Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/wise2.spec'], chrootPath='/var/lib/mock/f33-build-134302-41529/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=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/wise2.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 Package glib-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `glib-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'glib-2.0', required by 'virtual:world', not found Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1580428800 Wrote: /builddir/build/SRPMS/wise2-2.4.1-10.fc33.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/wise2.spec'], chrootPath='/var/lib/mock/f33-build-134302-41529/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=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/wise2.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=1580428800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.LsTHNb + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf wise2.4.1 + /usr/bin/gzip -dc /builddir/build/SOURCES/wise2.4.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd wise2.4.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (wise2-build.patch):' Patch #0 (wise2-build.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/makefile patching file src/welcome.csh + echo 'Patch #1 (wise2-isnumber.patch):' Patch #1 (wise2-isnumber.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/models/phasemodel.c Patch #2 (wise2-glib2.patch): + echo 'Patch #2 (wise2-glib2.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/makefile patching file src/snp/makefile patching file src/corba/makefile patching file src/models/makefile patching file src/dnaindex/makefile patching file src/dnaindex/assembly/makefile patching file src/dynlibsrc/makefile patching file src/network/makefile patching file src/other_programs/makefile patching file src/base/makefile patching file src/HMMer2/Makefile Patch #3 (wise2-getline.patch): + echo 'Patch #3 (wise2-getline.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/HMMer2/sqio.c Patch #4 (wise2-ld--as-needed.patch): + echo 'Patch #4 (wise2-ld--as-needed.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/models/makefile + chmod a-x src/external/mott/mott_api.c + chmod a-x src/external/mott/mott_api.h + chmod a-x src/external/mott/gaplib.c + chmod a-x src/external/mott/gapstat.h + sed -i s#/usr/local/bin/perl#/usr/bin/perl# docs/gettex.pl + chmod -x test_data/rrm.HMM + for i in base dynlibsrc dyc + cp src/base/LICENSE LICENSE.base + for i in base dynlibsrc dyc + cp src/dynlibsrc/LICENSE LICENSE.dynlibsrc + for i in base dynlibsrc dyc + cp src/dyc/LICENSE LICENSE.dyc + cp src/models/GNULICENSE LICENSE.GPL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Cj0mLe + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + export 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + make -C src CC=gcc 'CFLAGS= -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L' all make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' (cd base ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libwisebase.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/base' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseconfig.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisestring.c wisestring.dy: In function 'Wise2_breakstring_protect': wisestring.dy:632:14: warning: variable 'c' set but not used [-Wunused-but-set-variable] 632 | auto char c; | ^ wisestring.dy: In function 'Wise2_show_text': wisestring.dy:761:9: warning: 'pushpoi' may be used uninitialized in this function [-Wmaybe-uninitialized] 761 | line=pushpoi+1; | ~~~~^~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseerror.c wiseerror.dy: In function 'Wise2_show_message_stack': wiseerror.dy:176:16: warning: unused variable 'count' [-Wunused-variable] 176 | register int count; | ^~~~~ wiseerror.dy:175:16: warning: unused variable 'j' [-Wunused-variable] 175 | register int j; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisememman.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisefile.c wisefile.dy: In function 'Wise2_myfclose': wisefile.dy:72:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'FILE *' [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * wisefile.dy: In function 'Wise2_append_file_to_path': wisefile.dy:141:10: warning: variable 'runner' set but not used [-Wunused-but-set-variable] 141 | char * runner; | ^~~~~~ In file included from /usr/include/string.h:495, from wisebase.h:8, from wisefile.h:6, from wisefile.c:4: In function 'strncpy', inlined from 'Wise2_openfile' at wisefile.dy:212:3: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 12 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiserandom.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisetime.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseoverlay.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisestreaminterface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L commandline.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/base' (cd HMMer2 ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libhmmer.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c alphabet.c alphabet.c: In function 'DigitizeAlignment': alphabet.c:237:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ alphabet.c: In function 'P7CountSymbol': alphabet.c:264:13: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | counters[symidx] += wt; | ^ In file included from /usr/include/string.h:495, from alphabet.c:16: In function 'strncpy', inlined from 'SetAlphabet' at alphabet.c:108:5: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c core_algorithms.c core_algorithms.c: In function 'P7ViterbiTrace': core_algorithms.c:420:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized] 420 | int k; /* position in model (1..M) */ | ^ core_algorithms.c: In function 'P7ParsingViterbi': core_algorithms.c:958:11: warning: 'cur' may be used uninitialized in this function [-Wmaybe-uninitialized] 958 | sc = xmx[cur][XMC] + hmm->xsc[XTC][MOVE]; | ^ core_algorithms.c: In function 'P7WeeViterbi': core_algorithms.c:1082:19: warning: 't2' may be used uninitialized in this function [-Wmaybe-uninitialized] 1082 | tassign[s2] = t2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1081:19: warning: 'k2' may be used uninitialized in this function [-Wmaybe-uninitialized] 1081 | kassign[s2] = k2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1240:10: warning: 'ret_sc' may be used uninitialized in this function [-Wmaybe-uninitialized] 1240 | return ret_sc; | ^~~~~~ core_algorithms.c: In function 'Plan7ESTViterbi': core_algorithms.c:1312:24: warning: 'codon' may be used uninitialized in this function [-Wmaybe-uninitialized] 1312 | mmx[i][k] += hmm->dnam[codon][k]; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c debug.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c emit.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c emulation.c In file included from emulation.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c histogram.c histogram.c: In function 'PrintASCIIHistogram': histogram.c:200:8: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] 200 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.c: In function 'EVDMaxLikelyFit': histogram.c:1251:14: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized] 1251 | mu = -1. * log(esum / total) / lambda; | ^~~~~~~~~~~~~~~~~ histogram.c: In function 'ExtremeValueFitHistogram': histogram.c:659:35: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] 659 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c hmmio.c hmmio.c: In function 'read_asc19hmm': hmmio.c:847:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 847 | if ((s = Getword(fp, sqdARG_INT)) == NULL) goto FAILURE; M = atoi(s); /* model length */ | ^~ hmmio.c:847:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 847 | if ((s = Getword(fp, sqdARG_INT)) == NULL) goto FAILURE; M = atoi(s); /* model length */ | ^ hmmio.c:849:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 849 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; Plan7SetName(hmm, s); /* name */ | ^~ hmmio.c:849:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 849 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; Plan7SetName(hmm, s); /* name */ | ^~~~~~~~~~~~ hmmio.c:850:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 850 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; s2upper(s); /* alphabet type */ | ^~ hmmio.c:850:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 850 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; s2upper(s); /* alphabet type */ | ^~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c mathsupport.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c masks.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c misc.c In file included from misc.c:25: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c modelmakers.c modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:238:11: warning: variable 't_me' set but not used [-Wunused-but-set-variable] 238 | float t_me; /* estimate for an internal M->E transition */ | ^~~~ At top level: modelmakers.c:850:1: warning: 'print_matassign' defined but not used [-Wunused-function] 850 | print_matassign(int *matassign, int alen) | ^~~~~~~~~~~~~~~ modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:378:18: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized] 378 | matassign[i] &= ~ASSIGN_INSERT; | ^~ modelmakers.c:362:27: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized] 362 | if (isgap(aseqs[idx][j-1])) | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c plan7.c plan7.c: In function 'Plan7ESTConfig': plan7.c:793:10: warning: 'tripnull' may be used uninitialized in this function [-Wmaybe-uninitialized] 793 | float *tripnull; /* UNFINISHED!!! */ | ^~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c plan9.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c prior.c prior.c: In function 'P7ReadPrior': prior.c:102:12: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c tophits.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c trace.c In file included from trace.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c aligneval.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c alignio.c alignio.c: In function 'ReadAlignedFASTA': alignio.c:143:16: warning: 'aseq' may be used uninitialized in this function [-Wmaybe-uninitialized] 143 | *ret_aseq = aseq; | ~~~~~~~~~~~~~^~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c cluster.c cluster.c: In function 'Cluster': cluster.c:256:10: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized] 256 | if (i != Np-2) | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c dayhoff.c dayhoff.c: In function 'ParsePAMFile': dayhoff.c:164:32: warning: 'scale' may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (gotscale) *ret_scale = scale; | ~~~~~~~~~~~^~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c file.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c getopt.c getopt.c: In function 'Getopt': getopt.c:118:25: warning: 'opti' may be used uninitialized in this function [-Wmaybe-uninitialized] 118 | *ret_optname = opt[opti].name; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c gnuregex.c gnuregex.c:35: warning: "_GNU_SOURCE" redefined 35 | #define _GNU_SOURCE | : note: this is the location of the previous definition gnuregex.c: In function 'regex_compile': gnuregex.c:1613:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 1613 | if (COMPILE_STACK_EMPTY) | ^ gnuregex.c:1633:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 1633 | if (COMPILE_STACK_EMPTY) | ^ gnuregex.c: In function 're_match_2': gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:4061:19: warning: variable 'sdummy' set but not used [-Wunused-but-set-variable] 4061 | char *sdummy; | ^~~~~~ gnuregex.c:4060:28: warning: variable 'pdummy' set but not used [-Wunused-but-set-variable] 4060 | unsigned char *pdummy; | ^~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c interleaved.c interleaved.c: In function 'ReadInterleaved': interleaved.c:427:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] 427 | free(blocks); | ^~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c iupac.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c msf.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c revcomp.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c selex.c selex.c: In function 'ReadSELEX': selex.c:445:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] 445 | free(blocks); | ^~~~~~~~~~~~ selex.c:68:12: warning: 'num' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | int num; /* number of seqs read */ | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sqerror.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sqio.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_ctype.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_math.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_string.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c stack.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c translate.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c types.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c weight.c weight.c: In function 'GSCWeights': weight.c:71:21: warning: 'rwt' may be used uninitialized in this function [-Wmaybe-uninitialized] 71 | lwt[i] = rwt[i] = 0.0; | ~~~~~~~^~~~~ weight.c: In function 'VoronoiWeights': weight.c:291:24: warning: 'best' may be used uninitialized in this function [-Wmaybe-uninitialized] 291 | ainfo->wgt[best] += 1.0; | ^~ ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libdyna.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ aln.c aln.dy: In function 'Wise2_swallow_AlnColumn_multiple': aln.dy:580:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 580 | register int i; | ^ aln.dy: In function 'Wise2_mapped_ascii_AlnBlock': aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ aln.dy: In function 'Wise2_read_dumped_ascii_AlnColumn_line': aln.dy:918:11: warning: variable 'base' set but not used [-Wunused-but-set-variable] 918 | char ** base, **bstr; | ^~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dnamatrix.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ probability.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ alnrange.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ alnconvert.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ basematrix.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shattermatrix.c shattermatrix.dy: In function 'Wise2_new_ShatterMatrixComponent': shattermatrix.dy:124:7: warning: unused variable 'j' [-Wunused-variable] 124 | int j; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_show_PackAln_Debug': matrixdebug.dy:67:7: warning: unused variable 'cum' [-Wunused-variable] 67 | int cum; | ^~~ matrixdebug.dy:66:7: warning: unused variable 'j' [-Wunused-variable] 66 | int j,k; | ^ matrixdebug.dy: In function 'Wise2_user_DebugMatrix': matrixdebug.dy:208:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dpenvelope.c dpenvelope.dy: In function 'Wise2_read_DPEnvelope': dpenvelope.dy:98:11: warning: variable 'base' set but not used [-Wunused-but-set-variable] 98 | char ** base; | ^~~~ dpenvelope.dy: In function 'Wise2_overlap_DPUnit': dpenvelope.dy:68:1: warning: control reaches end of non-void function [-Wreturn-type] 68 | } | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dbsearchimpl.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dprunimpl.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexsequence.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexevalset.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexconsensi.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequence.c sequence.dy: In function 'Wise2_read_fasta_Sequence': sequence.dy:767:11: warning: unused variable 'seen_weight' [-Wunused-variable] 767 | boolean seen_weight = 0; | ^~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequencestream.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ seqalign.c seqalign.dy: In function 'Wise2_read_selex_SeqAlign': seqalign.dy:421:18: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized] 421 | for(seq = buffer+pos;*seq;seq++) { | ~~~~~~^~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hitlist.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsp.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspstream.c hspstream.dy: In function 'Wise2_typed_LinearHSPmanager_from_Stream': hspstream.dy:109:7: warning: unused variable 'i' [-Wunused-variable] 109 | int i; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codon.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ compmat.c compmat.dy: In function 'Wise2_write_Blast_CompMat_alphabet.part.0': compmat.dy:307:3: warning: 'minnumbers[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 307 | fprintf(ofp,"% d",minnumbers[0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codonmatrix.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codonmapper.c codonmapper.dy: In function 'Wise2_new_CodonMapper': codonmapper.dy:379:10: warning: variable 'total_freq' set but not used [-Wunused-but-set-variable] 379 | double total_freq; | ^~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequencedb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hscore.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ seqlookup.c seqlookup.dy: In function 'Wise2_load_SequenceDB_SeqLookupLoadPara': seqlookup.dy:143:7: warning: variable 'base' set but not used [-Wunused-but-set-variable] 143 | int base[5]; | ^~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ arrayseqlookup.c arrayseqlookup.dy: In function 'Wise2_add_ArraySeqHead': arrayseqlookup.dy:294:24: warning: variable 'temp' set but not used [-Wunused-but-set-variable] 294 | ArraySeqLookupUnit * temp; | ^~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genericindexresult.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ linkedlist_lookpos.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ singlenumberspace.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ histogram.c histogram.dy: In function 'Wise2_PrintASCIIHistogram': histogram.dy:276:8: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] 276 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.dy: In function 'Wise2_EVDMaxLikelyFit': histogram.dy:1325:14: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized] 1325 | mu = -1. * log(esum / total) / lambda; | ^~~~~~~~~~~~~~~~~ histogram.dy: In function 'Wise2_ExtremeValueFitHistogram': histogram.dy:647:35: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] 647 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ searchstatinterface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ searchstatlookup.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteindb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ protein.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ pairbase.c pairbase.dy: In function 'Wise2_diagonal_tweak_PairBaseCodonModel': pairbase.dy:48:7: warning: unused variable 'codon_b' [-Wunused-variable] 48 | int codon_b; | ^~~~~~~ pairbase.dy:47:7: warning: unused variable 'codon_a' [-Wunused-variable] 47 | int codon_a; | ^~~~~~~ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModel': pairbase.dy:106:18: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | m->codon[p] = 0.0; | ~~~~~~~~~~~~^~~~~ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModelScore': pairbase.dy:148:18: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] 148 | m->codon[p] = NEGI; gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ pairbaseseq.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomicdb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ randommodel.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ randomdb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomic.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ cdna.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ cdnadb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dna.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ embl.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ gene.c gene.dy: In function 'Wise2_write_Embl_FT_Gene': gene.dy:404:11: warning: 'tr' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | if( tr->ex_len > 1 ) { | ~~^~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ transcript.c transcript.dy: In function 'Wise2_show_Transcript': transcript.dy:170:23: warning: unused variable 'sf' [-Wunused-variable] 170 | SupportingFeature * sf; | ^~ transcript.dy:169:7: warning: unused variable 'k' [-Wunused-variable] 169 | int k; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ translation.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ btcanvas.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ asciibtcanvas.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libdyna_glib.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function 'Wise2_lookup_subseqhash_ghash': subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function 'Wise2_add_seq_subseqhash_ghash': subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function 'Wise2_add_direct_number_subseqhash_ghash': subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ intallocator.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteinstreamedindex.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shadowseq.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shadowseqindex.c shadowseqindex.dy: In function 'Wise2_dump_stats_ShadowSequenceIndex': shadowseqindex.dy:285:15: warning: format '%f' expects argument of type 'double', but argument 4 has type 'long unsigned int' [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsphandler.c hsphandler.dy: In function 'Wise2_truncated_LinearHSPmanager': hsphandler.dy:278:13: warning: variable 'worst' set but not used [-Wunused-but-set-variable] 278 | HSPset ** worst; | ^~~~~ hsphandler.dy: In function 'Wise2_new_consistent_HSPset': hsphandler.dy:342:7: warning: variable 'eaten' set but not used [-Wunused-but-set-variable] 342 | int eaten; | ^~~~~ hsphandler.dy: In function 'Wise2_new_LinearHSPmanager_simple_heuristic': hsphandler.dy:387:7: warning: unused variable 'j' [-Wunused-variable] 387 | int j; | ^ hsphandler.dy:386:7: warning: unused variable 'i' [-Wunused-variable] 386 | int i; | ^ hsphandler.dy: In function 'Wise2_new_HSP_QuerySeqHSP': hsphandler.dy:786:15: warning: variable 'pause_j' set but not used [-Wunused-but-set-variable] 786 | int pause_i,pause_j; | ^~~~~~~ hsphandler.dy:786:7: warning: variable 'pause_i' set but not used [-Wunused-but-set-variable] 786 | int pause_i,pause_j; | ^~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspscaninterface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function 'Wise2_one_off_two_hit_HSPscan_query_direct': hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:192:9: warning: unused variable 'k' [-Wunused-variable] 192 | int i,k,j; | ^ hsp2hitscan.dy:185:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 185 | int score; | ^~~~~ hsp2hitscan.dy:183:7: warning: variable 'no' set but not used [-Wunused-but-set-variable] 183 | int no; | ^~ hsp2hitscan.dy:182:18: warning: unused variable 'head' [-Wunused-variable] 182 | ArraySeqHead * head; | ^~~~ hsp2hitscan.dy:181:7: warning: unused variable 'start_base' [-Wunused-variable] 181 | int start_base; | ^~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupscan.c hsplookupscan.dy: In function 'Wise2_one_off_HSPscan_scan_query_direct': hsplookupscan.dy:144:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 144 | char newseq[5]; | ^~~~~~ hsplookupscan.dy:143:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 143 | int score; | ^~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function 'Wise2_one_off_ordered_HSPscan_scan_query_direct': hsplookupthreaded.dy:263:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int hsplookupthreaded.dy:136:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 136 | int score; | ^~~~~ hsplookupthreaded.dy:116:22: warning: unused variable 'hsp_para' [-Wunused-variable] 116 | LineariseHSPPara * hsp_para; | ^~~~~~~~ hsplookupthreaded.dy: In function 'Wise2_hsp_thread_worker': hsplookupthreaded.dy:659:27: warning: variable 'asl' set but not used [-Wunused-but-set-variable] 659 | auto ArraySeqLookup * asl; | ^~~ hsplookupthreaded.dy:627:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 627 | char newseq[5]; | ^~~~~~ hsplookupthreaded.dy:621:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 621 | int score; | ^~~~~ hsplookupthreaded.dy: In function 'Wise2_merge_HSPmanager': hsplookupthreaded.dy:567:1: warning: control reaches end of non-void function [-Wreturn-type] 567 | } | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ hspthreadeddb.dy:154:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Wise2_HSPDatabaseSegment *' [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspscanruntime.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsptwohitscan.c hsptwohitscan.dy: In function 'Wise2_twohit_one_off_HSPscan_scan_query_direct': hsptwohitscan.dy:113:7: warning: variable 'has_seen' set but not used [-Wunused-but-set-variable] 113 | int has_seen; | ^~~~~~~~ hsptwohitscan.dy:105:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 105 | char newseq[5]; | ^~~~~~ hsptwohitscan.dy:104:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 104 | int score; | ^~~~~ hsptwohitscan.dy: In function 'Wise2_add_to_TwoHitBuffer': hsptwohitscan.dy:354:7: warning: unused variable 'j' [-Wunused-variable] 354 | int j; | ^ hsptwohitscan.dy:353:7: warning: unused variable 'i' [-Wunused-variable] 353 | int i; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteinindexcons.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dnaindexcons.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd mott; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all) make[2]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 64 | free(freq0); | ^~~~ mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' mott_api.c:5:1: note: include '' or provide a declaration of 'free' 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' 104 | free(freqA); | ^~~~ mott_api.c:104:7: note: include '' or provide a declaration of 'free' mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' 144 | free(h+hmin); | ^~~~ mott_api.c:144:5: note: include '' or provide a declaration of 'free' mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' 155 | free(h+hmin); | ^~~~ mott_api.c:155:5: note: include '' or provide a declaration of 'free' mott_api.c:150:9: warning: unused variable 'n' [-Wunused-variable] 150 | int n; | ^ mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: implicit declaration of function 'calloc' [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^~~~~~ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' mott_api.c:179:16: note: include '' or provide a declaration of 'calloc' mott_api.c: In function 'PseudoResidueFrequencies2': mott_api.c:207:12: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^~~~~~~ mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' 230 | double *freq = (double*)calloc(256, sizeof(double)); | ^~~~~~ mott_api.c:230:27: note: include '' or provide a declaration of 'calloc' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c -o gaplib.o gaplib.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[2]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd socket ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libwisesocket.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/socket' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:55:10: warning: unused variable 'ofp' [-Wunused-variable] 55 | FILE * ofp; | ^~~ functionserver.dy: In function 'Wise2_new_FunctionServer': functionserver.dy:216:21: warning: unused variable 'name' [-Wunused-variable] 216 | struct sockaddr * name; | ^~~~ functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ functionclient.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ anonobj.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ transferinterface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/socket' (cd dnaindex ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function 'Wise2_show_KmerAssemblyNode': kmer_assembly.dy:296:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function 'Wise2_remove_sequence_label_KmerAssemblyLink': kmer_assembly.dy:365:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'KmerAssemblyLink *' [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format '%d' expects a matching 'int' argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function 'Wise2_insert_by_kmer_KmerHashIndex': kmer_hash.dy:252:7: warning: unused variable 'i' [-Wunused-variable] 252 | int i; | ^ kmer_hash.dy: In function 'Wise2_free_KmerHashIndex': kmer_hash.dy:318:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_count.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models dnamapping.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function 'Wise2_untangle_KmerAssembly': kmer_assembly_untangler.dy:120:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t' {aka 'long long int'} [-Wformat=] kmer_assembly_untangler.dy:157:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:101:22: warning: variable 'link_set' set but not used [-Wunused-but-set-variable] 101 | KmerAssemblyLink * link_set[1024]; | ^~~~~~~~ kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:444:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected 'int *' but argument is of type 'long int *' 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function 'Wise2_lift_forward_tangled_KmerAssemblyPath': kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t' {aka 'long long int'} [-Wformat=] In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.dy: In function 'Wise2_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.h:102:31: warning: 'newpath' may be used uninitialized in this function [-Wmaybe-uninitialized] 102 | #define free_KmerAssemblyPath Wise2_free_KmerAssemblyPath | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:363:22: note: 'newpath' was declared here 363 | KmerAssemblyPath * newpath; | ^~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c kmer_assembly_contig.dy: In function 'Wise2_KmerAssemblyContigSet_from_KmerAssemblyIndex': kmer_assembly_contig.dy:66:27: warning: unused variable 'final' [-Wunused-variable] 66 | KmerAssemblyContigSet * final; | ^~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function 'Wise2_mark_tangles_KmerAssembly': kmer_assembly_error.dy:93:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function 'Wise2_attempt_resolve_forward_error_KmerAssembly': kmer_assembly_error.dy:208:8: warning: unused variable 'next' [-Wunused-variable] 208 | char next[256]; | ^~~~ kmer_assembly_error.dy: In function 'Wise2_extend_indel_path_KmerAssembly': kmer_assembly_error.dy:351:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int *' [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: returning 'void *' from a function with return type 'boolean' {aka 'int'} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' (cd network ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/network' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c wise_proteinindex_server.c: In function 'main': wise_proteinindex_server.c:93:10: warning: unused variable 'temp' [-Wunused-variable] 93 | char * temp; | ^~~~ wise_proteinindex_server.c:91:10: warning: unused variable 'ior_file' [-Wunused-variable] 91 | char * ior_file; | ^~~~~~~~ wise_proteinindex_server.c:84:7: warning: unused variable 'count' [-Wunused-variable] 84 | int count = 0; | ^~~~~ wise_proteinindex_server.c:76:7: warning: unused variable 'ret' [-Wunused-variable] 76 | int ret; | ^~~ wise_proteinindex_server.c:75:14: warning: unused variable 'seq' [-Wunused-variable] 75 | Sequence * seq; | ^~~ wise_proteinindex_server.c:70:7: warning: unused variable 'i' [-Wunused-variable] 70 | int i; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c client_multihspscan.dy: In function 'Wise2_new_multiclient_HSPScanInterface': client_multihspscan.dy:128:1: warning: control reaches end of non-void function [-Wreturn-type] 128 | } | ^ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/network' (cd models ; make CC="gcc" CFLAGS="-c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/models' gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnal.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnaalign.c dnaalign.c: In function 'Wise2_calculate_shatter_DnaAlign': dnaalign.c:336:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 336 | int j; | ^~ dnaalign.c:335:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 335 | int i; | ^~ dnaalign.c:333:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 333 | boolean calculate_shatter_DnaAlign(DnaAlign * mat,DPEnvelope * dpenv) | ^~~~ dnaalign.c: In function 'Wise2_serial_search_DnaAlign': dnaalign.c:621:9: warning: unused variable 'db_status' [-Wunused-variable] 621 | * | ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:900:19: warning: unused variable 'de' [-Wunused-variable] 900 | */ | ^ dnaalign.c: In function 'Wise2_max_special_strip_DnaAlign': dnaalign.c:1799:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1799 | * Return [UNKN ] Undocumented return value [int] | ^~~~~~ dnaalign.c:1798:9: warning: unused variable 'temp' [-Wunused-variable] 1798 | * | ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:961:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 961 | } | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqaligndisplay.c gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ psw.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ proteinsw.c proteinsw.c: In function 'Wise2_calculate_shatter_ProteinSW': proteinsw.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ proteinsw.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ proteinsw.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:824:19: warning: unused variable 'de' [-Wunused-variable] 824 | ProteinSW * mat; | ^~ proteinsw.c: In function 'Wise2_max_special_strip_ProteinSW': proteinsw.c:1678:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1678 | { | ^ proteinsw.c:1677:9: warning: unused variable 'temp' [-Wunused-variable] 1677 | int max_special_strip_ProteinSW(ProteinSW * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:885:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 885 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sw_wrap.c sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinSW': sw_wrap.dy:355:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 355 | Search_Return_Type ret; | ^~~ sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinABC': sw_wrap.dy:407:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 407 | Search_Return_Type ret; | ^~~ sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinBA': sw_wrap.dy:460:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 460 | Search_Return_Type ret; | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ abc.c abc.c: In function 'Wise2_calculate_shatter_abc': abc.c:123:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 123 | int lenj; | ^~~ abc.c:122:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 122 | int leni; | ^~~ abc.c:120:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 120 | int k; | ^~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:822:19: warning: unused variable 'de' [-Wunused-variable] 822 | abc * mat; | ^ abc.c: In function 'Wise2_max_special_strip_abc': abc.c:1687:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1687 | { | ^ abc.c:1686:9: warning: unused variable 'temp' [-Wunused-variable] 1686 | int max_special_strip_abc(abc * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:883:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 883 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pba.c pba.c: In function 'Wise2_calculate_shatter_ProteinBlockAligner': pba.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 126 | int lenj; | ^~~ pba.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 125 | int leni; | ^~~ pba.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 123 | int k; | ^~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:929:19: warning: unused variable 'de' [-Wunused-variable] 929 | ProteinBlockAligner * mat; | ^~ pba.c: In function 'Wise2_max_special_strip_ProteinBlockAligner': pba.c:1884:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1884 | { | ^ pba.c:1883:9: warning: unused variable 'temp' [-Wunused-variable] 1883 | int max_special_strip_ProteinBlockAligner(ProteinBlockAligner * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:990:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 990 | | ^ gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pswdb.c gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function 'make_SeqAlign_from_align': dbac.c:413:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~^ ~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld dbac.c: In function 'main': dbac.c:463:7: warning: unused variable 'score' [-Wunused-variable] 463 | int score; | ^~~~~ dbac.c:460:19: warning: unused variable 'dmat' [-Wunused-variable] 460 | DnaMatchBlock * dmat; | ^~~~ dbac.c: In function 'showPFF': dbac.c:250:43: warning: 'currMatch' may be used uninitialized in this function [-Wmaybe-uninitialized] 250 | *(currMatch/0.25)))/log(2); | ~~~~~~~~~~^~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dba.c dba.c: In function 'Wise2_calculate_shatter_DnaMatchBlock': dba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ dba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ dba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ dba.c: In function 'Wise2_serial_search_DnaMatchBlock': dba.c:467:9: warning: unused variable 'db_status' [-Wunused-variable] 467 | Search_Return_Type serial_search_DnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp65,DnaMatrix* comp75,DnaMatrix* comp85,DnaMatrix* comp95,Score g,Score u,Score v,Score s,Score b) | ^~~~~~~~~ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:801:19: warning: unused variable 'de' [-Wunused-variable] 801 | DnaMatchBlock * mat; | ^~ dba.c: In function 'Wise2_max_special_strip_DnaMatchBlock': dba.c:1943:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1943 | { | ^ dba.c:1942:9: warning: unused variable 'temp' [-Wunused-variable] 1942 | int max_special_strip_DnaMatchBlock(DnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:862:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 862 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ slimdba.c slimdba.c: In function 'Wise2_calculate_shatter_SlimDnaMatchBlock': slimdba.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ slimdba.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ slimdba.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ slimdba.c: In function 'Wise2_serial_search_SlimDnaMatchBlock': slimdba.c:359:9: warning: unused variable 'db_status' [-Wunused-variable] 359 | Search_Return_Type serial_search_SlimDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp65,Score g,Score u,Score v,Score s,Score b) | ^~~~~~~~~ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:588:19: warning: unused variable 'de' [-Wunused-variable] 588 | SlimDnaMatchBlock * mat; | ^~ slimdba.c: In function 'Wise2_max_special_strip_SlimDnaMatchBlock': slimdba.c:1469:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1469 | { | ^ slimdba.c:1468:9: warning: unused variable 'temp' [-Wunused-variable] 1468 | int max_special_strip_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:649:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 649 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ bigdba.c bigdba.c: In function 'Wise2_calculate_shatter_BigDnaMatchBlock': bigdba.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ bigdba.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ bigdba.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ bigdba.c: In function 'Wise2_serial_search_BigDnaMatchBlock': bigdba.c:507:9: warning: unused variable 'db_status' [-Wunused-variable] 507 | Search_Return_Type serial_search_BigDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp55,DnaMatrix* comp65,DnaMatrix* comp75,DnaMatrix* comp85,DnaMatrix* comp95,Score g,Score g65,Score g55,Score u,Score v,Score s,Score b) | ^~~~~~~~~ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:880:19: warning: unused variable 'de' [-Wunused-variable] 880 | BigDnaMatchBlock * mat; | ^~ bigdba.c: In function 'Wise2_max_special_strip_BigDnaMatchBlock': bigdba.c:2117:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2117 | { | ^ bigdba.c:2116:9: warning: unused variable 'temp' [-Wunused-variable] 2116 | int max_special_strip_BigDnaMatchBlock(BigDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:941:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 941 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbadisplay.c dbadisplay.dy: In function 'Wise2_show_pretty_dba_align_btcanvas': dbadisplay.dy:71:11: warning: variable 'is_reversed' set but not used [-Wunused-but-set-variable] 71 | boolean is_reversed; | ^~~~~~~~~~~ dbadisplay.dy:285:45: warning: 'end_alc' may be used uninitialized in this function [-Wmaybe-uninitialized] 285 | sprintf(buffer,"-%d",two->offset - (end_alc->alu[1]->start+1)); | ~~~~~~~^~~~~ gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser21.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparameter.c geneparameter.dy: In function 'Wise2_GeneParameter21_from_GeneModel': geneparameter.dy:132:25: warning: unused variable 'cse' [-Wunused-variable] 132 | ComplexSequenceEval * cse; | ^~~ geneparameter.dy:131:25: warning: unused variable 'rmds' [-Wunused-variable] 131 | RandomModelDNAScore * rmds; | ^~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestats.c genestats.dy: In function 'Wise2_get_genestat_emission': genestats.dy:753:10: warning: unused variable 'd' [-Wunused-variable] 753 | double d; | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisehsp.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneutil.c geneutil.dy: In function 'Wise2_add_Genes_to_GenomicRegion_new': geneutil.dy:92:15: warning: unused variable 'intron_start' [-Wunused-variable] 92 | AlnColumn * intron_start; | ^~~~~~~~~~~~ geneutil.dy:82:7: warning: unused variable 'count' [-Wunused-variable] 82 | int count = 0; | ^~~~~ geneutil.dy: In function 'Wise2_Gene_from_AlnColumn_new': geneutil.dy:446:20: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized] 446 | exon_end = prev->alu[1]->end +1 - out->start; | ~~~~^~~~~ geneutil.dy:504:16: warning: 'ex' may be used uninitialized in this function [-Wmaybe-uninitialized] 504 | out->end = ex->end + out->start; | ~~^~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneoutput.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatemodel.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genefrequency.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ splicesitemodeler.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise4.c genewise4.c: In function 'Wise2_calculate_shatter_GeneWise4': genewise4.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 126 | int lenj; | ^~~ genewise4.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 125 | int leni; | ^~~ genewise4.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 123 | int k; | ^~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1068:19: warning: unused variable 'de' [-Wunused-variable] 1068 | GeneWise4 * mat; | ^~ genewise4.c: In function 'Wise2_max_special_strip_GeneWise4': genewise4.c:2217:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2217 | { | ^ genewise4.c:2216:9: warning: unused variable 'temp' [-Wunused-variable] 2216 | int max_special_strip_GeneWise4(GeneWise4 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1129:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1129 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise6.c genewise6.c: In function 'Wise2_calculate_shatter_GeneWise6': genewise6.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ genewise6.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ genewise6.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1180:19: warning: unused variable 'de' [-Wunused-variable] 1180 | GeneWise6 * mat; | ^~ genewise6.c: In function 'Wise2_max_special_strip_GeneWise6': genewise6.c:2417:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2417 | { | ^ genewise6.c:2416:9: warning: unused variable 'temp' [-Wunused-variable] 2416 | int max_special_strip_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1241:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1241 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestretch6.c genestretch6.c: In function 'Wise2_calculate_shatter_GeneStretch6': genestretch6.c:130:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 130 | int lenj; | ^~~ genestretch6.c:129:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 129 | int leni; | ^~~ genestretch6.c:127:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 127 | int k; | ^~ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1339:19: warning: unused variable 'de' [-Wunused-variable] 1339 | GeneStretch6 * mat; | ^~ genestretch6.c: In function 'Wise2_PackAln_calculate_Small_GeneStretch6': genestretch6.c:1839:19: warning: unused variable 'pau' [-Wunused-variable] 1839 | int score; | ^ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1400:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1400 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise21.c genewise21.c: In function 'Wise2_calculate_shatter_GeneWise21': genewise21.c:154:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 154 | int lenj; | ^~~ genewise21.c:153:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 153 | int leni; | ^~~ genewise21.c:151:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 151 | int k; | ^~ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2606:19: warning: unused variable 'de' [-Wunused-variable] 2606 | GeneWise21 * mat; | ^~ genewise21.c: In function 'Wise2_PackAln_calculate_Small_GeneWise21': genewise21.c:3507:19: warning: unused variable 'pau' [-Wunused-variable] 3507 | int score; | ^ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2667:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 2667 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop21.c geneloop21.c: In function 'Wise2_calculate_shatter_GeneLoop21': geneloop21.c:147:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 147 | int lenj; | ^~~ geneloop21.c:146:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 146 | int leni; | ^~~ geneloop21.c:144:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 144 | int k; | ^~ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2280:19: warning: unused variable 'de' [-Wunused-variable] 2280 | GeneLoop21 * mat; | ^~ geneloop21.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop21': geneloop21.c:3093:19: warning: unused variable 'pau' [-Wunused-variable] 3093 | int score; | ^ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2341:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 2341 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop6.c geneloop6.c: In function 'Wise2_calculate_shatter_GeneLoop6': geneloop6.c:129:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 129 | int lenj; | ^~~ geneloop6.c:128:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 128 | int leni; | ^~~ geneloop6.c:126:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 126 | int k; | ^~ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1268:19: warning: unused variable 'de' [-Wunused-variable] 1268 | GeneLoop6 * mat; | ^~ geneloop6.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop6': geneloop6.c:1742:19: warning: unused variable 'pau' [-Wunused-variable] 1742 | int score; | ^ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1329:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1329 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genephase6.c genephase6.c: In function 'Wise2_calculate_shatter_GenePhase6': genephase6.c:215:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 215 | int lenj; | ^~~ genephase6.c:214:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 214 | int leni; | ^~~ genephase6.c:212:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 212 | int k; | ^~ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1492:19: warning: unused variable 'de' [-Wunused-variable] 1492 | GenePhase6 * mat; | ^~ genephase6.c: In function 'Wise2_PackAln_calculate_Small_GenePhase6': genephase6.c:2052:19: warning: unused variable 'pau' [-Wunused-variable] 2052 | int score; | ^ genephase6.c: In function 'Wise2_thread_loop_GenePhase6': genephase6.c:873:1: warning: control reaches end of non-void function [-Wreturn-type] 873 | { | ^ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1553:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1553 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlite.c gwlite.c: In function 'Wise2_calculate_shatter_GeneLiteModel': gwlite.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ gwlite.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ gwlite.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1117:19: warning: unused variable 'de' [-Wunused-variable] 1117 | GeneLiteModel * mat; | ^~ gwlite.c: In function 'Wise2_max_special_strip_GeneLiteModel': gwlite.c:2294:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2294 | { | ^ gwlite.c:2293:9: warning: unused variable 'temp' [-Wunused-variable] 2293 | int max_special_strip_GeneLiteModel(GeneLiteModel * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1178:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1178 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlitemodel.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwrap.c gwrap.dy: In function 'Wise2_Hscore_from_TSM_genewise': gwrap.dy:527:25: warning: unused variable 'tempcse' [-Wunused-variable] 527 | ComplexSequenceEval * tempcse; | ^~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ matchsum.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwrap.c estwrap.dy: In function 'Wise2_Hscore_from_TSM_estwise': estwrap.dy:269:22: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 269 | Search_Return_Type ret; | ^~~ estwrap.dy: In function 'Wise2_AlnBlock_from_TSM_estwise_wrap': estwrap.dy:138:14: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 138 | AlnBlock * out; | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodel.c genewisemodel.c: In function 'Wise2_pack_GeneWiseScore': genewisemodel.dy:114:10: warning: 'out' is used uninitialized in this function [-Wuninitialized] 114 | return out; | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_ProteinIntronList': phasemodel.dy:65:10: warning: unused variable 'run2' [-Wunused-variable] 65 | char * run2; | ^~~~ phasemodel.dy:64:10: warning: unused variable 'run1' [-Wunused-variable] 64 | char * run1; | ^~~~ phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:233:7: warning: unused variable 'j' [-Wunused-variable] 233 | int j; | ^ phasemodel.dy:231:14: warning: unused variable 'input' [-Wunused-variable] 231 | Sequence * input; | ^~~~~ phasemodel.dy:241:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:871, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function 'fgets', inlined from 'Wise2_read_fasta_PhasedProtein' at phasemodel.dy:241:3: /usr/include/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ cdparser.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function 'Wise2_write_intron_desc': genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwise3.c estwise3.c: In function 'Wise2_calculate_shatter_EstWise3': estwise3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estwise3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estwise3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1144:19: warning: unused variable 'de' [-Wunused-variable] 1144 | EstWise3 * mat; | ^ estwise3.c: In function 'Wise2_max_special_strip_EstWise3': estwise3.c:2402:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2402 | { | ^ estwise3.c:2401:9: warning: unused variable 'temp' [-Wunused-variable] 2401 | int max_special_strip_EstWise3(EstWise3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1205:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1205 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslim3.c estslim3.c: In function 'Wise2_calculate_shatter_EstSlim3': estslim3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estslim3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estslim3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:936:19: warning: unused variable 'de' [-Wunused-variable] 936 | EstSlim3 * mat; | ^ estslim3.c: In function 'Wise2_max_special_strip_EstSlim3': estslim3.c:1894:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1894 | { | ^ estslim3.c:1893:9: warning: unused variable 'temp' [-Wunused-variable] 1893 | int max_special_strip_EstSlim3(EstSlim3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:997:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 997 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estloop3.c estloop3.c: In function 'Wise2_calculate_shatter_EstLoop3': estloop3.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 125 | int lenj; | ^~~ estloop3.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 124 | int leni; | ^~~ estloop3.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 122 | int k; | ^~ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1312:19: warning: unused variable 'de' [-Wunused-variable] 1312 | EstLoop3 * mat; | ^ estloop3.c: In function 'Wise2_PackAln_calculate_Small_EstLoop3': estloop3.c:1809:19: warning: unused variable 'pau' [-Wunused-variable] 1809 | int score; | ^ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1373:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1373 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estfrag3.c estfrag3.c: In function 'Wise2_calculate_shatter_EstFrag3': estfrag3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estfrag3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estfrag3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:965:19: warning: unused variable 'de' [-Wunused-variable] 965 | EstFrag3 * mat; | ^ estfrag3.c: In function 'Wise2_max_special_strip_EstFrag3': estfrag3.c:2242:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2242 | { | ^ estfrag3.c:2241:9: warning: unused variable 'temp' [-Wunused-variable] 2241 | int max_special_strip_EstFrag3(EstFrag3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:1026:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1026 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslimloop.c estslimloop.c: In function 'Wise2_calculate_shatter_EstSlimLoop3': estslimloop.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 125 | int lenj; | ^~~ estslimloop.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 124 | int leni; | ^~~ estslimloop.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 122 | int k; | ^~ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1114:19: warning: unused variable 'de' [-Wunused-variable] 1114 | EstSlimLoop3 * mat; | ^~ estslimloop.c: In function 'Wise2_PackAln_calculate_Small_EstSlimLoop3': estslimloop.c:1535:19: warning: unused variable 'pau' [-Wunused-variable] 1535 | int score; | ^ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1175:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1175 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwquickdb.c gwquickdb.dy: In function 'Wise2_init_GeneWiseQuickDB': gwquickdb.dy:46:1: warning: control reaches end of non-void function [-Wreturn-type] 46 | } | ^ gwquickdb.dy: In function 'Wise2_reload_GeneWiseQuickDB': gwquickdb.dy:65:1: warning: control reaches end of non-void function [-Wreturn-type] 65 | } | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatedb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pfamhmmer1db.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pwmdna.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodeldb.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqhit.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ standardout.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser4.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estquick3.c estquick3.c: In function 'Wise2_calculate_shatter_EstQuick3': estquick3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estquick3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estquick3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:860:19: warning: unused variable 'de' [-Wunused-variable] 860 | EstQuick3 * mat; | ^~ estquick3.c: In function 'Wise2_max_special_strip_EstQuick3': estquick3.c:1766:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1766 | { | ^ estquick3.c:1765:9: warning: unused variable 'temp' [-Wunused-variable] 1765 | int max_special_strip_EstQuick3(EstQuick3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:921:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 921 | | ^ gcc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function 'build_objects': genewise.c:446:10: warning: unused variable 'ifp' [-Wunused-variable] 446 | FILE * ifp; | ^~~ gcc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/dyna.h:53, from threestatemodel.h:7, from wise2xhmmer2.h:24, from genewisedb.c:4: genewisedb.c: In function 'show_output': ../dynlibsrc/genomicregion.h:453:35: warning: 'cgr' may be used uninitialized in this function [-Wmaybe-uninitialized] 453 | #define add_Gene_to_GenomicRegion Wise2_add_Gene_to_GenomicRegion | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genewisedb.c:216:19: note: 'cgr' was declared here 216 | GenomicRegion * cgr; | ^~~ gcc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/seqalign.h:6, from wise2xhmmer2.h:23, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized in this function [-Wmaybe-uninitialized] 665 | #define add_SequenceSet Wise2_add_SequenceSet | ^~~~~~~~~~~~~~~~~~~~~ estwisedb.c:183:17: note: 'set' was declared here 183 | SequenceSet * set; | ^~~ In file included from estwisedb.c:16: estwrap.h:166:36: warning: 'anchored' may be used uninitialized in this function [-Wmaybe-uninitialized] 166 | #define write_mul_estwise_AlnBlock Wise2_write_mul_estwise_AlnBlock | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ estwisedb.c:182:14: note: 'anchored' was declared here 182 | AlnBlock * anchored; | ^~~~~~~~ gcc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function 'main': genomewise.c:95:10: warning: unused variable 'divide_string' [-Wunused-variable] 95 | char * divide_string = "//"; | ^~~~~~~~~~~~~ genomewise.c:81:7: warning: unused variable 'kbyte' [-Wunused-variable] 81 | int kbyte = 10000; | ^~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise9.c genomewise9.c: In function 'Wise2_calculate_shatter_GenomeWise9': genomewise9.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 137 | int lenj; | ^~~ genomewise9.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 136 | int leni; | ^~~ genomewise9.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 134 | int k; | ^~ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1331:19: warning: unused variable 'de' [-Wunused-variable] 1331 | GenomeWise9 * mat; | ^~ genomewise9.c: In function 'Wise2_PackAln_calculate_Small_GenomeWise9': genomewise9.c:1895:19: warning: unused variable 'pau' [-Wunused-variable] 1895 | int score; | ^ genomewise9.c: In function 'Wise2_thread_loop_GenomeWise9': genomewise9.c:745:1: warning: control reaches end of non-void function [-Wreturn-type] 745 | { | ^ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1392:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1392 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genome_evidence.c genome_evidence.dy: In function 'Wise2_free_GenomeEvidenceUnit': genome_evidence.dy:61:1: warning: control reaches end of non-void function [-Wreturn-type] 61 | } | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment to 'int (*)(void *)' from incompatible pointer type 'Wise2_EstEvidence * (*)(Wise2_EstEvidence *)' [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ est_evidence.dy: In function 'Wise2_est_start_pot': est_evidence.dy:183:7: warning: unused variable 'i' [-Wunused-variable] 183 | int i; | ^ est_evidence.dy: In function 'Wise2_est_stop_pot': est_evidence.dy:203:7: warning: unused variable 'i' [-Wunused-variable] 203 | int i; | ^ gcc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function 'make_PairBaseCodonModelScore': sywise.c:64:10: warning: unused variable 'ifp' [-Wunused-variable] 64 | FILE * ifp; | ^~~ sywise.c: In function 'show_score_sequence': sywise.c:117:37: warning: array subscript has type 'char' [-Wchar-subscripts] 117 | match_score = m->base[pbs->seq[alc->alu[1]->start+1]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c:118:38: warning: array subscript has type 'char' [-Wchar-subscripts] 118 | match_score += m->base[pbs->seq[alc->alu[1]->start+2]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c:119:38: warning: array subscript has type 'char' [-Wchar-subscripts] 119 | match_score += m->base[pbs->seq[alc->alu[1]->start+3]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c: In function 'main': sywise.c:212:11: warning: unused variable 'show_gene_raw' [-Wunused-variable] 212 | boolean show_gene_raw = 0; | ^~~~~~~~~~~~~ sywise.c:211:11: warning: unused variable 'show_trans' [-Wunused-variable] 211 | boolean show_trans = 1; | ^~~~~~~~~~ sywise.c:204:27: warning: variable 'std_opt' set but not used [-Wunused-but-set-variable] 204 | StandardOutputOptions * std_opt; | ^~~~~~~ sywise.c:202:13: warning: unused variable 'trans' [-Wunused-variable] 202 | Protein * trans; | ^~~~~ sywise.c:201:19: warning: variable 'gr2' set but not used [-Wunused-but-set-variable] 201 | GenomicRegion * gr2; | ^~~ sywise.c:183:13: warning: unused variable 'score_mat' [-Wunused-variable] 183 | CompMat * score_mat; | ^~~~~~~~~ sywise.c:168:7: warning: unused variable 'i' [-Wunused-variable] 168 | int i; | ^ In file included from sywise.c:1: sywise20.h:328:46: warning: 'pal' may be used uninitialized in this function [-Wmaybe-uninitialized] 328 | #define convert_PackAln_to_AlnBlock_SyWise20 Wise2_convert_PackAln_to_AlnBlock_SyWise20 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sywise.c:196:13: note: 'pal' was declared here 196 | PackAln * pal; | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise20.c sywise20.c: In function 'Wise2_calculate_shatter_SyWise20': sywise20.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 137 | int lenj; | ^~~ sywise20.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 136 | int leni; | ^~~ sywise20.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 134 | int k; | ^~ sywise20.c: In function 'Wise2_serial_search_SyWise20': sywise20.c:789:9: warning: unused variable 'db_status' [-Wunused-variable] 789 | Search_Return_Type serial_search_SyWise20(Hscore * out,SyExonScore* exonmodel,ComplexSequence* seq ,PairBaseCodonModelScore* codon,PairBaseModelScore* nonc,PairBaseCodonModelScore* start,PairBaseCodonModelScore* stop,Score intron_open,Score gene_open,Score nonc_cost) | ^~~~~~~~~ sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1355:19: warning: unused variable 'de' [-Wunused-variable] 1355 | SyWise20 * mat; | ^ sywise20.c: In function 'Wise2_PackAln_calculate_Small_SyWise20': sywise20.c:1943:19: warning: unused variable 'pau' [-Wunused-variable] 1943 | int score; | ^ sywise20.c: In function 'Wise2_thread_loop_SyWise20': sywise20.c:764:1: warning: control reaches end of non-void function [-Wreturn-type] 764 | { | ^ sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1416:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1416 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ syexonmodel.c gcc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function 'pseudo_gene_assessment': pseudowise.c:99:32: warning: array subscript has type 'char' [-Wchar-subscripts] 99 | if( protein->comp[aa][pep->seq[pep_pos]] < 0 ) { | ~~~~~~~~^~~~~~~~~ pseudowise.c:57:9: warning: unused variable 'j' [-Wunused-variable] 57 | int i,j; | ^ pseudowise.c:57:7: warning: unused variable 'i' [-Wunused-variable] 57 | int i,j; | ^ pseudowise.c: In function 'main': pseudowise.c:180:7: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 180 | int offset; | ^~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise7.c pseudowise7.c: In function 'Wise2_calculate_shatter_PseudoWise7': pseudowise7.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ pseudowise7.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ pseudowise7.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1207:19: warning: unused variable 'de' [-Wunused-variable] 1207 | PseudoWise7 * mat; | ^~ pseudowise7.c: In function 'Wise2_max_special_strip_PseudoWise7': pseudowise7.c:2471:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2471 | { | ^ pseudowise7.c:2470:9: warning: unused variable 'temp' [-Wunused-variable] 2470 | int max_special_strip_PseudoWise7(PseudoWise7 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1268:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 1268 | | ^ gcc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localdba.c localdba.c: In function 'Wise2_calculate_shatter_LocalDnaMatchBlock': localdba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ localdba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ localdba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ localdba.c: In function 'Wise2_serial_search_LocalDnaMatchBlock': localdba.c:487:9: warning: unused variable 'db_status' [-Wunused-variable] 487 | Search_Return_Type serial_search_LocalDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,LocalCisHitScore* lchs) | ^~~~~~~~~ localdba.c: In function 'Wise2_PackAln_bestmemory_LocalDnaMatchBlock': localdba.c:841:19: warning: unused variable 'de' [-Wunused-variable] 841 | LocalDnaMatchBlock * mat; | ^~ localdba.c: In function 'Wise2_max_special_strip_LocalDnaMatchBlock': localdba.c:1984:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1984 | { | ^ localdba.c:1983:9: warning: unused variable 'temp' [-Wunused-variable] 1983 | int max_special_strip_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ localdba.c: In function 'Wise2_PackAln_bestmemory_LocalDnaMatchBlock': localdba.c:902:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 902 | | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c localcishit.dy: In function 'Wise2_expand_to_subhits_LocalCisHitSet': localcishit.dy:91:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 91 | int score; | ^~~~~ localcishit.dy:90:7: warning: unused variable 'score_start' [-Wunused-variable] 90 | int score_start; | ^~~~~~~~~~~ localcishit.dy:89:7: warning: unused variable 'tend' [-Wunused-variable] 89 | int tend; | ^~~~ localcishit.dy:88:7: warning: unused variable 'qend' [-Wunused-variable] 88 | int qend; | ^~~~ localcishit.dy:87:7: warning: variable 'tstart' set but not used [-Wunused-but-set-variable] 87 | int tstart; | ^~~~~~ localcishit.dy:86:7: warning: variable 'qstart' set but not used [-Wunused-but-set-variable] 86 | int qstart; | ^~~~~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localcispara.c gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment to 'char' from 'void *' makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;iseed = temp; | ~~~~~~~~~~^~~~~~ transfactor.dy: In function 'Wise2_read_ben_IUPAC_TransFactorSet': transfactor.dy:680:21: warning: '%s' directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); | ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:871, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 529 bytes into a destination of size 512 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ transfactor.dy: In function 'Wise2_calculate_TransFactorMatchSet': transfactor.dy:437:9: warning: 'cutoff' may be used uninitialized in this function [-Wmaybe-uninitialized] 437 | if( rev_prob > cutoff ) { | ^ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pairwiseshortdna.c pairwiseshortdna.dy: In function 'Wise2_query_to_reverse_target': pairwiseshortdna.dy:56:11: warning: variable 'reverse_tree' set but not used [-Wunused-but-set-variable] 56 | GTree * reverse_tree; | ^~~~~~~~~~~~ pairwiseshortdna.dy:55:11: warning: variable 'forward_tree' set but not used [-Wunused-but-set-variable] 55 | GTree * forward_tree; | ^~~~~~~~~~~~ gcc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:73:7: warning: unused variable 'c' [-Wunused-variable] 73 | int c; | ^ scanwisep.c:72:7: warning: unused variable 'ret' [-Wunused-variable] 72 | int ret; | ^~~ scanwisep.c:70:14: warning: unused variable 'seq' [-Wunused-variable] 70 | Sequence * seq; | ^~~ scanwisep.c: In function 'HitPair_from_HSPset_sw': scanwisep.c:305:7: warning: unused variable 'i' [-Wunused-variable] 305 | int i; | ^ scanwisep.c: In function 'HitList_from_LinearHSPmanager_sw': scanwisep.c:326:30: warning: unused variable 'conv' [-Wunused-variable] 326 | struct convert_data_fulldp conv; | ^~~~ scanwisep.c: In function 'main': scanwisep.c:476:25: warning: variable 'ssl' set but not used [-Wunused-but-set-variable] 476 | SearchStatInterface * ssl; | ^~~ scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:144:10: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 144 | return out; | ^~~ gcc -c -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 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c hsp2aln_sw.dy: In function 'Wise2_worker_thread_LM2HitList': hsp2aln_sw.dy:119:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 119 | if( tm->current_pos >= tm->input->len || tm->para->no_hitalns > 0 && tm->current_pos > tm->para->no_hitalns || | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: creating libmodel.a make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/models' make bin make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /builddir/build/BUILD/wise2.4.1/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' make: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.wPDvyb + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 ++ dirname /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 ~/build/BUILD/wise2.4.1/src/bin ~/build/BUILD/wise2.4.1 + cd wise2.4.1 + pushd src/bin + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dba /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dnal /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwise /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwisedb /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewise /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewisedb /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 promoterwise /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 scanwise /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 scanwise_server /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 psw /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 pswdb /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin ~/build/BUILD/wise2.4.1 + popd + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/wise2 ~/build/BUILD/wise2.4.1/wisecfg ~/build/BUILD/wise2.4.1 + pushd wisecfg + install -pm 644 BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd cb.tmf codon.martian codon.table gene.stat gon120.bla gon160.bla gon200.bla gon250.bla gon350.bla human.gf human.gp human.stats idenity.bla methods pb.gf pombe.gf tm.pri wag55 wag65 wag75 wag85 wise.2 wise.per worm.gf /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/wise2 + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/wise2/examples + pushd test_data ~/build/BUILD/wise2.4.1/test_data ~/build/BUILD/wise2.4.1 + install -pm 644 HOX.HMM Q8NAN2.dna Q8NAN2.pep README alignwise.gen db.hmm dummy_hox.dna epo.genomic epo.pep fugu.gen fugu_human.pep hn_est.fa human.genomic jason.dna jason.pep keratin_intron.human keratin_intron.mouse pep.fa phased_roa1.pep road.pep rpo_fugu.gen rpo_h_f.anchor rpo_h_m.anchor rpo_h_r.anchor rpo_human.gen rpo_human.intron rpo_human.pep rpo_mouse.gen rpo_rat.gen rrm.HMM rua1.pep vav.dna vav_promoter.human vav_promoter.mouse xeno.cdna xeno.pep /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/wise2/examples + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/etc/profile.d + echo 'export WISECONFIGDIR=/usr/share/wise2/' + echo 'setenv WISECONFIGDIR /usr/share/wise2/' + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 2.4.1-10.fc33 --unique-debug-suffix -2.4.1-10.fc33.riscv64 --unique-debug-src-base wise2-2.4.1-10.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/wise2.4.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/dba extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/dba explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/estwise explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/dnal explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/estwisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/estwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/dnal extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/estwisedb explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/genewise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/genewise explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/genewisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/genewisedb explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/promoterwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/promoterwise explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/psw extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/psw explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/pswdb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/pswdb explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/scanwise explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/scanwise_server extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/scanwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/bin/scanwise_server original debug info size: 40352kB, size after compression: 36356kB /usr/lib/rpm/sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. 22705 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /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 *** WARNING: ./usr/src/debug/wise2-2.4.1-10.fc33.riscv64/src/base/wiseoverlay.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-10.fc33.riscv64/src/base/wisememman.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-10.fc33.riscv64/src/base/wisefile.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-10.fc33.riscv64/src/base/wisetime.dy is executable but has no shebang, removing executable bit Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.elae4d + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + export WISECONFIGDIR=/builddir/build/BUILD/wise2.4.1/wisecfg + WISECONFIGDIR=/builddir/build/BUILD/wise2.4.1/wisecfg + make -C src test make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' cd test ; perl testman.pl -cf ../wisecfg < short.test >>> Doing promoterwise promoterwise standard test >>> Calling [../bin/promoterwise -silent pw.human pw.mouse > TEMP-PW] >>> promoterwise ... Failed >>> Doing basic-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] >>> basic-cdna ... Failed >>> Doing basic-genomic genomic test case (protein v genomic), all outputs >>> Calling [../bin/genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Warning Error Attempting to access CompMat with aminoacid numbers 190:0 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:1 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:2 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:3 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:4 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:5 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:6 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:7 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:8 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:9 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:10 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:11 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:12 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:13 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:14 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:15 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:16 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:17 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:18 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:19 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:20 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:21 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:22 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:23 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:24 (they must be bound between 0:26, returning 0 here Warning Error Attempting to access CompMat with aminoacid numbers 190:25 (they must be bound between 0:26, returning 0 here >>> basic-genomic ... Failed >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] Warning Error Strangely truncated line in fasta file >>> hmm-binary-cdna ... Failed >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match >>> Calling [../bin/genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] Warning Error Strangely truncated line in fasta file Information In making HSHNCPA1 a genomic sequence, converted 3 bases (0.7%) to N's from non ATGCN GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna ... Passed >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match >>> Calling [../bin/estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] Warning Error Strangely truncated line in fasta file Information In making HSHNCPA1 a cdna sequence, converted 3 bases (0.7%) to N's from non ATGCN EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna-est ... Failed >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs >>> Calling [../bin/genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] Warning Error Strangely truncated line in fasta file >>> hmm-ascii-genomic ... Failed >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] Warning Error DB searching: just finished [Query Pos: 0] [Target Pos: 5] Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file >>> genewise-db ... Passed >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] Warning Error DB searching: just finished [Query Pos: 0] [Target Pos: 5] Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file >>> genewise-db-lite ... Passed >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] Warning Error DB searching: just finished [Query Pos: 0] [Target Pos: 5] Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file >>> estwise-db ... Passed >>> Doing pswdb Protein smith waterman db search >>> Calling [../bin/pswdb road.pep pep.fa -quiet > TEMP ] Warning Error Strangely truncated line in fasta file Warning Error DB searching: just finished [Query Pos: 0] [Target Pos: 1] Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file >>> pswdb ... Failed >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching >>> Calling [../bin/genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] Warning Error Strangely truncated line in fasta file >>> genewisedb-pfam-mode ... Failed Tests failed PLEASE: email ewan birney (birney@sanger.ac.uk) with the test.results file make: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' + RPM_EC=0 ++ jobs -p + exit 0 Processing files: wise2-2.4.1-10.fc33.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.JGfAEe + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2 + cp -pr README /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.io1JNc + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.base /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dynlibsrc /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dyc /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.GPL /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: config(wise2) = 2.4.1-10.fc33 wise2 = 2.4.1-10.fc33 wise2(riscv-64) = 2.4.1-10.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) rtld(GNU_HASH) Processing files: wise2-doc-2.4.1-10.fc33.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SLnl5b + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-doc + cp -pr docs /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.1lbxCc + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2-doc + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/licenses/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-doc = 2.4.1-10.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-examples-2.4.1-10.fc33.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.eSJ2sc + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-examples + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-examples + cp -pr test_data/README /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64/usr/share/doc/wise2-examples + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-examples = 2.4.1-10.fc33 wise2-examples(riscv-64) = 2.4.1-10.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debugsource-2.4.1-10.fc33.riscv64 Provides: wise2-debugsource = 2.4.1-10.fc33 wise2-debugsource(riscv-64) = 2.4.1-10.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debuginfo-2.4.1-10.fc33.riscv64 Provides: debuginfo(build-id) = 03aa00bd57723e8af983c20d5c4e30a62ae2f9fe debuginfo(build-id) = 166887f178267e397afec43c664ea6e64f4813bb debuginfo(build-id) = 3f582f8d6a352ba37794ebbb0a1359fe84f16ad4 debuginfo(build-id) = 424de06444b7dadf000b0a23f02bdbb1a575c843 debuginfo(build-id) = 80f9bfa39dd8dd23b5ff8e9ae9f0e0abcd0cf891 debuginfo(build-id) = b4b7bc2b8f025ed435f698a34f0f52540031a9d0 debuginfo(build-id) = b7a5cfa2de60987f6b666f0609f3c8d692d030a8 debuginfo(build-id) = c851a07c552b1dab7057cdba17bcdf1b28d6d8e4 debuginfo(build-id) = cb2411cefc71f0458c06e2efdfdb908e204672d1 debuginfo(build-id) = cd1851a2fbe0b827b8084c82161a4654f4e1ba83 debuginfo(build-id) = e1a887a30970b43df185cba52d4a402c6665fbb6 wise2-debuginfo = 2.4.1-10.fc33 wise2-debuginfo(riscv-64) = 2.4.1-10.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: wise2-debugsource(riscv-64) = 2.4.1-10.fc33 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 Wrote: /builddir/build/RPMS/wise2-doc-2.4.1-10.fc33.noarch.rpm Wrote: /builddir/build/RPMS/wise2-examples-2.4.1-10.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-2.4.1-10.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-debugsource-2.4.1-10.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-debuginfo-2.4.1-10.fc33.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.KOnBHc + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-10.fc33.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0