Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f31-build-115595-34500/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1548979200 Wrote: /builddir/build/SRPMS/lagan-2.0-25.fc31.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f31-build-115595-34500/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1548979200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.l7V1fs + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf lagan20 + /usr/bin/gzip -dc /builddir/build/SOURCES/lagan20.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd lagan20 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (lagan20-chris.patch):' Patch #0 (lagan20-chris.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .chris --fuzz=0 patching file Readmes/README.FIRST patching file Readmes/README.shuffle patching file Readmes/README.chaos patching file Readmes/README.lagan patching file src/utils/scorealign.c patching file src/utils/Glue.cpp patching file src/utils/mrun.pl patching file src/utils/mrunfile.pl patching file src/utils/mrunpairs.pl patching file src/utils/mviz.pl patching file src/mlagan.c patching file src/prolagan.c patching file src/slagan-mfa.pl patching file src/supermap.pl patching file src/xmfa2mfa.pl patching file utils/mrunpairs.pl patching file utils/draft.pl patching file utils/mrunfile.pl patching file utils/mviz.pl patching file utils/mrun.pl patching file slagan.pl patching file lagan.pl patching file rechaos.pl patching file slagan-mfa.pl patching file supermap.pl patching file xmfa2mfa.pl patching file src/glocal/rightinfluence.cpp patching file src/glocal/score.cpp + sed -i 's/^CC .*$/CC = gcc $(RPM_OPT_FLAGS)/; BUILDSTDERR: s/^CPP .*$/CPP = g++ $(RPM_OPT_FLAGS)/' Makefile + sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c src/utils/bin2bl.c src/utils/bin2mf.c src/utils/cextract.c src/utils/contigorder.c src/utils/cstat.c src/utils/fa2xfa.c src/utils/getbounds.c src/utils/getcontigpos.c src/utils/getlength.c src/utils/getoverlap.c src/utils/overlay.c src/utils/rc.c src/utils/scorealign.c src/utils/scorecontigs.c src/utils/seqmerge.c + sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/utils/Glue.cpp src/utils/dotplot.cpp + sed -i 's|$ENV{LAGAN_DIR}|"/usr/lib64/lagan"|g' anal_gloc.pl lagan.pl rechaos.pl slagan-mfa.pl slagan.pl supermap.pl xmfa2mfa.pl src/anal_gloc.pl src/lagan.pl src/rechaos.pl src/slagan-mfa.pl src/slagan.pl src/supermap.pl src/xmfa2mfa.pl utils/cmerge2.pl utils/draft.pl utils/flipchaos.pl utils/mextract.pl utils/mf2bin.pl utils/mpretty.pl utils/mproject.pl utils/mrun.pl utils/mrunfile.pl utils/mrunpairs.pl utils/msplit.pl utils/mviz.pl src/utils/cmerge2.pl src/utils/draft.pl src/utils/mextract.pl src/utils/mf2bin.pl src/utils/mpretty.pl src/utils/mproject.pl src/utils/mrun.pl src/utils/mrunfile.pl src/utils/mrunpairs.pl src/utils/mviz.pl + sed -i 's|$LAGAN_DIR|/usr/lib64/lagan|g' Readmes/README.shuffle src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c + sed -i s/getline/GetLine/g src/anchors.c + rm prolagan + chmod -x src/glocal/Makefile src/glocal/default.score src/glocal/glocal src/glocal/glocal.cpp src/glocal/glocal.h src/glocal/io.cpp src/glocal/io.h src/glocal/leftinfluence.cpp src/glocal/leftinfluence.h src/glocal/rightinfluence.cpp src/glocal/rightinfluence.cpp.chris src/glocal/rightinfluence.h src/glocal/score.cpp src/glocal/score.cpp.chris src/glocal/score.h src/glocal/structs.h src/glocal/test.score + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BzldMu + umask 022 + cd /builddir/build/BUILD + cd lagan20 + make -j4 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' (cd src; make) make[1]: Entering directory '/builddir/build/BUILD/lagan20/src' gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../anchors anchors.c skiplist.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../order order.c diagmatrix.c filebuffer.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG BUILDSTDERR: order.c: In function 'readAncFile': BUILDSTDERR: order.c:237:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] BUILDSTDERR: 237 | if ((tt->seq1start >= s1start && tt->seq1end <= s1end || s1start == 0 && s1end == 0) && BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: order.c:238:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] BUILDSTDERR: 238 | (tt->seq2start >= s2start && tt->seq2end <= s2end || s2start == 0 && s2end == 0)){ BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: order.c: In function 'mkBarrel': BUILDSTDERR: order.c:274:7: warning: unused variable 'incr' [-Wunused-variable] BUILDSTDERR: 274 | int incr; BUILDSTDERR: | ^~~~ BUILDSTDERR: order.c: In function 'doAlign': BUILDSTDERR: order.c:409:5: warning: implicit declaration of function 'printMFAAlign'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration] BUILDSTDERR: 409 | printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); BUILDSTDERR: | ^~~~~~~~~~~~~ BUILDSTDERR: | printBinAlign BUILDSTDERR: order.c:411:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printTextAlign'? [-Wimplicit-function-declaration] BUILDSTDERR: 411 | printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); BUILDSTDERR: | ^~~~~~~~~~~~~~ BUILDSTDERR: | printTextAlign BUILDSTDERR: anchors.c: In function 'hptrcomp': BUILDSTDERR: anchors.c:49:7: warning: unused variable 'jt' [-Wunused-variable] BUILDSTDERR: 49 | int jt = ((hptr*)p2)->isstart; BUILDSTDERR: | ^~ BUILDSTDERR: order.c: In function 'getChain': BUILDSTDERR: order.c:486:7: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 486 | int temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: order.c: In function 'saveNeck': BUILDSTDERR: order.c:561:6: warning: unused variable 'second' [-Wunused-variable] BUILDSTDERR: 561 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); BUILDSTDERR: | ^~~~~~ BUILDSTDERR: order.c:560:9: warning: unused variable 'first' [-Wunused-variable] BUILDSTDERR: 560 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), BUILDSTDERR: | ^~~~~ BUILDSTDERR: order.c: In function 'joinAligns': BUILDSTDERR: order.c:586:10: warning: unused variable 'n' [-Wunused-variable] BUILDSTDERR: 586 | align *n = a->nextalign, *t; BUILDSTDERR: | ^ BUILDSTDERR: anchors.c: In function 'doOutput': BUILDSTDERR: anchors.c:171:17: warning: unused variable 'bestscore' [-Wunused-variable] BUILDSTDERR: 171 | int chl=0, i, bestscore=-1; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: anchors.c:171:14: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 171 | int chl=0, i, bestscore=-1; BUILDSTDERR: | ^ BUILDSTDERR: anchors.c:168:7: warning: variable 'len' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 168 | int len; BUILDSTDERR: | ^~~ BUILDSTDERR: order.c: In function 'printBinAlign': BUILDSTDERR: order.c:718:23: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 718 | left = lets[seq1[s1++]]; BUILDSTDERR: | ~~~~^~~~~~ BUILDSTDERR: order.c:720:24: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 720 | right = lets[seq2[s2++]]; BUILDSTDERR: | ~~~~^~~~~~ BUILDSTDERR: order.c: In function 'printMFAAlign': BUILDSTDERR: order.c:773:27: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 773 | int nm=0, nga=0, ngb=0, nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: order.c:773:7: warning: unused variable 'nm' [-Wunused-variable] BUILDSTDERR: 773 | int nm=0, nga=0, ngb=0, nlets=0; BUILDSTDERR: | ^~ BUILDSTDERR: order.c: In function 'printXMFAAlign': BUILDSTDERR: order.c:805:27: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 805 | int nm=0, nga=0, ngb=0, nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: order.c:805:7: warning: unused variable 'nm' [-Wunused-variable] BUILDSTDERR: 805 | int nm=0, nga=0, ngb=0, nlets=0; BUILDSTDERR: | ^~ BUILDSTDERR: order.c: In function 'readfile': BUILDSTDERR: order.c:61:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 61 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: order.c: In function 'readSubstMatrix': BUILDSTDERR: order.c:145:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 145 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: order.c:149:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 149 | fscanf (file, "%d", &gapstart); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: order.c:150:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 150 | fscanf (file, "%d", &gapcont); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: anchors.c: In function 'GetLine': BUILDSTDERR: anchors.c:232:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 232 | fgets(temp, 1024, infile); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: mlagan.c: In function 'hptrcomp': BUILDSTDERR: mlagan.c:38:7: warning: unused variable 'jt' [-Wunused-variable] BUILDSTDERR: 38 | int jt = ((hptr*)p2)->isstart; BUILDSTDERR: | ^~ BUILDSTDERR: mlagan.c: In function 'readfile': BUILDSTDERR: mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] BUILDSTDERR: 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: mlagan.c: In function 'getAnchsFromFile': BUILDSTDERR: mlagan.c:161:29: warning: unused variable 'first' [-Wunused-variable] BUILDSTDERR: 161 | hll *myres = 0, *tt = 0, *first = 0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: mlagan.c: In function 'generateAnchors': BUILDSTDERR: mlagan.c:213:8: warning: unused variable 'flip' [-Wunused-variable] BUILDSTDERR: 213 | char flip = 0; BUILDSTDERR: | ^~~~ BUILDSTDERR: mlagan.c:211:10: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 211 | align* temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: mlagan.c: In function 'remakeHLL': BUILDSTDERR: mlagan.c:310:10: warning: unused variable 'bestscore' [-Wunused-variable] BUILDSTDERR: 310 | int i, bestscore=-1; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: mlagan.c:310:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 310 | int i, bestscore=-1; BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c:309:20: warning: unused variable 't3' [-Wunused-variable] BUILDSTDERR: 309 | hll *temp, *t2, *t3; BUILDSTDERR: | ^~ BUILDSTDERR: mlagan.c:309:15: warning: unused variable 't2' [-Wunused-variable] BUILDSTDERR: 309 | hll *temp, *t2, *t3; BUILDSTDERR: | ^~ BUILDSTDERR: mlagan.c:307:7: warning: unused variable 'len' [-Wunused-variable] BUILDSTDERR: 307 | int len; BUILDSTDERR: | ^~~ BUILDSTDERR: order.c: In function 'printBinAlign': BUILDSTDERR: order.c:725:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 725 | } BUILDSTDERR: | ^ BUILDSTDERR: order.c: In function 'printTextAlign': BUILDSTDERR: order.c:769:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 769 | } BUILDSTDERR: | ^ BUILDSTDERR: order.c: In function 'printMFAAlign': BUILDSTDERR: order.c:801:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 801 | } BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c: In function 'iterativeImprovement': BUILDSTDERR: mlagan.c:485:10: warning: unused variable 'readd' [-Wunused-variable] BUILDSTDERR: 485 | align *readd, *old, *new; BUILDSTDERR: | ^~~~~ BUILDSTDERR: mlagan.c:483:12: warning: unused variable 'oldscore' [-Wunused-variable] BUILDSTDERR: 483 | int i=0, oldscore, cutoff; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: order.c: In function 'printXMFAAlign': BUILDSTDERR: fchaos.c: In function 'removeDups': BUILDSTDERR: fchaos.c:302:24: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 302 | hll *i, *j, *jprev, *temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: order.c:833:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 833 | } BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c: In function 'treeToRPN': BUILDSTDERR: mlagan.c:528:16: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 528 | int i=0; int j, k; BUILDSTDERR: | ^ BUILDSTDERR: fchaos.c: In function 'readfile': BUILDSTDERR: fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args] BUILDSTDERR: 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c: In function 'chain': BUILDSTDERR: fchaos.c:401:16: warning: unused variable 'd2' [-Wunused-variable] BUILDSTDERR: 401 | int i, d1=0, d2=0; BUILDSTDERR: | ^~ BUILDSTDERR: fchaos.c:401:10: warning: unused variable 'd1' [-Wunused-variable] BUILDSTDERR: 401 | int i, d1=0, d2=0; BUILDSTDERR: | ^~ BUILDSTDERR: fchaos.c:401:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 401 | int i, d1=0, d2=0; BUILDSTDERR: | ^ BUILDSTDERR: fchaos.c: In function 'findPrev': BUILDSTDERR: fchaos.c:440:7: warning: unused variable 'doneset' [-Wunused-variable] BUILDSTDERR: 440 | int doneset = 0; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: fchaos.c: In function 'doAlgo': BUILDSTDERR: fchaos.c:543:24: warning: unused variable 'bestdbaseloc' [-Wunused-variable] BUILDSTDERR: 543 | int bestqueryloc=-1, bestdbaseloc=-1, numhits; BUILDSTDERR: | ^~~~~~~~~~~~ BUILDSTDERR: fchaos.c:543:7: warning: unused variable 'bestqueryloc' [-Wunused-variable] BUILDSTDERR: 543 | int bestqueryloc=-1, bestdbaseloc=-1, numhits; BUILDSTDERR: | ^~~~~~~~~~~~ BUILDSTDERR: fchaos.c:542:9: warning: unused variable 'bestscore' [-Wunused-variable] BUILDSTDERR: 542 | float bestscore=-1, baseval; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: mlagan.c: In function 'main': BUILDSTDERR: mlagan.c:1067:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] BUILDSTDERR: 1067 | printXMFAAlign(outfile, final); BUILDSTDERR: | ^~~~~~~~~~~~~~ BUILDSTDERR: | printFASTAAlign BUILDSTDERR: mlagan.c:942:8: warning: unused variable 'command' [-Wunused-variable] BUILDSTDERR: 942 | char command[256]; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: mlagan.c:941:24: warning: unused variable 'y' [-Wunused-variable] BUILDSTDERR: 941 | int i = 1, j = 1, x, y; BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c:941:21: warning: unused variable 'x' [-Wunused-variable] BUILDSTDERR: 941 | int i = 1, j = 1, x, y; BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c:939:14: warning: unused variable 'seqfile' [-Wunused-variable] BUILDSTDERR: 939 | FileBuffer seqfile; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: fchaos.c: In function 'main': BUILDSTDERR: fchaos.c:885:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 885 | int i; BUILDSTDERR: | ^ BUILDSTDERR: fchaos.c: In function 'saveScore': BUILDSTDERR: fchaos.c:970:7: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 970 | int temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: mlagan.c: In function 'readfile': BUILDSTDERR: mlagan.c:79:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 79 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c: In function 'savenfreeLList': BUILDSTDERR: fchaos.c:1137:9: warning: variable 'j' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 1137 | int i,j; BUILDSTDERR: | ^ BUILDSTDERR: mlagan.c: In function 'treeToRPN': BUILDSTDERR: mlagan.c:565:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 565 | } BUILDSTDERR: | ^ BUILDSTDERR: fchaos.c: In function 'readfile': BUILDSTDERR: fchaos.c:344:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 344 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c: In function 'readSubstMatrix': BUILDSTDERR: fchaos.c:622:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c:627:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 627 | fscanf (file, "%d", &gappenstart); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c:628:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 628 | fscanf (file, "%d", &gappenext); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: anchors.c: In function 'findBestChain': BUILDSTDERR: anchors.c:164:10: warning: 'bestptr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 164 | return (hll*)bestptr->myelem; BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: skiplist.c: In function 'printSLE': BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] BUILDSTDERR: 12 | printf(" %d %x\n", tbp->index, tbp->myelem); BUILDSTDERR: | ~^ ~~~~~~~~~~~ BUILDSTDERR: | | | BUILDSTDERR: | unsigned int void * BUILDSTDERR: | %p BUILDSTDERR: skiplist.c: In function 'makeSkLst': BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 33 | int i; BUILDSTDERR: | ^ BUILDSTDERR: skiplist.c: In function 'SLinsert': BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable] BUILDSTDERR: 100 | sle* prev = SLfind(trgt, index), *tbe; BUILDSTDERR: | ^~~ BUILDSTDERR: mlagan.c: In function 'buildTree': BUILDSTDERR: mlagan.c:597:12: warning: 'mlj' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 597 | int mli, mlj; BUILDSTDERR: | ^~~ BUILDSTDERR: mlagan.c:597:7: warning: 'mli' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 597 | int mli, mlj; BUILDSTDERR: | ^~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG BUILDSTDERR: prolagan.c: In function 'hptrcomp': BUILDSTDERR: prolagan.c:41:7: warning: unused variable 'jt' [-Wunused-variable] BUILDSTDERR: 41 | int jt = ((hptr*)p2)->isstart; BUILDSTDERR: | ^~ BUILDSTDERR: prolagan.c: In function 'readfile': BUILDSTDERR: prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] BUILDSTDERR: 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: prolagan.c: In function 'appendAlignProfile': BUILDSTDERR: prolagan.c:163:9: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 163 | int i,j,k; BUILDSTDERR: | ^ BUILDSTDERR: prolagan.c: In function 'readProfile': BUILDSTDERR: prolagan.c:198:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] BUILDSTDERR: 198 | while ( myseq = FileRead( with_gaps,0,0,VER_MLAGAN )) { BUILDSTDERR: | ^~~~~ BUILDSTDERR: prolagan.c: In function 'getAnchsFromFile': BUILDSTDERR: prolagan.c:246:29: warning: unused variable 'first' [-Wunused-variable] BUILDSTDERR: 246 | hll *myres = 0, *tt = 0, *first = 0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: prolagan.c: In function 'generateAnchors': BUILDSTDERR: prolagan.c:298:8: warning: unused variable 'flip' [-Wunused-variable] BUILDSTDERR: 298 | char flip = 0; BUILDSTDERR: | ^~~~ BUILDSTDERR: prolagan.c:296:10: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 296 | align* temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: prolagan.c: In function 'remakeHLL': BUILDSTDERR: prolagan.c:395:10: warning: unused variable 'bestscore' [-Wunused-variable] BUILDSTDERR: 395 | int i, bestscore=-1; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: prolagan.c:395:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 395 | int i, bestscore=-1; BUILDSTDERR: | ^ BUILDSTDERR: prolagan.c:394:20: warning: unused variable 't3' [-Wunused-variable] BUILDSTDERR: 394 | hll *temp, *t2, *t3; BUILDSTDERR: | ^~ BUILDSTDERR: prolagan.c:394:15: warning: unused variable 't2' [-Wunused-variable] BUILDSTDERR: 394 | hll *temp, *t2, *t3; BUILDSTDERR: | ^~ BUILDSTDERR: prolagan.c:392:7: warning: unused variable 'len' [-Wunused-variable] BUILDSTDERR: 392 | int len; BUILDSTDERR: | ^~~ BUILDSTDERR: prolagan.c: In function 'processAnchors': BUILDSTDERR: prolagan.c:539:36: warning: unused variable 'uni' [-Wunused-variable] BUILDSTDERR: 539 | align *first, *second, *result, *uni; BUILDSTDERR: | ^~~ BUILDSTDERR: prolagan.c: In function 'iterativeImprovement': BUILDSTDERR: prolagan.c:587:10: warning: unused variable 'readd' [-Wunused-variable] BUILDSTDERR: 587 | align *readd, *old, *new; BUILDSTDERR: | ^~~~~ BUILDSTDERR: prolagan.c:585:12: warning: unused variable 'oldscore' [-Wunused-variable] BUILDSTDERR: 585 | int i=0, oldscore, cutoff; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: prolagan.c: In function 'treeToRPN': BUILDSTDERR: prolagan.c:630:16: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 630 | int i=0; int j, k; BUILDSTDERR: | ^ BUILDSTDERR: prolagan.c: In function 'main': BUILDSTDERR: prolagan.c:1087:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] BUILDSTDERR: 1087 | printXMFAAlign(outfile, final); BUILDSTDERR: | ^~~~~~~~~~~~~~ BUILDSTDERR: | printFASTAAlign BUILDSTDERR: prolagan.c:966:8: warning: unused variable 'table' [-Wunused-variable] BUILDSTDERR: 966 | hll* table[MAX_SEQ][MAX_SEQ]; BUILDSTDERR: | ^~~~~ BUILDSTDERR: prolagan.c:960:8: warning: unused variable 'command' [-Wunused-variable] BUILDSTDERR: 960 | char command[256]; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: prolagan.c:954:14: warning: unused variable 'seqfile' [-Wunused-variable] BUILDSTDERR: 954 | FileBuffer seqfile; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: prolagan.c: In function 'readfile': BUILDSTDERR: prolagan.c:79:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 79 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: prolagan.c: In function 'treeToRPN': BUILDSTDERR: prolagan.c:667:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 667 | } BUILDSTDERR: | ^ BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr': BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable] BUILDSTDERR: 155 | char res; BUILDSTDERR: | ^~~ BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable] BUILDSTDERR: 154 | int dn = x+y-1, loc; BUILDSTDERR: | ^~~ BUILDSTDERR: fchaos.c: In function 'doTranslated': BUILDSTDERR: fchaos.c:865:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 865 | procPairs(currquery, currdbase); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: fchaos.c: In function 'main': BUILDSTDERR: fchaos.c:955:7: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 955 | procPairs(currquery, currdbase); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c: In function 'getAnchsFromAlign': BUILDSTDERR: multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable] BUILDSTDERR: 104 | float peakfrac; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable] BUILDSTDERR: 103 | char ingap = 0, isfrst = 1; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable] BUILDSTDERR: 99 | int currscore=0, oldscore, peakscore; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable] BUILDSTDERR: 99 | int currscore=0, oldscore, peakscore; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c: In function 'unifyAlign': BUILDSTDERR: multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable] BUILDSTDERR: 188 | int s1 = 0, s2 = 0, tgs, tgc; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable] BUILDSTDERR: 188 | int s1 = 0, s2 = 0, tgs, tgc; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable] BUILDSTDERR: 187 | int i,j,k, cbc, brcount; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable] BUILDSTDERR: 187 | int i,j,k, cbc, brcount; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c: In function 'getChain': BUILDSTDERR: multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 247 | int temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'saveNeck': BUILDSTDERR: multial.c:358:6: warning: unused variable 'second' [-Wunused-variable] BUILDSTDERR: 358 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c:357:9: warning: unused variable 'first' [-Wunused-variable] BUILDSTDERR: 357 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c: In function 'joinAligns': BUILDSTDERR: multial.c:381:10: warning: unused variable 'n' [-Wunused-variable] BUILDSTDERR: 381 | align *n = a->nextalign, *t; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'openGap': BUILDSTDERR: multial.c:594:25: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 594 | int alopen, pen, sav, i; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable] BUILDSTDERR: 594 | int alopen, pen, sav, i; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c: In function 'mkBarrel': BUILDSTDERR: multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable] BUILDSTDERR: 615 | int incr; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'doNW': BUILDSTDERR: multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 811 | int numNecks =0, oldneck =0; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable] BUILDSTDERR: 808 | char rh, ptr=0, isneck; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:807:14: warning: unused variable 'b' [-Wunused-variable] BUILDSTDERR: 807 | align* a, *b; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable] BUILDSTDERR: 805 | int tt, prevgap; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable] BUILDSTDERR: 805 | int tt, prevgap; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable] BUILDSTDERR: 804 | int gapend[3]; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c: In function 'removeSeqByName': BUILDSTDERR: multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 1062 | seq *removed; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c: In function 'getSeqNum': BUILDSTDERR: multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable] BUILDSTDERR: 1073 | seq *removed; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c: In function 'remapHLLs': BUILDSTDERR: multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] BUILDSTDERR: 1262 | if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF || BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable] BUILDSTDERR: 1104 | int mybp, i, *searchint, stmybp, mylen, olen, osize; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'hllJoin': BUILDSTDERR: multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1352 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 1352 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'minHLL': BUILDSTDERR: multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1368 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'mergeHLLs': BUILDSTDERR: multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1408 | int i, j, mscore; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 1408 | int i, j, mscore; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printTextAlign': BUILDSTDERR: multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1466 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1465 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1465 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: In function 'printFASTAAlign': BUILDSTDERR: multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1525 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1524 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1524 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: In function 'printXMFAAlign': BUILDSTDERR: multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1553 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1552 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1552 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: At top level: BUILDSTDERR: multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static BUILDSTDERR: 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static BUILDSTDERR: 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static BUILDSTDERR: 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static BUILDSTDERR: 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static BUILDSTDERR: 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static BUILDSTDERR: 563 | return matchcache[v(other->cnts[0][ow]) | BUILDSTDERR: | ^~~~~~~~~~ BUILDSTDERR: multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static BUILDSTDERR: 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static BUILDSTDERR: 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | BUILDSTDERR: | ^~~~~~~~~~ BUILDSTDERR: multial.c: In function 'scoreLocal': BUILDSTDERR: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 84 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'readSubstMatrix': BUILDSTDERR: multial.c:478:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 478 | fscanf (file, "%d", &k); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c:486:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 486 | fscanf (file, "%d", &gapstart); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c:487:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 487 | fscanf (file, "%d", &gapcont); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c: In function 'removeSeqByName': BUILDSTDERR: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1068 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printTextAlign': BUILDSTDERR: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1521 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printFASTAAlign': BUILDSTDERR: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1549 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printXMFAAlign': BUILDSTDERR: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1579 | } BUILDSTDERR: | ^ BUILDSTDERR: thrtrie.c: In function 'makeAlpha': BUILDSTDERR: thrtrie.c:33:15: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 33 | indeces[*alpha] = i; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: thrtrie.c:35:19: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 35 | else indeces [*alpha] = i++; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: thrtrie.c: In function 'lookup': BUILDSTDERR: thrtrie.c:42:17: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 42 | return indeces[c]; BUILDSTDERR: | ^ BUILDSTDERR: thrtrie.c: In function 'insertString': BUILDSTDERR: thrtrie.c:174:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 174 | int i, j, wordlen = root->height, letprev, letcurr; BUILDSTDERR: | ^ BUILDSTDERR: In file included from thrtrie.c:13: BUILDSTDERR: mempage.c: In function 'MPallfree': BUILDSTDERR: mempage.c:48:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 48 | } BUILDSTDERR: | ^ BUILDSTDERR: filebuffer.c: In function 'FileRead': BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] BUILDSTDERR: 123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: skiplist.c: In function 'printSLE': BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] BUILDSTDERR: 12 | printf(" %d %x\n", tbp->index, tbp->myelem); BUILDSTDERR: | ~^ ~~~~~~~~~~~ BUILDSTDERR: | | | BUILDSTDERR: | unsigned int void * BUILDSTDERR: | %p BUILDSTDERR: skiplist.c: In function 'makeSkLst': BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 33 | int i; BUILDSTDERR: | ^ BUILDSTDERR: skiplist.c: In function 'SLinsert': BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable] BUILDSTDERR: 100 | sle* prev = SLfind(trgt, index), *tbe; BUILDSTDERR: | ^~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2mf utils/bin2mf.c BUILDSTDERR: multial.c: In function 'getAnchsFromAlign': BUILDSTDERR: multial.c:104:9: warning: unused variable 'peakfrac' [-Wunused-variable] BUILDSTDERR: 104 | float peakfrac; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:103:19: warning: unused variable 'isfrst' [-Wunused-variable] BUILDSTDERR: 103 | char ingap = 0, isfrst = 1; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c:99:30: warning: unused variable 'peakscore' [-Wunused-variable] BUILDSTDERR: 99 | int currscore=0, oldscore, peakscore; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: multial.c:99:20: warning: unused variable 'oldscore' [-Wunused-variable] BUILDSTDERR: 99 | int currscore=0, oldscore, peakscore; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c: In function 'unifyAlign': BUILDSTDERR: multial.c:188:28: warning: unused variable 'tgc' [-Wunused-variable] BUILDSTDERR: 188 | int s1 = 0, s2 = 0, tgs, tgc; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c:188:23: warning: unused variable 'tgs' [-Wunused-variable] BUILDSTDERR: 188 | int s1 = 0, s2 = 0, tgs, tgc; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c:187:19: warning: unused variable 'brcount' [-Wunused-variable] BUILDSTDERR: 187 | int i,j,k, cbc, brcount; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:187:14: warning: unused variable 'cbc' [-Wunused-variable] BUILDSTDERR: 187 | int i,j,k, cbc, brcount; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c: In function 'getChain': BUILDSTDERR: multial.c:247:7: warning: unused variable 'temp' [-Wunused-variable] BUILDSTDERR: 247 | int temp; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'saveNeck': BUILDSTDERR: multial.c:358:6: warning: unused variable 'second' [-Wunused-variable] BUILDSTDERR: 358 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c:357:9: warning: unused variable 'first' [-Wunused-variable] BUILDSTDERR: 357 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c: In function 'joinAligns': BUILDSTDERR: multial.c:381:10: warning: unused variable 'n' [-Wunused-variable] BUILDSTDERR: 381 | align *n = a->nextalign, *t; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'openGap': BUILDSTDERR: multial.c:594:25: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 594 | int alopen, pen, sav, i; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:594:15: warning: unused variable 'pen' [-Wunused-variable] BUILDSTDERR: 594 | int alopen, pen, sav, i; BUILDSTDERR: | ^~~ BUILDSTDERR: multial.c: In function 'mkBarrel': BUILDSTDERR: multial.c:615:7: warning: unused variable 'incr' [-Wunused-variable] BUILDSTDERR: 615 | int incr; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'doNW': BUILDSTDERR: multial.c:811:20: warning: variable 'oldneck' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 811 | int numNecks =0, oldneck =0; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:808:8: warning: unused variable 'rh' [-Wunused-variable] BUILDSTDERR: 808 | char rh, ptr=0, isneck; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:807:14: warning: unused variable 'b' [-Wunused-variable] BUILDSTDERR: 807 | align* a, *b; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:805:11: warning: unused variable 'prevgap' [-Wunused-variable] BUILDSTDERR: 805 | int tt, prevgap; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c:805:7: warning: unused variable 'tt' [-Wunused-variable] BUILDSTDERR: 805 | int tt, prevgap; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:804:7: warning: unused variable 'gapend' [-Wunused-variable] BUILDSTDERR: 804 | int gapend[3]; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: multial.c: In function 'removeSeqByName': BUILDSTDERR: multial.c:1062:8: warning: variable 'removed' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 1062 | seq *removed; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c: In function 'getSeqNum': BUILDSTDERR: multial.c:1073:8: warning: unused variable 'removed' [-Wunused-variable] BUILDSTDERR: 1073 | seq *removed; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: multial.c: In function 'remapHLLs': BUILDSTDERR: multial.c:1262:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] BUILDSTDERR: 1262 | if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF || BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1104:43: warning: unused variable 'olen' [-Wunused-variable] BUILDSTDERR: 1104 | int mybp, i, *searchint, stmybp, mylen, olen, osize; BUILDSTDERR: | ^~~~ BUILDSTDERR: multial.c: In function 'hllJoin': BUILDSTDERR: multial.c:1352:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1352 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1352:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 1352 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'minHLL': BUILDSTDERR: multial.c:1368:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1368 | int i, j; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'mergeHLLs': BUILDSTDERR: multial.c:1408:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 1408 | int i, j, mscore; BUILDSTDERR: | ^ BUILDSTDERR: multial.c:1408:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 1408 | int i, j, mscore; BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printTextAlign': BUILDSTDERR: multial.c:1466:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1466 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1465:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1465 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1465:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1465 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: In function 'printFASTAAlign': BUILDSTDERR: multial.c:1525:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1525 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1524:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1524 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1524:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1524 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: In function 'printXMFAAlign': BUILDSTDERR: multial.c:1553:7: warning: unused variable 'nlets' [-Wunused-variable] BUILDSTDERR: 1553 | int nlets=0; BUILDSTDERR: | ^~~~~ BUILDSTDERR: multial.c:1552:13: warning: unused variable 's2' [-Wunused-variable] BUILDSTDERR: 1552 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c:1552:7: warning: unused variable 's1' [-Wunused-variable] BUILDSTDERR: 1552 | int s1=0, s2=0, c, k, i; BUILDSTDERR: | ^~ BUILDSTDERR: multial.c: At top level: BUILDSTDERR: multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static BUILDSTDERR: 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static BUILDSTDERR: 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static BUILDSTDERR: 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static BUILDSTDERR: 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static BUILDSTDERR: 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static BUILDSTDERR: 563 | return matchcache[v(other->cnts[0][ow]) | BUILDSTDERR: | ^~~~~~~~~~ BUILDSTDERR: multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static BUILDSTDERR: 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static BUILDSTDERR: 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | BUILDSTDERR: | ^~~~~~~~~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/bin2bl utils/bin2bl.c BUILDSTDERR: multial.c: In function 'scoreLocal': BUILDSTDERR: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 84 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'readSubstMatrix': BUILDSTDERR: multial.c:478:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 478 | fscanf (file, "%d", &k); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c:486:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 486 | fscanf (file, "%d", &gapstart); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c:487:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 487 | fscanf (file, "%d", &gapcont); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: multial.c: In function 'removeSeqByName': BUILDSTDERR: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1068 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printTextAlign': BUILDSTDERR: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1521 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printFASTAAlign': BUILDSTDERR: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1549 | } BUILDSTDERR: | ^ BUILDSTDERR: multial.c: In function 'printXMFAAlign': BUILDSTDERR: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 1579 | } BUILDSTDERR: | ^ BUILDSTDERR: utils/bin2bl.c: In function 'main': BUILDSTDERR: utils/bin2bl.c:52:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] BUILDSTDERR: 52 | if (argv[1][0] == '-') BUILDSTDERR: | ^ BUILDSTDERR: utils/bin2bl.c:22:7: warning: unused variable 'width' [-Wunused-variable] BUILDSTDERR: 22 | int width = 60; BUILDSTDERR: | ^~~~~ BUILDSTDERR: global.c: In function 'ismatch': BUILDSTDERR: global.c:12:17: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 12 | return indeces[a] == indeces[b]; BUILDSTDERR: | ^ BUILDSTDERR: global.c:12:31: warning: array subscript has type 'char' [-Wchar-subscripts] BUILDSTDERR: 12 | return indeces[a] == indeces[b]; BUILDSTDERR: | ^ BUILDSTDERR: global.c: In function 'global': BUILDSTDERR: global.c:34:31: warning: unused variable 'score' [-Wunused-variable] BUILDSTDERR: 34 | int mm = end2 - start2 + 1, score; BUILDSTDERR: | ^~~~~ BUILDSTDERR: global.c: In function 'printalign': BUILDSTDERR: global.c:172:1: warning: control reaches end of non-void function [-Wreturn-type] BUILDSTDERR: 172 | } BUILDSTDERR: | ^ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/cextract utils/cextract.c BUILDSTDERR: utils/cextract.c: In function 'getLength': BUILDSTDERR: utils/cextract.c:16:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 16 | fgets (buffer, 1024, file); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: utils/cextract.c: In function 'readfile': BUILDSTDERR: utils/cextract.c:41:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 41 | fgets (buffer, 1024, file); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: translate.c: In function 'toPeptide': BUILDSTDERR: translate.c:9:10: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 9 | int i, j, sum=0, mask = 0; BUILDSTDERR: | ^ BUILDSTDERR: utils/cextract.c:59:8: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 59 | if (ch == '>') ungetc (ch, file); BUILDSTDERR: | ^ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o ../utils/cstat utils/cstat.c BUILDSTDERR: filebuffer.c: In function 'FileRead': BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] BUILDSTDERR: 123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: utils/cstat.c: In function 'cntlets': BUILDSTDERR: utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] BUILDSTDERR: 51 | if (!isspace(currchar)) { BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: utils/cstat.c:52:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] BUILDSTDERR: 52 | currchar = toupper(currchar); BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: utils/cstat.c: In function 'main': BUILDSTDERR: utils/cstat.c:234:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 234 | int i; BUILDSTDERR: | ^ BUILDSTDERR: utils/cstat.c: In function 'cntlets': BUILDSTDERR: utils/cstat.c:44:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 44 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: utils/cstat.c: In function 'readseq': BUILDSTDERR: utils/cstat.c:67:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 67 | fgets(temp, 255, input); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: /usr/bin/ld: /tmp/ccTn9NAo.o: in function `chain': BUILDSTDERR: /builddir/build/BUILD/lagan20/src/fchaos.c:412: undefined reference to `findPrev' BUILDSTDERR: collect2: error: ld returned 1 exit status BUILDSTDERR: make[1]: *** [Makefile:14: ../chaos] Error 1 BUILDSTDERR: make[1]: *** Waiting for unfinished jobs.... BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr': BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable] BUILDSTDERR: 155 | char res; BUILDSTDERR: | ^~~ BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable] BUILDSTDERR: 154 | int dn = x+y-1, loc; BUILDSTDERR: | ^~~ BUILDSTDERR: skiplist.c: In function 'printSLE': BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] BUILDSTDERR: 12 | printf(" %d %x\n", tbp->index, tbp->myelem); BUILDSTDERR: | ~^ ~~~~~~~~~~~ BUILDSTDERR: | | | BUILDSTDERR: | unsigned int void * BUILDSTDERR: | %p BUILDSTDERR: skiplist.c: In function 'makeSkLst': BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 33 | int i; BUILDSTDERR: | ^ BUILDSTDERR: skiplist.c: In function 'SLinsert': BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable] BUILDSTDERR: 100 | sle* prev = SLfind(trgt, index), *tbe; BUILDSTDERR: | ^~~ BUILDSTDERR: diagmatrix.c: In function 'DMsetPtr': BUILDSTDERR: diagmatrix.c:155:8: warning: unused variable 'res' [-Wunused-variable] BUILDSTDERR: 155 | char res; BUILDSTDERR: | ^~~ BUILDSTDERR: diagmatrix.c:154:19: warning: unused variable 'loc' [-Wunused-variable] BUILDSTDERR: 154 | int dn = x+y-1, loc; BUILDSTDERR: | ^~~ BUILDSTDERR: filebuffer.c: In function 'FileRead': BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] BUILDSTDERR: 123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: skiplist.c: In function 'printSLE': BUILDSTDERR: skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] BUILDSTDERR: 12 | printf(" %d %x\n", tbp->index, tbp->myelem); BUILDSTDERR: | ~^ ~~~~~~~~~~~ BUILDSTDERR: | | | BUILDSTDERR: | unsigned int void * BUILDSTDERR: | %p BUILDSTDERR: skiplist.c: In function 'makeSkLst': BUILDSTDERR: skiplist.c:33:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 33 | int i; BUILDSTDERR: | ^ BUILDSTDERR: skiplist.c: In function 'SLinsert': BUILDSTDERR: skiplist.c:100:37: warning: unused variable 'tbe' [-Wunused-variable] BUILDSTDERR: 100 | sle* prev = SLfind(trgt, index), *tbe; BUILDSTDERR: | ^~~ BUILDSTDERR: filebuffer.c: In function 'FileRead': BUILDSTDERR: filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] BUILDSTDERR: 123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? BUILDSTDERR: | ^~~~~~~ make[1]: Leaving directory '/builddir/build/BUILD/lagan20/src' BUILDSTDERR: make: *** [Makefile:2: all] Error 2 RPM build errors: BUILDSTDERR: error: Bad exit status from /var/tmp/rpm-tmp.BzldMu (%build) BUILDSTDERR: Bad exit status from /var/tmp/rpm-tmp.BzldMu (%build) Child return code was: 1 EXCEPTION: [Error()] Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/mockbuild/trace_decorator.py", line 96, in trace result = func(*args, **kw) File "/usr/lib/python3.7/site-packages/mockbuild/util.py", line 700, in do raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode) mockbuild.exception.Error: Command failed: # bash --login -c /usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/lagan.spec