Mock Version: 2.15 Mock Version: 2.15 Mock Version: 2.15 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/wise2.spec'], chrootPath='/var/lib/mock/f38-build-693987-85046/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': 'C.UTF-8'}shell=Falselogger=timeout=1209600uid=991gid=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': 'C.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=1674259200 Wrote: /builddir/build/SRPMS/wise2-2.4.1-17.fc38.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/f38-build-693987-85046/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': 'C.UTF-8'}shell=Falselogger=timeout=1209600uid=991gid=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': 'C.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1674259200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OkztJM + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf wise2.4.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/wise2.4.1.tar.gz + 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 -f -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 -f -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 -f -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 + echo 'Patch #3 (wise2-getline.patch):' Patch #3 (wise2-getline.patch): + /usr/bin/patch --no-backup-if-mismatch -f -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 -f -p1 --fuzz=0 patching file src/models/makefile + echo 'Patch #6 (wise2-c99.patch):' Patch #6 (wise2-c99.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/HMMer2/prior.c patching file src/external/mott/mott_api.c + 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.M8Kycw + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd wise2.4.1 + export 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + make -C src CC=gcc 'CFLAGS= -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L' all make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' (cd base ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libwisebase.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/base' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiseconfig.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisestring.c wisestring.dy: In function 'Wise2_breakstring_protect': wisestring.dy:632:21: warning: variable 'c' set but not used [-Wunused-but-set-variable] 632 | auto char c; | ^ wisestring.dy: In function 'Wise2_show_text': wisestring.dy:771:23: warning: 'pushpoi' may be used uninitialized [-Wmaybe-uninitialized] 771 | line=pushpoi+1; | ~~~~^~~~~~~~~~ wisestring.dy:741:9: note: 'pushpoi' was declared here 741 | char *pushpoi; | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisememman.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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; | ^~~~~~ wisefile.dy: In function 'Wise2_openfile': wisefile.dy:212:3: warning: 'strncpy' specified bound 12 equals destination size [-Wstringop-truncation] 212 | strncpy(prot,passedprot,12); | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiserandom.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisetime.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiseoverlay.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisestreaminterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L commandline.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libhmmer.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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; | ^ alphabet.c: In function 'SetAlphabet': alphabet.c:108:5: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 108 | strncpy(Alphabet, "ACGTUNRYMKSWHBVDX", 17); | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c core_algorithms.c core_algorithms.c: In function 'P7ViterbiTrace': core_algorithms.c:513:20: warning: 'k' may be used uninitialized [-Wmaybe-uninitialized] 513 | sc = imx[i+1][k] - hmm->isc[(int) dsq[i+1]][k]; | ^ core_algorithms.c:420:7: note: 'k' was declared here 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 [-Wmaybe-uninitialized] 958 | sc = xmx[cur][XMC] + hmm->xsc[XTC][MOVE]; | ^ core_algorithms.c:846:10: note: 'cur' was declared here 846 | int cur, prv; /* indices for rolling dp matrix */ | ^~~ core_algorithms.c: In function 'P7WeeViterbi': core_algorithms.c:1081:19: warning: 'k2' may be used uninitialized [-Wmaybe-uninitialized] 1081 | kassign[s2] = k2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1432:16: note: 'k2' was declared here 1432 | int k2; | ^~ core_algorithms.c:1082:19: warning: 't2' may be used uninitialized [-Wmaybe-uninitialized] 1082 | tassign[s2] = t2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1433:16: note: 't2' was declared here 1433 | enum p7stype t2; | ^~ core_algorithms.c:1240:10: warning: 'ret_sc' may be used uninitialized [-Wmaybe-uninitialized] 1240 | return ret_sc; | ^~~~~~ core_algorithms.c:1047:16: note: 'ret_sc' was declared here 1047 | float ret_sc; /* optimal score over complete seq */ | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c debug.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c emit.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c histogram.c histogram.c: In function 'PrintASCIIHistogram': histogram.c:223:26: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 223 | for (num = 0; lowbound > h->lowscore; lowbound--) | ~~~~~~~~~^~~~~~~~~~~~~ histogram.c:200:8: note: 'lowbound' was declared here 200 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.c: In function 'EVDMaxLikelyFit': histogram.c:1249:13: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1249 | total += mult; | ~~~~~~^~~~~~~ histogram.c:1171:10: note: 'total' was declared here 1171 | double total; | ^~~~~ histogram.c: In function 'ExtremeValueFitHistogram': histogram.c:659:42: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 659 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ histogram.c:576:10: note: 'z' was declared here 576 | int z; /* number of censored samples */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c mathsupport.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c masks.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 */ | ^~~~ modelmakers.c: At top level: modelmakers.c:850:1: warning: 'print_matassign' defined but not used [-Wunused-function] 850 | print_matassign(int *matassign, int alen) | ^~~~~~~~~~~~~~~ In file included from structs.h:22, from modelmakers.c:29: modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:362:27: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized] 362 | if (isgap(aseqs[idx][j-1])) | ^ modelmakers.c:224:14: note: 'j' was declared here 224 | int i, j; /* positions in alignment */ | ^ modelmakers.c:378:14: warning: 'first' may be used uninitialized [-Wmaybe-uninitialized] 378 | matassign[i] &= ~ASSIGN_INSERT; | ~~~~~~~~~^~~ modelmakers.c:235:11: note: 'first' was declared here 235 | int first, last; /* positions of first and last cols [1..alen] */ | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c plan7.c plan7.c: In function 'Plan7ESTConfig': plan7.c:793:10: warning: 'tripnull' may be used uninitialized [-Wmaybe-uninitialized] 793 | float *tripnull; /* UNFINISHED!!! */ | ^~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c plan9.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c prior.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c tophits.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c aligneval.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c alignio.c alignio.c: In function 'ReadAlignedFASTA': alignio.c:143:16: warning: 'aseq' may be used uninitialized [-Wmaybe-uninitialized] 143 | *ret_aseq = aseq; | ~~~~~~~~~~~~~^~~~~~ alignio.c:109:11: note: 'aseq' was declared here 109 | char **aseq; /* aligned sequences */ | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c cluster.c cluster.c: In function 'Cluster': cluster.c:210:31: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized] 210 | tree[Np-2].right = coord[j]; | ^ cluster.c:152:17: note: 'j' was declared here 152 | int i, j; /* coords of minimum difference */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c dayhoff.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c file.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c getopt.c getopt.c: In function 'Getopt': getopt.c:118:25: warning: 'opti' may be used uninitialized [-Wmaybe-uninitialized] 118 | *ret_optname = opt[opti].name; | ^ getopt.c:62:7: note: 'opti' was declared here 62 | int opti; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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, | ^~~~~~~~~~~~~~~~~ gnuregex.c: In function 'regex_compile': gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c interleaved.c interleaved.c: In function 'ReadInterleaved': interleaved.c:427:3: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 427 | free(blocks); | ^~~~~~~~~~~~ interleaved.c:283:6: note: 'blocks' was declared here 283 | } *blocks; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c iupac.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c msf.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c revcomp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c selex.c selex.c: In function 'ReadSELEX': selex.c:215:25: warning: 'num' may be used uninitialized [-Wmaybe-uninitialized] 215 | aseqs = (char **) MallocOrDie (num * sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selex.c:68:12: note: 'num' was declared here 68 | int num; /* number of seqs read */ | ^~~ selex.c:74:6: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 74 | } *blocks; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sqerror.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sqio.c sqio.c: In function 'SeqfileFormat': sqio.c:1033:11: warning: the comparison will always evaluate as 'false' for the address of 'sp' will never be NULL [-Waddress] 1033 | if (sp==NULL || *sp=='\0') | ^~ sqio.c:1010:9: note: 'sp' declared here 1010 | char sp[LINEBUFLEN]; | ^~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_ctype.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_math.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_string.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c stack.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c translate.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c types.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c weight.c weight.c: In function 'GSCWeights': weight.c:79:3: warning: 'rwt' may be used uninitialized [-Wmaybe-uninitialized] 79 | downweight(tree, ainfo->nseq, lwt, rwt, fwt, ainfo->nseq); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ weight.c:43:17: note: 'rwt' was declared here 43 | float *lwt, *rwt; /* weight on left, right of this tree node */ | ^~~ weight.c: In function 'VoronoiWeights': weight.c:291:17: warning: 'best' may be used uninitialized [-Wmaybe-uninitialized] 291 | ainfo->wgt[best] += 1.0; | ~~~~~~~~~~^~~~~~ weight.c:163:11: note: 'best' was declared here 163 | int best; /* index of nearest real sequence */ | ^~~~ 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libdyna.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dnamatrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ probability.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ alnrange.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ alnconvert.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ basematrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dbsearchimpl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dprunimpl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexsequence.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexevalset.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexconsensi.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ sequencestream.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ seqalign.c seqalign.dy: In function 'Wise2_read_selex_SeqAlign': seqalign.dy:421:25: warning: 'pos' may be used uninitialized [-Wmaybe-uninitialized] 421 | for(seq = buffer+pos;*seq;seq++) { | ~~~~~~^~~~ seqalign.dy:350:7: note: 'pos' was declared here 350 | int pos; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hitlist.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ codon.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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' may be used uninitialized [-Wmaybe-uninitialized] 307 | fprintf(ofp,"% d",minnumbers[0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compmat.dy:268:7: note: 'minnumbers' declared here 268 | int minnumbers[26]; | ^~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ codonmatrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ sequencedb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hscore.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genericindexresult.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ linkedlist_lookpos.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ singlenumberspace.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ histogram.c histogram.dy: In function 'Wise2_PrintASCIIHistogram': histogram.dy:299:26: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 299 | for (num = 0; lowbound > h->lowscore; lowbound--) | ~~~~~~~~~^~~~~~~~~~~~~ histogram.dy:276:8: note: 'lowbound' was declared here 276 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.dy: In function 'Wise2_EVDMaxLikelyFit': histogram.dy:1323:13: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1323 | total += mult; | ~~~~~~^~~~~~~ histogram.dy:1245:10: note: 'total' was declared here 1245 | double total; | ^~~~~ histogram.dy: In function 'Wise2_ExtremeValueFitHistogram': histogram.dy:647:42: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 647 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ histogram.dy:545:10: note: 'z' was declared here 545 | int z; /* number of censored samples */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ searchstatinterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ searchstatlookup.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteindb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ protein.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:106:25: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 106 | m->codon[p] = 0.0; | ~~~~~~~~~~~~^~~~~ pairbase.dy:96:7: note: 'p' was declared here 96 | int p; | ^ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModelScore': pairbase.dy:148:25: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 148 | m->codon[p] = NEGI; pairbase.dy:138:7: note: 'p' was declared here 138 | int p; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ pairbaseseq.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genomicdb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ randommodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ randomdb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genomic.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ cdna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ cdnadb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ embl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 404 | if( tr->ex_len > 1 ) { | ~~^~~~~~~~ gene.dy:364:16: note: 'tr' was declared here 364 | Transcript * tr; | ^~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ translation.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ btcanvas.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ asciibtcanvas.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libdyna_glib.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ intallocator.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteinstreamedindex.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ shadowseq.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspscaninterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} 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=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} 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=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} 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=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspscanruntime.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteinindexcons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dnaindexcons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all) make[2]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c -o mott_api.o mott_api.c mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:152:9: warning: unused variable 'n' [-Wunused-variable] 152 | int n; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c -o gaplib.o gaplib.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libwisesocket.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/socket' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:129:11: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ functionclient.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ anonobj.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ transferinterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_count.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models dnamapping.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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=] 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: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:568:82: 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=] 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: In function 'Wise2_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.h:102:31: warning: 'newpath' may be used uninitialized [-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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:351:24: 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/network' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnal.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 961 | } | ^ dnaalign.c:899:15: note: 'out' was declared here 899 | * | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ psw.c In file included from /usr/include/stdio.h:906, from ../base/wisebase.h:6, from ../dynlibsrc/packaln.h:7, from ../dynlibsrc/dyna.h:12, from proteinsw.h:6, from sw_wrap.h:6, from psw.c:8: In function 'fprintf', inlined from 'main' at psw.c:241:5: /usr/include/bits/stdio2.h:79:10: warning: 'qend' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ psw.c: In function 'main': psw.c:60:7: note: 'qend' was declared here 60 | int qend; | ^~~~ In function 'fprintf', inlined from 'main' at psw.c:241:5: /usr/include/bits/stdio2.h:79:10: warning: 'tend' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ psw.c: In function 'main': psw.c:62:7: note: 'tend' was declared here 62 | int tend; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 885 | | ^ proteinsw.c:823:15: note: 'out' was declared here 823 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 883 | | ^ abc.c:821:15: note: 'out' was declared here 821 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 990 | | ^ pba.c:928:15: note: 'out' was declared here 928 | long long total; | ^~~ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:259:38: warning: 'currMatch' may be used uninitialized [-Wmaybe-uninitialized] 259 | *( ((1-currMatch)/3)/0.25 )))/log(2); | ~~^~~~~~~~~~~ dbac.c:169:10: note: 'currMatch' was declared here 169 | double currMatch; | ^~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 862 | | ^ dba.c:800:15: note: 'out' was declared here 800 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 649 | | ^ slimdba.c:587:15: note: 'out' was declared here 587 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 941 | | ^ bigdba.c:879:15: note: 'out' was declared here 879 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:278:34: warning: 'end_alc' may be used uninitialized [-Wmaybe-uninitialized] 278 | sprintf(buffer,"%d",end_alc->alu[0]->start+1); | ~~~~~~~^~~~~ dbadisplay.dy:64:15: note: 'end_alc' was declared here 64 | AlnColumn * end_alc; | ^~~~~~~ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser21.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisehsp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:504:16: warning: 'ex' may be used uninitialized [-Wmaybe-uninitialized] 504 | out->end = ex->end + out->start; | ~~^~~~~ geneutil.dy:367:10: note: 'ex' was declared here 367 | Exon * ex; | ^~ geneutil.dy:446:20: warning: 'prev' may be used uninitialized [-Wmaybe-uninitialized] 446 | exon_end = prev->alu[1]->end +1 - out->start; | ~~~~^~~~~ geneutil.dy:381:15: note: 'prev' was declared here 381 | AlnColumn * prev; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneoutput.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatemodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genefrequency.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ splicesitemodeler.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1129 | | ^ genewise4.c:1067:15: note: 'out' was declared here 1067 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1241 | | ^ genewise6.c:1179:15: note: 'out' was declared here 1179 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1400 | | ^ genestretch6.c:1338:15: note: 'out' was declared here 1338 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 2667 | | ^ genewise21.c:2605:15: note: 'out' was declared here 2605 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 2341 | | ^ geneloop21.c:2279:15: note: 'out' was declared here 2279 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1329 | | ^ geneloop6.c:1267:15: note: 'out' was declared here 1267 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1553 | | ^ genephase6.c:1491:15: note: 'out' was declared here 1491 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1178 | | ^ gwlite.c:1116:15: note: 'out' was declared here 1116 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlitemodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ matchsum.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:244:10: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 244 | return out; | ^~~ estwrap.dy:138:14: note: 'out' was declared here 138 | AlnBlock * out; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodel.c genewisemodel.dy: In function 'Wise2_pack_GeneWiseScore': genewisemodel.dy:114:10: warning: 'out' is used uninitialized [-Wuninitialized] 114 | return out; | ^~~ genewisemodel.dy:112:10: note: 'out' was declared here 112 | char * out; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:906, 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:215:12: warning: call to '*__fgets_chk' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 215 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ cdparser.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1205 | | ^ estwise3.c:1143:15: note: 'out' was declared here 1143 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 997 | | ^ estslim3.c:935:15: note: 'out' was declared here 935 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1373 | | ^ estloop3.c:1311:15: note: 'out' was declared here 1311 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1026 | | ^ estfrag3.c:964:15: note: 'out' was declared here 964 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1175 | | ^ estslimloop.c:1113:15: note: 'out' was declared here 1113 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatedb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pfamhmmer1db.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pwmdna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodeldb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqhit.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ standardout.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser4.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 921 | | ^ estquick3.c:859:15: note: 'out' was declared here 859 | long long total; | ^~~ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` In function 'Wise2_GeneWiseCodonModel_from_GeneFrequencies', inlined from 'Wise2_GeneParameter21_from_GeneFrequency21' at geneparameter.dy:205:15: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` In function 'Wise2_GeneWiseCodonModel_from_GeneFrequencies', inlined from 'Wise2_GeneParameter21_from_GeneFrequency21' at geneparameter.dy:205:15, inlined from 'Wise2_GeneParameter21_wrap' at gwrap.dy:76:9, inlined from 'build_db_objects' at genewisedb.c:554:11: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/dyna.h:29, from threestatemodel.h:7, from wise2xhmmer2.h:24, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/aln.h:222:34: warning: 'anchored' may be used uninitialized [-Wmaybe-uninitialized] 222 | #define add_to_anchored_AlnBlock Wise2_add_to_anchored_AlnBlock estwisedb.c:182:14: note: 'anchored' was declared here 182 | AlnBlock * anchored; | ^~~~~~~~ In file included from ../dynlibsrc/seqalign.h:6, from wise2xhmmer2.h:23: ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized [-Wmaybe-uninitialized] 665 | #define add_SequenceSet Wise2_add_SequenceSet estwisedb.c:183:17: note: 'set' was declared here 183 | SequenceSet * set; | ^~~ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1392 | | ^ genomewise9.c:1330:15: note: 'out' was declared here 1330 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1416 | | ^ sywise20.c:1354:15: note: 'out' was declared here 1354 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function 'pseudo_gene_assessment': pseudowise.c:99:39: 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 1268 | | ^ pseudowise7.c:1206:15: note: 'out' was declared here 1206 | long long total; | ^~~ 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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 [-Wmaybe-uninitialized] 902 | | ^ localdba.c:840:15: note: 'out' was declared here 840 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localcispara.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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:838:14: note: 'temp' was declared here 838 | SeqAlign * 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 494 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); | ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:906, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: In function 'sprintf', inlined from 'Wise2_read_ben_IUPAC_TransFactorSet' at transfactor.dy:680:5: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 9 and 530 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ transfactor.dy: In function 'Wise2_calculate_TransFactorMatchSet': transfactor.dy:427:9: warning: 'cutoff' may be used uninitialized [-Wmaybe-uninitialized] 427 | if( prob > cutoff ) { | ^ transfactor.dy:366:10: note: 'cutoff' was declared here 366 | double cutoff; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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.XoXVE9 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 ++ dirname /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX ~/build/BUILD/wise2.4.1/src/bin ~/build/BUILD/wise2.4.1 + cd wise2.4.1 + pushd src/bin + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.riscv64/usr/bin + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/wise2 + pushd wisecfg ~/build/BUILD/wise2.4.1/wisecfg ~/build/BUILD/wise2.4.1 + 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/wise2-2.4.1-17.fc38.riscv64/usr/share/wise2 + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.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/wise2-2.4.1-17.fc38.riscv64/usr/share/wise2/examples + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/etc/profile.d + echo 'export WISECONFIGDIR=/usr/share/wise2/' + echo 'setenv WISECONFIGDIR /usr/share/wise2/' + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 2.4.1-17.fc38 --unique-debug-suffix -2.4.1-17.fc38.riscv64 --unique-debug-src-base wise2-2.4.1-17.fc38.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/wise2.4.1 extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/estwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/dba extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/dnal extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/estwisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/genewise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/genewisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/promoterwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/psw extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/pswdb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/scanwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/bin/scanwise_server original debug info size: 81616kB, size after compression: 78164kB /usr/bin/sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. 23175 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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/wise2-2.4.1-17.fc38.riscv64/src/base/wisetime.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-17.fc38.riscv64/src/base/wisememman.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-17.fc38.riscv64/src/base/wiseoverlay.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-17.fc38.riscv64/src/base/wisefile.dy is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.nDJIPV + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + 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 FATAL: No support for non-protein, non-nucleic acid alphabets. >>> Bad exit status - 256 (system - ) >>> 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: wise2-2.4.1-17.fc38.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.WrpJ7Y + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2 + cp -pr README /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.3g4Rot + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.base /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dynlibsrc /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dyc /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.GPL /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: config(wise2) = 2.4.1-17.fc38 wise2 = 2.4.1-17.fc38 wise2(riscv-64) = 2.4.1-17.fc38 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) libc.so.6(GLIBC_2.34)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) rtld(GNU_HASH) Processing files: wise2-doc-2.4.1-17.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.nbS76t + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-doc + cp -pr docs /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.ZpRwRY + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2-doc + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/licenses/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-doc = 2.4.1-17.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-examples-2.4.1-17.fc38.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.oOw7bN + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-examples + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-examples + cp -pr test_data/README /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64/usr/share/doc/wise2-examples + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-examples = 2.4.1-17.fc38 wise2-examples(riscv-64) = 2.4.1-17.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debugsource-2.4.1-17.fc38.riscv64 Provides: wise2-debugsource = 2.4.1-17.fc38 wise2-debugsource(riscv-64) = 2.4.1-17.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debuginfo-2.4.1-17.fc38.riscv64 Provides: debuginfo(build-id) = 14a0e33f4e34718a755fc503c80ef4889766fc59 debuginfo(build-id) = 1b357e4e5731b2b8df2d90927406276afc84cf1a debuginfo(build-id) = 2add94753032c45aca0eee5c9106aff0d75d32fa debuginfo(build-id) = 471d5b14bd8320ba94758851dda15b60d0c2c810 debuginfo(build-id) = 552253d13913deec8b591c481dd9c0cd9b531216 debuginfo(build-id) = 6424c22b680999b9bfb2cb914c41ed85ba648a1c debuginfo(build-id) = 71b3542019e58fd9c293d3b2dfe07f9d9260691e debuginfo(build-id) = 808225d969b23a2af273abb1d5a4e4fab959281b debuginfo(build-id) = dea80ea7a65e3b359703bf3519f32b67c13cfbfb debuginfo(build-id) = e325f1c3fbd826803f076726edaf1d0955245741 debuginfo(build-id) = f57920c4b8e17b9093d66cc44ab281972b1307fe wise2-debuginfo = 2.4.1-17.fc38 wise2-debuginfo(riscv-64) = 2.4.1-17.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: wise2-debugsource(riscv-64) = 2.4.1-17.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 Wrote: /builddir/build/RPMS/wise2-examples-2.4.1-17.fc38.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-doc-2.4.1-17.fc38.noarch.rpm Wrote: /builddir/build/RPMS/wise2-2.4.1-17.fc38.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-debuginfo-2.4.1-17.fc38.riscv64.rpm Wrote: /builddir/build/RPMS/wise2-debugsource-2.4.1-17.fc38.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.iymLjv + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-17.fc38.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.FzQmQj + umask 022 + cd /builddir/build/BUILD + rm -rf wise2.4.1 wise2.4.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0