDERR:    52 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
BUILDSTDERR:       |                                                        ~^
BUILDSTDERR:       |                                                         |
BUILDSTDERR:       |                                                         char *
BUILDSTDERR: utils/contigorder.c: In function 'solveOrder':
BUILDSTDERR: utils/contigorder.c:176:30: warning: unused variable 'ptr' [-Wunused-variable]
BUILDSTDERR:   176 |   int **best, *first, *last, ptr, newScore, **scoreOf;
BUILDSTDERR:       |                              ^~~
BUILDSTDERR: utils/contigorder.c: In function 'getFileInfo':
BUILDSTDERR: utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    19 |   fscanf (file, "numContigs = %d\n", numContigs);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    20 |   fscanf (file, "seqLen = %d\n", seqLen);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/contigorder.c:26:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    26 |  fscanf (file, "%&d", &dummy);
BUILDSTDERR:       |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/contigorder.c: In function 'getScores':
BUILDSTDERR: utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    56 |   fscanf (file, "numContigs = %*d\n");
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    57 |   fscanf (file, "seqLen = %*d\n");
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/contigorder.c:63:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    63 |  fscanf (file, "%d", &((*score)[i][j]));
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/getbounds utils/getbounds.c
BUILDSTDERR: utils/getbounds.c: In function 'main':
BUILDSTDERR: utils/getbounds.c:32:27: warning: unused variable 'ext' [-Wunused-variable]
BUILDSTDERR:    32 |   int S1B, S1E, S2B, S2E, ext, len1, len2;
BUILDSTDERR:       |                           ^~~
BUILDSTDERR: utils/getbounds.c: In function 'getLength':
BUILDSTDERR: utils/getbounds.c:18:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    18 |   fgets (buffer, 1024, file);
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:       |                   ^~~
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/getlength utils/getlength.c
BUILDSTDERR: utils/contigorder.c: In function 'solveOrder':
BUILDSTDERR: utils/contigorder.c:249:63: warning: 'bestRange' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   249 |       for (j = 0; k && j < numRanges; j++) if (last[j] < first[bestRange]){
BUILDSTDERR:       |                                                               ^
BUILDSTDERR: utils/contigorder.c:251:22: warning: 'bestState' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   251 |  if (newScore == best[bestState][bestRange]){
BUILDSTDERR:       |                      ^
BUILDSTDERR: utils/getlength.c: In function 'main':
BUILDSTDERR: utils/getlength.c:20:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    20 |   fgets (buffer, BUF_SIZE, 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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/rc utils/rc.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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/seqmerge utils/seqmerge.c
BUILDSTDERR: utils/seqmerge.c: In function 'main':
BUILDSTDERR: utils/seqmerge.c:33:15: warning: suggest parentheses around comparison in operand of '^' [-Wparentheses]
BUILDSTDERR:    33 |   if (written ^ 60 != 0) printf ("\n");
BUILDSTDERR:       |               ^
BUILDSTDERR: utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    19 |     fgets (buffer, 1024, file);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/rc.c: In function 'main':
BUILDSTDERR: utils/rc.c:39:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    39 |   fgets(temp, 255, stdin);
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/scorealign utils/scorealign.c -lm
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/scorecontigs utils/scorecontigs.c -lm
BUILDSTDERR: utils/scorealign.c: In function 'getSequence':
BUILDSTDERR: utils/scorealign.c:262:8: warning: variable 'prevch' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   262 |   char prevch = '~';
BUILDSTDERR:       |        ^~~~~~
BUILDSTDERR: utils/scorealign.c: In function 'getSequences':
BUILDSTDERR: utils/scorealign.c:322:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
BUILDSTDERR:   322 |   while (newseq = getSequence (file, &si, &ss, &se, &sd, &sc)){
BUILDSTDERR:       |          ^~~~~~
BUILDSTDERR: utils/scorealign.c:310:7: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   310 |   int i, si, ss, se;
BUILDSTDERR:       |       ^
BUILDSTDERR: utils/scorealign.c: In function 'processSequences':
BUILDSTDERR: utils/scorealign.c:353:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   353 |   int i, j;
BUILDSTDERR:       |          ^
BUILDSTDERR: utils/scorealign.c: In function 'getSequence':
BUILDSTDERR: utils/scorealign.c:266:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   266 |   fgets (line, 1024, file);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorealign.c: In function 'readScoreMatrix':
BUILDSTDERR: utils/scorealign.c:411:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   411 |   fgets (line, 1024, file);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorealign.c:419:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   419 |     fscanf (file, "%1s", &(line[0]));
BUILDSTDERR:       |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorealign.c:421:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   421 |       fscanf (file, "%d", &k);
BUILDSTDERR:       |       ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorealign.c:426:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   426 |   fscanf (file, "%d%d", &gapopen, &gapcont);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorecontigs.c: In function 'analyze':
BUILDSTDERR: utils/scorecontigs.c:345:13: warning: unused variable 'k' [-Wunused-variable]
BUILDSTDERR:   345 |   int i, j, k;
BUILDSTDERR:       |             ^
BUILDSTDERR: utils/scorecontigs.c: In function 'main':
BUILDSTDERR: utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=]
BUILDSTDERR:   385 |     if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){
BUILDSTDERR:       |                                     ~^                                                            ~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR:       |                                      |                                                            |
BUILDSTDERR:       |                                      char *                                                       char (*)[1024]
BUILDSTDERR: utils/scorecontigs.c: In function 'cntlets':
BUILDSTDERR: utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    56 |   fgets(temp, 1024, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/scorecontigs.c: In function 'readseq':
BUILDSTDERR: utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    82 |   fgets (temp, 1024, input);
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:       |                   ^~~
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/getcontigpos utils/getcontigpos.c
BUILDSTDERR: utils/getcontigpos.c: In function 'print':
BUILDSTDERR: utils/getcontigpos.c:66:46: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:    66 |   int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
BUILDSTDERR:       |                                              ^
BUILDSTDERR: utils/getcontigpos.c:66:33: warning: unused variable 'written' [-Wunused-variable]
BUILDSTDERR:    66 |   int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
BUILDSTDERR:       |                                 ^~~~~~~
BUILDSTDERR: utils/getcontigpos.c: In function 'getLength':
BUILDSTDERR: utils/getcontigpos.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/getcontigpos.c: In function 'readfile':
BUILDSTDERR: utils/getcontigpos.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: utils/getcontigpos.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    59 |     if (ch == '>') ungetc (ch, file);
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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/fa2xfa utils/fa2xfa.c
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/Glue utils/Glue.cpp
BUILDSTDERR: utils/fa2xfa.c: In function 'print':
BUILDSTDERR: utils/fa2xfa.c:81:36: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:    81 |   int i = 0, pos = 0, written = 0, j = 0;
BUILDSTDERR:       |                                    ^
BUILDSTDERR: utils/fa2xfa.c:81:14: warning: unused variable 'pos' [-Wunused-variable]
BUILDSTDERR:    81 |   int i = 0, pos = 0, written = 0, j = 0;
BUILDSTDERR:       |              ^~~
BUILDSTDERR: utils/fa2xfa.c: In function 'getLength':
BUILDSTDERR: utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    30 |   fgets (buffer, 1024, file);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/fa2xfa.c: In function 'readfile':
BUILDSTDERR: utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    55 |     fgets (buffer, 1024, file);
BUILDSTDERR:       |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/dotplot utils/dotplot.cpp
BUILDSTDERR: utils/fa2xfa.c:74:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    74 |     if (ch == '>') ungetc (ch, file);
BUILDSTDERR:       |        ^
BUILDSTDERR: utils/dotplot.cpp: In function 'int main(int, char**)':
BUILDSTDERR: utils/dotplot.cpp:6:27: warning: variable 'pa' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:     6 |   int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
BUILDSTDERR:       |                           ^~
BUILDSTDERR: utils/dotplot.cpp:6:31: warning: variable 'pb' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:     6 |   int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
BUILDSTDERR:       |                               ^~
BUILDSTDERR: utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    37 |     fgets (buffer, 105, file);
BUILDSTDERR:       |     ~~~~~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    74 |     fgets (buffer, 105, file);
BUILDSTDERR:       |     ~~~~~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    97 |     fgets (buffer, 105, 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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/overlay utils/overlay.c
BUILDSTDERR: utils/overlay.c: In function 'read_align':
BUILDSTDERR: utils/overlay.c:102:30: warning: unused variable 'tt' [-Wunused-variable]
BUILDSTDERR:   102 |   char currchar, checkchar, *tt;
BUILDSTDERR:       |                              ^~
BUILDSTDERR: utils/overlay.c: In function 'read_sequences':
BUILDSTDERR: utils/overlay.c:177:19: warning: unused variable 'breaker' [-Wunused-variable]
BUILDSTDERR:   177 |   int i, j, kmer, breaker;
BUILDSTDERR:       |                   ^~~~~~~
BUILDSTDERR: utils/overlay.c:177:13: warning: unused variable 'kmer' [-Wunused-variable]
BUILDSTDERR:   177 |   int i, j, kmer, breaker;
BUILDSTDERR:       |             ^~~~
BUILDSTDERR: utils/overlay.c:177:10: warning: unused variable 'j' [-Wunused-variable]
BUILDSTDERR:   177 |   int i, j, kmer, breaker;
BUILDSTDERR:       |          ^
BUILDSTDERR: utils/overlay.c: In function 'main':
BUILDSTDERR: utils/overlay.c:233:16: warning: unused variable 'test' [-Wunused-variable]
BUILDSTDERR:   233 |   float ttree, test;
BUILDSTDERR:       |                ^~~~
BUILDSTDERR: utils/overlay.c:233:9: warning: unused variable 'ttree' [-Wunused-variable]
BUILDSTDERR:   233 |   float ttree, test;
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: utils/overlay.c:232:7: warning: unused variable 'moved' [-Wunused-variable]
BUILDSTDERR:   232 |   int moved, i;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: utils/overlay.c:231:8: warning: unused variable 'string_tree' [-Wunused-variable]
BUILDSTDERR:   231 |   char string_tree[16537]; //noone will ever need more :)))
BUILDSTDERR:       |        ^~~~~~~~~~~
BUILDSTDERR: utils/overlay.c: In function 'read_align':
BUILDSTDERR: utils/overlay.c:110:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   110 |   fgets(temp, 255, input);
BUILDSTDERR:       |   ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from utils/overlay.c:5:
BUILDSTDERR: In function 'strncpy',
BUILDSTDERR:     inlined from 'read_align' at utils/overlay.c:135:5:
BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/overlay.c: In function 'read_align':
BUILDSTDERR: utils/overlay.c:135:45: note: length computed here
BUILDSTDERR:   135 |     strncpy(allseqs[target]->seqname, temp, strlen(temp)+1);
BUILDSTDERR:       |                                             ^~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp: In function 'void readScoreMatrix(char*)':
BUILDSTDERR: utils/Glue.cpp:33:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
BUILDSTDERR:    33 |   lagan_dir = "/usr/lib64/lagan";
BUILDSTDERR:       |               ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp: In function 'void calculateScoreMatrix(int)':
BUILDSTDERR: utils/Glue.cpp:60:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
BUILDSTDERR:    60 |   char *alpha = "ATCG";
BUILDSTDERR:       |                 ^~~~~~
BUILDSTDERR: utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
BUILDSTDERR:    11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
BUILDSTDERR:       |                                ^~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp:68:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE'
BUILDSTDERR:    68 |     readScoreMatrix (NUCLEOTIDE_MATRIX_FILE);
BUILDSTDERR:       |                      ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp: In function 'int countLets(SafeVector<char>&)':
BUILDSTDERR: utils/Glue.cpp:228:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
BUILDSTDERR:   228 |     if (data[i] >= 'A' && data[i] <= 'Z' || data[i] >= 'a' && data[i] <= 'z')
BUILDSTDERR: utils/Glue.cpp: In function 'int main(int, char**)':
BUILDSTDERR: utils/Glue.cpp:372:19: warning: variable 'end1' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   372 |   int begin1 = 1, end1 = 1;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: utils/Glue.cpp: In function 'void readScoreMatrix(char*)':
BUILDSTDERR: utils/Glue.cpp:40:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    40 |   fgets (line, 1024, file);
BUILDSTDERR:       |   ~~~~~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp:48:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    48 |     fscanf (file, "%1s", &(line[0]));
BUILDSTDERR:       |     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp:50:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    50 |       fscanf (file, "%d", &k);
BUILDSTDERR:       |       ~~~~~~~^~~~~~~~~~~~~~~~
BUILDSTDERR: utils/Glue.cpp:55:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    55 |   fscanf (file, "%d%d", &gapopen, &gapcont);
BUILDSTDERR:       |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I./ -c leftinfluence.cpp
BUILDSTDERR: In file included from ./leftinfluence.h:4,
BUILDSTDERR:                  from leftinfluence.cpp:1:
BUILDSTDERR: leftinfluence.cpp: In function 'void InitLI(LI*, long long int)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: leftinfluence.cpp:135:22: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   135 |  if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
BUILDSTDERR:       |                      ^~~~~~~~~~~
BUILDSTDERR: In file included from ./rightinfluence.h:4,
BUILDSTDERR:                  from rightinfluence.cpp:1:
BUILDSTDERR: rightinfluence.cpp: In function 'void initRI(RI*, long long int)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: rightinfluence.cpp:9:22: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:     9 |  if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
BUILDSTDERR:       |                      ^~~~~~~~~~~
BUILDSTDERR: rightinfluence.cpp: In function 'long long int RICommitEndPoint(RI*, Fragment*)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: rightinfluence.cpp:119:85: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   119 | int possibleCase = NEGATIVE << DOWNSTRANDSHIFT | NEGATIVE <<UPSTRANDSHIFT | LEFT << RELPOSSHIFT;
BUILDSTDERR:       |                                                                                     ^~~~~~~~~~~
BUILDSTDERR: leftinfluence.cpp: In function 'void printState(LI*)':
BUILDSTDERR: leftinfluence.cpp:619:16: warning: variable 'colCount' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   619 |  long long int colCount, diagCount, ownerCount;
BUILDSTDERR:       |                ^~~~~~~~
BUILDSTDERR: leftinfluence.cpp:619:26: warning: variable 'diagCount' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   619 |  long long int colCount, diagCount, ownerCount;
BUILDSTDERR:       |                          ^~~~~~~~~
BUILDSTDERR: leftinfluence.cpp:619:37: warning: variable 'ownerCount' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   619 |  long long int colCount, diagCount, ownerCount;
BUILDSTDERR:       |                                     ^~~~~~~~~~
BUILDSTDERR: In file included from ./score.h:4,
BUILDSTDERR:                  from glocal.cpp:1:
BUILDSTDERR: glocal.cpp: In function 'int main(int, char**)':
BUILDSTDERR: ./structs.h:31:50: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    31 | #define TOTALSHIFT UPSTRANDBITS + DOWNSTRANDBITS + RELPOSBITS
BUILDSTDERR:       |                                                  ^
BUILDSTDERR: glocal.cpp:64:16: note: in expansion of macro 'TOTALSHIFT'
BUILDSTDERR:    64 |  for (i=0;i<1<<TOTALSHIFT;i++) {
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: glocal.cpp: In function 'long long int startPointHandler()':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: glocal.cpp:131:86: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   131 |   possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
BUILDSTDERR:       |                                                                                      ^~~~~~~~~~~
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: glocal.cpp:142:87: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   142 |   possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos << RELPOSSHIFT;
BUILDSTDERR:       |                                                                                       ^~~~~~~~~~~
BUILDSTDERR: glocal.cpp:120:8: warning: variable 'current_score' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   120 |  float current_score;
BUILDSTDERR:       |        ^~~~~~~~~~~~~
BUILDSTDERR: In file included from ./score.h:4,
BUILDSTDERR:                  from glocal.cpp:1:
BUILDSTDERR: glocal.cpp: In function 'long long int endPointHandler()':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: glocal.cpp:224:88: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   224 |     possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
BUILDSTDERR:       |                                                                                        ^~~~~~~~~~~
BUILDSTDERR: io.cpp: In function 'long long int getline(FILE*, hll*)':
BUILDSTDERR: io.cpp:60:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    60 |  fgets(temp, 1024, infile);
BUILDSTDERR:       |  ~~~~~^~~~~~~~~~~~~~~~~~~~
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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I./ -c score.cpp
BUILDSTDERR: In file included from score.cpp:1:
BUILDSTDERR: score.cpp: In function 'void createScoreFunctionObjects(char*)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: score.cpp:92:106: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:    92 |   cases[i]= charToCase(updir)<<UPSTRANDSHIFT | charToCase(downdir)<<DOWNSTRANDSHIFT |charToCase(relpos)<<RELPOSSHIFT;
BUILDSTDERR:       |                                                                                                          ^~~~~~~~~~~
BUILDSTDERR: score.cpp: In function 'float scoreAll(Fragment*, Fragment*, long long int)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: score.cpp:143:19: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   143 |   if (ret_case >> RELPOSSHIFT != UNRELATED) {
BUILDSTDERR:       |                   ^~~~~~~~~~~
BUILDSTDERR: score.cpp: In function 'float fragmentSetScore(Fragment*, Fragment*, LI*, RI*, long long int)':
BUILDSTDERR: ./structs.h:30:34: warning: suggest parentheses around '+' inside '<<' [-Wparentheses]
BUILDSTDERR:    30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
BUILDSTDERR:       |                                  ^
BUILDSTDERR: score.cpp:185:120: note: in expansion of macro 'RELPOSSHIFT'
BUILDSTDERR:   185 |   tempScore = scoreAll(owner,current, current->strand << DOWNSTRANDSHIFT | owner->strand <<UPSTRANDSHIFT | UNRELATED<< RELPOSSHIFT);
BUILDSTDERR:       |                                                                                                                        ^~~~~~~~~~~
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'
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.qgyDgT
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
+ cd lagan20
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
+ mkdir -p /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le//usr/bin /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le//usr/lib64/lagan/utils
+ install -m755 chaos /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin
+ install -m755 mlagan /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin
+ install -m755 prolagan /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin
+ install -m755 lagan.pl /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/lagan
+ install -m755 slagan.pl /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//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-2.0-27.fc32.ppc64le//usr/lib64/lagan/utils
+ install -m644 blosum62.txt blosum62s.txt nucmatrix.txt test.score /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le//usr/lib64/lagan
+ rm -f Readmes/README.FIRST.chris Readmes/README.chaos.chris Readmes/README.lagan.chris Readmes/README.shuffle.chris
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 2.0-27.fc32 --unique-debug-suffix -2.0-27.fc32.ppc64le --unique-debug-src-base lagan-2.0-27.fc32.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/lagan20
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/chaos
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/mlagan
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/chaos
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/anchors
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/mlagan
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/prolagan
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/anchors
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/bin/prolagan
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/glocal
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/glocal
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/order
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/Glue
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/order
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/Glue
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/bin2bl
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/bin2bl
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/bin2mf
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/bin2mf
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/cextract
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/cextract
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/contigorder
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/contigorder
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/dotplot
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/cstat
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/dotplot
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/cstat
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/fa2xfa
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/fa2xfa
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getbounds
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getbounds
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getcontigpos
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getcontigpos
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getlength
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getlength
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getoverlap
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/getoverlap
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/overlay
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/overlay
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/rc
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/rc
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/scorealign
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/scorealign
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/scorecontigs
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/scorecontigs
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/seqmerge
extracting debug info from /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/lib64/lagan/utils/seqmerge
original debug info size: 3776kB, size after compression: 3552kB
/usr/lib/rpm/sepdebugcrcfix: Updated 23 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 675 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/lagan 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/mviz.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/mpretty.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/draft.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/mproject.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/lib64/lagan/utils/mrun.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/anal_gloc.pl from /usr/bin/env perl to #!/usr/bin/perl
Processing files: lagan-2.0-27.fc32.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.nQD3pP
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ DOCDIR=/builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/share/doc/lagan
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/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-2.0-27.fc32.ppc64le/usr/share/doc/lagan
+ cp -pr sample.fasta sample.params /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le/usr/share/doc/lagan
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Provides: lagan = 2.0-27.fc32 lagan(ppc-64) = 2.0-27.fc32
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(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) perl(:VERSION) >= 5.5.0 perl(Cwd) perl(File::Basename) perl(File::Copy) perl(File::Path) perl(Getopt::Long) perl(IO::Handle) perl(IPC::Open2) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH)
Processing files: lagan-debugsource-2.0-27.fc32.ppc64le
Provides: lagan-debugsource = 2.0-27.fc32 lagan-debugsource(ppc-64) = 2.0-27.fc32
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: lagan-debuginfo-2.0-27.fc32.ppc64le
Provides: debuginfo(build-id) = 00b25183ed2d2ac6b0f95368d7c7763467526a37 debuginfo(build-id) = 15bfb66eab746247a5c2704a5e41ef8a5fceb55e debuginfo(build-id) = 235ea9ee1c700deb66b855602922e6c50f81e2e0 debuginfo(build-id) = 255fef4f77bdf26c254643b485d91d8e92109ba1 debuginfo(build-id) = 2b7ec183e5f0c2deb8240f076727983f2c20f2d0 debuginfo(build-id) = 2fc109e15fd6f29f164c68f8f86585e6480fd6e2 debuginfo(build-id) = 4639d8532bb0ba58c961c0d0d8b570946506e5b9 debuginfo(build-id) = 53d81ceec270180f73e93217c8b270d1bff7cb50 debuginfo(build-id) = 5afec8bb290c82f8840b65b2b1a8da78d902e5b2 debuginfo(build-id) = 5bde1e1a46b45c02401839b1b1e0019691b79934 debuginfo(build-id) = 6f03701f2b95c2cce6380fd508b189945fedffb8 debuginfo(build-id) = 7739a642ce0a002ae84d6d72291b09ce49bf8f68 debuginfo(build-id) = 7f4f86ad86587ce79f772e06178c90082c455a69 debuginfo(build-id) = 8e9b444fd15d58b4663c1384aa8bdfce5f151726 debuginfo(build-id) = 931aea9ef09e7f13b8c518280a93dc2080d6cca1 debuginfo(build-id) = b50d4334129c98717f7978fbc23c8aeed451d6f1 debuginfo(build-id) = b5d78c6b417955d29be8bf77ccff17118a86cb39 debuginfo(build-id) = ba068377fe09d1fc9e937ea4eb7d4ea6584fba6a debuginfo(build-id) = bcdb3c8bb0baa0b8d0b5fc2aa980b6001bcbe11d debuginfo(build-id) = d74b34bc4924141728654378aa8a3efbcdb38324 debuginfo(build-id) = dc6064b3dcd249e73303a6d7f201225d479a7a65 debuginfo(build-id) = e23ea51eca34a260143f0366c3d8fbaf65cdda0f debuginfo(build-id) = e4c216ebc6c7fbd0424752fbffad300110be5a4c lagan-debuginfo = 2.0-27.fc32 lagan-debuginfo(ppc-64) = 2.0-27.fc32
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: lagan-debugsource(ppc-64) = 2.0-27.fc32
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
Wrote: /builddir/build/RPMS/lagan-debugsource-2.0-27.fc32.ppc64le.rpm
Wrote: /builddir/build/RPMS/lagan-2.0-27.fc32.ppc64le.rpm
Wrote: /builddir/build/RPMS/lagan-debuginfo-2.0-27.fc32.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.63ivdQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/lagan-2.0-27.fc32.ppc64le
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Child return code was: 0