+ exec + rm -rf /rpmbuild + mkdir -p /rpmbuild + su -c 'rpmbuild -ba /builddir/build/SPECS/wise2.spec --define "debug_package %{nil}" --undefine _annotated_build --define "_missing_doc_files_terminate_build %{nil}" --define "_emacs_sitestartdir /usr/share/emacs/site-lisp/site-start.d" --define "_emacs_sitelispdir /usr/share/emacs/site-lisp" --nocheck ' mockbuild Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.7gJe4d + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf wise2.4.1 + /usr/bin/gzip -dc /builddir/build/SOURCES/wise2.4.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd wise2.4.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (wise2-build.patch):' Patch #0 (wise2-build.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/makefile patching file src/welcome.csh + echo 'Patch #1 (wise2-isnumber.patch):' Patch #1 (wise2-isnumber.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/models/phasemodel.c + echo 'Patch #2 (wise2-glib2.patch):' Patch #2 (wise2-glib2.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/makefile patching file src/snp/makefile patching file src/corba/makefile patching file src/models/makefile patching file src/dnaindex/makefile patching file src/dnaindex/assembly/makefile patching file src/dynlibsrc/makefile patching file src/network/makefile patching file src/other_programs/makefile patching file src/base/makefile patching file src/HMMer2/Makefile + echo 'Patch #3 (wise2-getline.patch):' Patch #3 (wise2-getline.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/HMMer2/sqio.c + echo 'Patch #4 (wise2-ld--as-needed.patch):' Patch #4 (wise2-ld--as-needed.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/models/makefile + chmod a-x src/external/mott/mott_api.c + chmod a-x src/external/mott/mott_api.h + chmod a-x src/external/mott/gaplib.c + chmod a-x src/external/mott/gapstat.h + sed -i s#/usr/local/bin/perl#/usr/bin/perl# docs/gettex.pl + chmod -x test_data/rrm.HMM + for i in base dynlibsrc dyc + cp src/base/LICENSE LICENSE.base + for i in base dynlibsrc dyc + cp src/dynlibsrc/LICENSE LICENSE.dynlibsrc + for i in base dynlibsrc dyc + cp src/dyc/LICENSE LICENSE.dyc + cp src/models/GNULICENSE LICENSE.GPL + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.RBrXqG + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + export 'LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + make -C src CC=gcc 'CFLAGS= -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L' all make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' (cd base ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libwisebase.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/base' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseconfig.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisestring.c wisestring.dy: In function 'Wise2_breakstring_protect': wisestring.dy:632:14: warning: variable 'c' set but not used [-Wunused-but-set-variable] auto char c; ^ wisestring.dy: In function 'Wise2_show_text': wisestring.dy:757:9: warning: 'pushpoi' may be used uninitialized in this function [-Wmaybe-uninitialized] push=(*pushpoi); ~~~~^~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseerror.c wiseerror.dy: In function 'Wise2_show_message_stack': wiseerror.dy:176:16: warning: unused variable 'count' [-Wunused-variable] register int count; ^~~~~ wiseerror.dy:175:16: warning: unused variable 'j' [-Wunused-variable] register int j; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisememman.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisefile.c wisefile.dy: In function 'Wise2_myfclose': wisefile.dy:72:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'FILE * {aka struct _IO_FILE *}' [-Wformat=] fprintf(stderr,"Closing %d\n",ofp); ^~~~~~~~~~~~~~ wisefile.dy: In function 'Wise2_append_file_to_path': wisefile.dy:141:10: warning: variable 'runner' set but not used [-Wunused-but-set-variable] char * runner; ^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiserandom.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisetime.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wiseoverlay.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L wisestreaminterface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L commandline.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/base' (cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libhmmer.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c alphabet.c alphabet.c: In function 'DigitizeAlignment': alphabet.c:237:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { ^~~~~~~~~~~~~~~~~~~~~~~~~~ alphabet.c: In function 'P7CountSymbol': alphabet.c:264:13: warning: array subscript has type 'char' [-Wchar-subscripts] counters[symidx] += wt; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c core_algorithms.c core_algorithms.c: In function 'P7ViterbiTrace': core_algorithms.c:420:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized] int k; /* position in model (1..M) */ ^ core_algorithms.c: In function 'P7ParsingViterbi': core_algorithms.c:846:10: warning: 'cur' may be used uninitialized in this function [-Wmaybe-uninitialized] int cur, prv; /* indices for rolling dp matrix */ ^~~ core_algorithms.c: In function 'P7WeeViterbi': core_algorithms.c:1108:10: warning: 't2' may be used uninitialized in this function [-Wmaybe-uninitialized] if (t2 == STC) ^ core_algorithms.c:1081:19: warning: 'k2' may be used uninitialized in this function [-Wmaybe-uninitialized] kassign[s2] = k2; ~~~~~~~~~~~~^~~~ core_algorithms.c:1240:10: warning: 'ret_sc' may be used uninitialized in this function [-Wmaybe-uninitialized] return ret_sc; ^~~~~~ core_algorithms.c: In function 'Plan7ESTViterbi': core_algorithms.c:1312:24: warning: 'codon' may be used uninitialized in this function [-Wmaybe-uninitialized] mmx[i][k] += hmm->dnam[codon][k]; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c debug.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c emit.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c emulation.c In file included from emulation.c:26:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c histogram.c histogram.c: In function 'PrintASCIIHistogram': histogram.c:200:8: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] int lowbound, lowcount; /* cutoffs on the low side */ ^~~~~~~~ histogram.c: In function 'EVDMaxLikelyFit': histogram.c:1251:14: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized] mu = -1. * log(esum / total) / lambda; ^~~~~~~~~~~~~~~~~ histogram.c: In function 'ExtremeValueFitHistogram': histogram.c:659:35: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); ~^~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c hmmio.c hmmio.c: In function 'read_asc19hmm': hmmio.c:847:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 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' 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] 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' 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] 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' if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; s2upper(s); /* alphabet type */ ^~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c mathsupport.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c masks.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c misc.c In file included from misc.c:25:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c modelmakers.c modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:238:11: warning: variable 't_me' set but not used [-Wunused-but-set-variable] float t_me; /* estimate for an internal M->E transition */ ^~~~ At top level: modelmakers.c:850:1: warning: 'print_matassign' defined but not used [-Wunused-function] print_matassign(int *matassign, int alen) ^~~~~~~~~~~~~~~ modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:378:18: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized] matassign[i] &= ~ASSIGN_INSERT; ^~ modelmakers.c:224:14: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized] int i, j; /* positions in alignment */ ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c plan7.c plan7.c: In function 'Plan7ESTConfig': plan7.c:793:10: warning: 'tripnull' may be used uninitialized in this function [-Wmaybe-uninitialized] float *tripnull; /* UNFINISHED!!! */ ^~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c plan9.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c prior.c prior.c: In function 'P7ReadPrior': prior.c:102:12: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; ^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c tophits.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c trace.c In file included from trace.c:26:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c aligneval.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c alignio.c alignio.c: In function 'ReadAlignedFASTA': alignio.c:143:16: warning: 'aseq' may be used uninitialized in this function [-Wmaybe-uninitialized] *ret_aseq = aseq; ~~~~~~~~~~~~~^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c cluster.c cluster.c: In function 'Cluster': cluster.c:210:31: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized] tree[Np-2].right = coord[j]; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c dayhoff.c dayhoff.c: In function 'ParsePAMFile': dayhoff.c:164:32: warning: 'scale' may be used uninitialized in this function [-Wmaybe-uninitialized] if (gotscale) *ret_scale = scale; ~~~~~~~~~~~^~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c file.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c getopt.c getopt.c: In function 'Getopt': getopt.c:62:7: warning: 'opti' may be used uninitialized in this function [-Wmaybe-uninitialized] int opti; ^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c gnuregex.c gnuregex.c:35:0: warning: "_GNU_SOURCE" redefined #define _GNU_SOURCE :0:0: 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] if (COMPILE_STACK_EMPTY) ^ gnuregex.c:1633:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 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] 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] 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] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] char *destination; \ ^ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] char *destination; \ ^ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] char *destination; \ ^ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~ gnuregex.c:4061:19: warning: variable 'sdummy' set but not used [-Wunused-but-set-variable] char *sdummy; ^~~~~~ gnuregex.c:4060:28: warning: variable 'pdummy' set but not used [-Wunused-but-set-variable] unsigned char *pdummy; ^~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] char *destination; \ ^ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] char *destination; \ ^ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c interleaved.c interleaved.c: In function 'ReadInterleaved': interleaved.c:427:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] free(blocks); ^~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c iupac.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c msf.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c revcomp.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c selex.c selex.c: In function 'ReadSELEX': selex.c:74:6: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] } *blocks; ^~~~~~ selex.c:231:15: warning: 'num' may be used uninitialized in this function [-Wmaybe-uninitialized] ainfo->nseq = num; ~~~~~~~~~~~~^~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sqerror.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sqio.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_ctype.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_math.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c sre_string.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c stack.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c translate.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c types.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c weight.c weight.c: In function 'GSCWeights': weight.c:43:17: warning: 'rwt' may be used uninitialized in this function [-Wmaybe-uninitialized] float *lwt, *rwt; /* weight on left, right of this tree node */ ^~~ weight.c: In function 'VoronoiWeights': weight.c:163:11: warning: 'best' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libdyna.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,ifp); ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ aln.c aln.dy: In function 'Wise2_swallow_AlnColumn_multiple': aln.dy:580:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] register int i; ^ aln.dy: In function 'Wise2_mapped_ascii_AlnBlock': aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 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] char ** base, **bstr; ^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dnamatrix.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ probability.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ alnrange.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ alnconvert.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ basematrix.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shattermatrix.c shattermatrix.dy: In function 'Wise2_new_ShatterMatrixComponent': shattermatrix.dy:124:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_show_PackAln_Debug': matrixdebug.dy:67:7: warning: unused variable 'cum' [-Wunused-variable] int cum; ^~~ matrixdebug.dy:66:7: warning: unused variable 'j' [-Wunused-variable] 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] fgets(buffer,MAXLINE,in); ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dpenvelope.c dpenvelope.dy: In function 'Wise2_read_DPEnvelope': dpenvelope.dy:98:11: warning: variable 'base' set but not used [-Wunused-but-set-variable] char ** base; ^~~~ dpenvelope.dy: In function 'Wise2_overlap_DPUnit': dpenvelope.dy:68:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dbsearchimpl.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dprunimpl.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexsequence.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexevalset.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ complexconsensi.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequence.c sequence.dy: In function 'Wise2_read_fasta_Sequence': sequence.dy:767:11: warning: unused variable 'seen_weight' [-Wunused-variable] boolean seen_weight = 0; ^~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequencestream.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ seqalign.c seqalign.dy: In function 'Wise2_read_selex_SeqAlign': seqalign.dy:421:18: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized] for(seq = buffer+pos;*seq;seq++) { ~~~~~~^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hitlist.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsp.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspstream.c hspstream.dy: In function 'Wise2_typed_LinearHSPmanager_from_Stream': hspstream.dy:109:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codon.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ compmat.c compmat.dy: In function 'Wise2_write_Blast_CompMat_alphabet': compmat.dy:307:3: warning: 'minnumbers[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] fprintf(ofp,"% d",minnumbers[0]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codonmatrix.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ codonmapper.c codonmapper.dy: In function 'Wise2_new_CodonMapper': codonmapper.dy:379:10: warning: variable 'total_freq' set but not used [-Wunused-but-set-variable] double total_freq; ^~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ sequencedb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hscore.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ seqlookup.c seqlookup.dy: In function 'Wise2_load_SequenceDB_SeqLookupLoadPara': seqlookup.dy:143:7: warning: variable 'base' set but not used [-Wunused-but-set-variable] int base[5]; ^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ arrayseqlookup.c arrayseqlookup.dy: In function 'Wise2_add_ArraySeqHead': arrayseqlookup.dy:294:24: warning: variable 'temp' set but not used [-Wunused-but-set-variable] ArraySeqLookupUnit * temp; ^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genericindexresult.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ linkedlist_lookpos.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ singlenumberspace.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ histogram.c histogram.dy: In function 'Wise2_PrintASCIIHistogram': histogram.dy:276:8: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] int lowbound, lowcount; /* cutoffs on the low side */ ^~~~~~~~ histogram.dy: In function 'Wise2_EVDMaxLikelyFit': histogram.dy:1325:14: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized] mu = -1. * log(esum / total) / lambda; ^~~~~~~~~~~~~~~~~ histogram.dy: In function 'Wise2_ExtremeValueFitHistogram': histogram.dy:647:35: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); ~^~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ searchstatinterface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ searchstatlookup.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteindb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ protein.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ pairbase.c pairbase.dy: In function 'Wise2_diagonal_tweak_PairBaseCodonModel': pairbase.dy:48:7: warning: unused variable 'codon_b' [-Wunused-variable] int codon_b; ^~~~~~~ pairbase.dy:47:7: warning: unused variable 'codon_a' [-Wunused-variable] int codon_a; ^~~~~~~ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModel': pairbase.dy:106:18: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] m->codon[p] = 0.0; ~~~~~~~~~~~~^~~~~ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModelScore': pairbase.dy:148:18: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] m->codon[p] = NEGI; gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ pairbaseseq.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomicdb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ randommodel.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ randomdb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomic.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ cdna.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ cdnadb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dna.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ embl.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,maxlen,ifp); ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ gene.c gene.dy: In function 'Wise2_write_Embl_FT_Gene': gene.dy:364:16: warning: 'tr' may be used uninitialized in this function [-Wmaybe-uninitialized] Transcript * tr; ^~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ transcript.c transcript.dy: In function 'Wise2_show_Transcript': transcript.dy:170:23: warning: unused variable 'sf' [-Wunused-variable] SupportingFeature * sf; ^~ transcript.dy:169:7: warning: unused variable 'k' [-Wunused-variable] int k; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ translation.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ btcanvas.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ asciibtcanvas.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libdyna_glib.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 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] 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] 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] 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] 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] g_hash_table_insert(h,(gpointer)seq_number,p); ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ intallocator.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteinstreamedindex.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shadowseq.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ shadowseqindex.c shadowseqindex.dy: In function 'Wise2_dump_stats_ShadowSequenceIndex': shadowseqindex.dy:285:15: warning: format '%f' expects argument of type 'double', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsphandler.c hsphandler.dy: In function 'Wise2_truncated_LinearHSPmanager': hsphandler.dy:278:13: warning: variable 'worst' set but not used [-Wunused-but-set-variable] 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] int eaten; ^~~~~ hsphandler.dy: In function 'Wise2_new_LinearHSPmanager_simple_heuristic': hsphandler.dy:387:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ hsphandler.dy:386:7: warning: unused variable 'i' [-Wunused-variable] 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] int pause_i,pause_j; ^~~~~~~ hsphandler.dy:786:7: warning: variable 'pause_i' set but not used [-Wunused-but-set-variable] int pause_i,pause_j; ^~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspscaninterface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function 'Wise2_one_off_two_hit_HSPscan_query_direct': hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t {aka long int}' [-Wformat=] fprintf(stderr,"START %d.%03du %d.%03ds \n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ use.ru_utime.tv_sec, ~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t {aka long int}' [-Wformat=] fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use.ru_utime.tv_sec, ~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t {aka long int}' [-Wformat=] fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use.ru_utime.tv_sec, ~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t {aka long int}' [-Wformat=] fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use.ru_utime.tv_sec, ~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t {aka long int}' [-Wformat=] hsp2hitscan.dy:192:9: warning: unused variable 'k' [-Wunused-variable] int i,k,j; ^ hsp2hitscan.dy:185:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ hsp2hitscan.dy:183:7: warning: variable 'no' set but not used [-Wunused-but-set-variable] int no; ^~ hsp2hitscan.dy:182:18: warning: unused variable 'head' [-Wunused-variable] ArraySeqHead * head; ^~~~ hsp2hitscan.dy:181:7: warning: unused variable 'start_base' [-Wunused-variable] int start_base; ^~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupscan.c hsplookupscan.dy: In function 'Wise2_one_off_HSPscan_scan_query_direct': hsplookupscan.dy:144:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] char newseq[5]; ^~~~~~ hsplookupscan.dy:143:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function 'Wise2_one_off_ordered_HSPscan_scan_query_direct': hsplookupthreaded.dy:263:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(stderr,"retrieved array with %d elements\n",current_oph); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hsplookupthreaded.dy:136:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ hsplookupthreaded.dy:116:22: warning: unused variable 'hsp_para' [-Wunused-variable] 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] auto ArraySeqLookup * asl; ^~~ hsplookupthreaded.dy:627:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] char newseq[5]; ^~~~~~ hsplookupthreaded.dy:621:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ hsplookupthreaded.dy: In function 'Wise2_merge_HSPmanager': hsplookupthreaded.dy:567:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 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 * {aka struct Wise2_HSPDatabaseSegment *}' [-Wformat=] fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hspscanruntime.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ hsptwohitscan.c hsptwohitscan.dy: In function 'Wise2_twohit_one_off_HSPscan_scan_query_direct': hsptwohitscan.dy:113:7: warning: variable 'has_seen' set but not used [-Wunused-but-set-variable] int has_seen; ^~~~~~~~ hsptwohitscan.dy:105:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] char newseq[5]; ^~~~~~ hsptwohitscan.dy:104:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ hsptwohitscan.dy: In function 'Wise2_add_to_TwoHitBuffer': hsptwohitscan.dy:354:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ hsptwohitscan.dy:353:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ proteinindexcons.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ dnaindexcons.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd mott; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all) make[2]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] free(freq0); ^~~~ mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' mott_api.c:64:3: note: include '' or provide a declaration of 'free' mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' free(freqA); ^~~~ mott_api.c:104:7: note: include '' or provide a declaration of 'free' mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' free(h+hmin); ^~~~ mott_api.c:144:5: note: include '' or provide a declaration of 'free' mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' free(h+hmin); ^~~~ mott_api.c:155:5: note: include '' or provide a declaration of 'free' mott_api.c:150:9: warning: unused variable 'n' [-Wunused-variable] int n; ^ mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: implicit declaration of function 'calloc' [-Wimplicit-function-declaration] h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^~~~~~ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' mott_api.c:179:16: note: include '' or provide a declaration of 'calloc' mott_api.c: In function 'PseudoResidueFrequencies2': mott_api.c:207:12: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] freq[toupper(seq[n])]++; ^~~~~~~ mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' double *freq = (double*)calloc(256, sizeof(double)); ^~~~~~ mott_api.c:230:27: note: include '' or provide a declaration of 'calloc' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -c -o gaplib.o gaplib.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[2]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd socket ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" libwisesocket.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/socket' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:55:10: warning: unused variable 'ofp' [-Wunused-variable] FILE * ofp; ^~~ functionserver.dy: In function 'Wise2_new_FunctionServer': functionserver.dy:216:21: warning: unused variable 'name' [-Wunused-variable] struct sockaddr * name; ^~~~ functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,9); ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,6); ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,5); ^~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ functionclient.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ anonobj.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ transferinterface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/socket' (cd dnaindex ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function 'Wise2_show_KmerAssemblyNode': kmer_assembly.dy:296:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ 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=] fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=] fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 * {aka struct KmerAssemblyLink *}' [-Wformat=] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ kmer_assembly.dy:367:20: warning: format '%d' expects a matching 'int' argument [-Wformat=] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function 'Wise2_insert_by_kmer_KmerHashIndex': kmer_hash.dy:252:7: warning: unused variable 'i' [-Wunused-variable] 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=] fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ 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=] fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_count.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models dnamapping.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 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=] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ 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=] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t {aka long long int}' [-Wformat=] kmer_assembly_untangler.dy:157:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ 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=] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ kmer_assembly_untangler.dy:101:22: warning: variable 'link_set' set but not used [-Wunused-but-set-variable] 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=] 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_assembly_untangler.dy:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^~~~~~~~~~~~~~~~~ In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.h:174:6: note: expected 'int *' but argument is of type 'long int *' 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=] 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_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t {aka long long int}' [-Wformat=] In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.dy: In function 'Wise2_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.h:102:31: warning: 'newpath' may be used uninitialized in this function [-Wmaybe-uninitialized] #define free_KmerAssemblyPath Wise2_free_KmerAssemblyPath ^~~~~~~~~~~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:363:22: note: 'newpath' was declared here KmerAssemblyPath * newpath; ^~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c kmer_assembly_contig.dy: In function 'Wise2_KmerAssemblyContigSet_from_KmerAssemblyIndex': kmer_assembly_contig.dy:66:27: warning: unused variable 'final' [-Wunused-variable] KmerAssemblyContigSet * final; ^~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function 'Wise2_mark_tangles_KmerAssembly': kmer_assembly_error.dy:93:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ 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=] fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ kmer_assembly_error.dy: In function 'Wise2_attempt_resolve_forward_error_KmerAssembly': kmer_assembly_error.dy:208:8: warning: unused variable 'next' [-Wunused-variable] char next[256]; ^~~~ kmer_assembly_error.dy: In function 'Wise2_extend_indel_path_KmerAssembly': kmer_assembly_error.dy:351:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int *' [-Wformat=] 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: return makes integer from pointer without a cast [-Wint-conversion] return NULL; ^~~~ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' (cd network ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/network' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c wise_proteinindex_server.c: In function 'main': wise_proteinindex_server.c:93:10: warning: unused variable 'temp' [-Wunused-variable] char * temp; ^~~~ wise_proteinindex_server.c:91:10: warning: unused variable 'ior_file' [-Wunused-variable] char * ior_file; ^~~~~~~~ wise_proteinindex_server.c:84:7: warning: unused variable 'count' [-Wunused-variable] int count = 0; ^~~~~ wise_proteinindex_server.c:76:7: warning: unused variable 'ret' [-Wunused-variable] int ret; ^~~ wise_proteinindex_server.c:75:14: warning: unused variable 'seq' [-Wunused-variable] Sequence * seq; ^~~ wise_proteinindex_server.c:70:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c client_multihspscan.dy: In function 'Wise2_new_multiclient_HSPScanInterface': client_multihspscan.dy:128:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/network' (cd models ; make CC="gcc" CFLAGS="-c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/models' gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnal.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnaalign.c dnaalign.c: In function 'Wise2_calculate_shatter_DnaAlign': dnaalign.c:336:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int j; ^~ dnaalign.c:335:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int i; ^~ dnaalign.c:333:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 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] * ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:900:19: warning: unused variable 'de' [-Wunused-variable] */ ^ dnaalign.c: In function 'Wise2_max_special_strip_DnaAlign': dnaalign.c:1799:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] * Return [UNKN ] Undocumented return value [int] ^~~~~~ dnaalign.c:1798:9: warning: unused variable 'temp' [-Wunused-variable] * ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:961:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] } ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqaligndisplay.c gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ psw.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ proteinsw.c proteinsw.c: In function 'Wise2_calculate_shatter_ProteinSW': proteinsw.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ proteinsw.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ proteinsw.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:824:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ proteinsw.c:1677:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_ProteinSW(ProteinSW * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:885:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sw_wrap.c sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinSW': sw_wrap.dy:355:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] 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] Search_Return_Type ret; ^~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ abc.c abc.c: In function 'Wise2_calculate_shatter_abc': abc.c:123:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ abc.c:122:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ abc.c:120:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:822:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ abc.c:1686:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_abc(abc * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:883:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pba.c pba.c: In function 'Wise2_calculate_shatter_ProteinBlockAligner': pba.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ pba.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ pba.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:929:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ pba.c:1883:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_ProteinBlockAligner(ProteinBlockAligner * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:990:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pswdb.c gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function 'make_SeqAlign_from_align': dbac.c:413:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=] fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); ~^ ~~~~~~~~~~~ %ld dbac.c: In function 'main': dbac.c:463:7: warning: unused variable 'score' [-Wunused-variable] int score; ^~~~~ dbac.c:460:19: warning: unused variable 'dmat' [-Wunused-variable] DnaMatchBlock * dmat; ^~~~ dbac.c: In function 'showPFF': dbac.c:250:43: warning: 'currMatch' may be used uninitialized in this function [-Wmaybe-uninitialized] *(currMatch/0.25)))/log(2); ~~~~~~~~~~^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dba.c dba.c: In function 'Wise2_calculate_shatter_DnaMatchBlock': dba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ dba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ dba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ dba.c: In function 'Wise2_serial_search_DnaMatchBlock': dba.c:467:9: warning: unused variable 'db_status' [-Wunused-variable] 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] 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] { ^ dba.c:1942:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_DnaMatchBlock(DnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:862:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ slimdba.c slimdba.c: In function 'Wise2_calculate_shatter_SlimDnaMatchBlock': slimdba.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ slimdba.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ slimdba.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ slimdba.c: In function 'Wise2_serial_search_SlimDnaMatchBlock': slimdba.c:359:9: warning: unused variable 'db_status' [-Wunused-variable] 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] 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] { ^ slimdba.c:1468:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:649:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ bigdba.c bigdba.c: In function 'Wise2_calculate_shatter_BigDnaMatchBlock': bigdba.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ bigdba.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ bigdba.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ bigdba.c: In function 'Wise2_serial_search_BigDnaMatchBlock': bigdba.c:507:9: warning: unused variable 'db_status' [-Wunused-variable] 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] 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] { ^ bigdba.c:2116:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_BigDnaMatchBlock(BigDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:941:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbadisplay.c dbadisplay.dy: In function 'Wise2_show_pretty_dba_align_btcanvas': dbadisplay.dy:71:11: warning: variable 'is_reversed' set but not used [-Wunused-but-set-variable] boolean is_reversed; ^~~~~~~~~~~ dbadisplay.dy:285:45: warning: 'end_alc' may be used uninitialized in this function [-Wmaybe-uninitialized] sprintf(buffer,"-%d",two->offset - (end_alc->alu[1]->start+1)); ~~~~~~~^~~~~ gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser21.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparameter.c geneparameter.dy: In function 'Wise2_GeneParameter21_from_GeneModel': geneparameter.dy:132:25: warning: unused variable 'cse' [-Wunused-variable] ComplexSequenceEval * cse; ^~~ geneparameter.dy:131:25: warning: unused variable 'rmds' [-Wunused-variable] RandomModelDNAScore * rmds; ^~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestats.c genestats.dy: In function 'Wise2_get_genestat_emission': genestats.dy:753:10: warning: unused variable 'd' [-Wunused-variable] double d; ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisehsp.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneutil.c geneutil.dy: In function 'Wise2_add_Genes_to_GenomicRegion_new': geneutil.dy:92:15: warning: unused variable 'intron_start' [-Wunused-variable] AlnColumn * intron_start; ^~~~~~~~~~~~ geneutil.dy:82:7: warning: unused variable 'count' [-Wunused-variable] int count = 0; ^~~~~ geneutil.dy: In function 'Wise2_Gene_from_AlnColumn_new': geneutil.dy:446:20: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized] exon_end = prev->alu[1]->end +1 - out->start; ~~~~^~~~~ geneutil.dy:367:10: warning: 'ex' may be used uninitialized in this function [-Wmaybe-uninitialized] Exon * ex; ^~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneoutput.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatemodel.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genefrequency.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ splicesitemodeler.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise4.c genewise4.c: In function 'Wise2_calculate_shatter_GeneWise4': genewise4.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genewise4.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genewise4.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1068:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ genewise4.c:2216:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_GeneWise4(GeneWise4 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1129:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise6.c genewise6.c: In function 'Wise2_calculate_shatter_GeneWise6': genewise6.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genewise6.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genewise6.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1180:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ genewise6.c:2416:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1241:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestretch6.c genestretch6.c: In function 'Wise2_calculate_shatter_GeneStretch6': genestretch6.c:130:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genestretch6.c:129:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genestretch6.c:127:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1339:19: warning: unused variable 'de' [-Wunused-variable] GeneStretch6 * mat; ^~ genestretch6.c: In function 'Wise2_PackAln_calculate_Small_GeneStretch6': genestretch6.c:1839:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1400:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise21.c genewise21.c: In function 'Wise2_calculate_shatter_GeneWise21': genewise21.c:154:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genewise21.c:153:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genewise21.c:151:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2606:19: warning: unused variable 'de' [-Wunused-variable] GeneWise21 * mat; ^~ genewise21.c: In function 'Wise2_PackAln_calculate_Small_GeneWise21': genewise21.c:3507:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2667:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop21.c geneloop21.c: In function 'Wise2_calculate_shatter_GeneLoop21': geneloop21.c:147:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ geneloop21.c:146:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ geneloop21.c:144:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2280:19: warning: unused variable 'de' [-Wunused-variable] GeneLoop21 * mat; ^~ geneloop21.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop21': geneloop21.c:3093:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2341:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop6.c geneloop6.c: In function 'Wise2_calculate_shatter_GeneLoop6': geneloop6.c:129:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ geneloop6.c:128:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ geneloop6.c:126:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1268:19: warning: unused variable 'de' [-Wunused-variable] GeneLoop6 * mat; ^~ geneloop6.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop6': geneloop6.c:1742:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1329:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genephase6.c genephase6.c: In function 'Wise2_calculate_shatter_GenePhase6': genephase6.c:215:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genephase6.c:214:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genephase6.c:212:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1492:19: warning: unused variable 'de' [-Wunused-variable] GenePhase6 * mat; ^~ genephase6.c: In function 'Wise2_PackAln_calculate_Small_GenePhase6': genephase6.c:2052:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ genephase6.c: In function 'Wise2_thread_loop_GenePhase6': genephase6.c:873:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1553:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlite.c gwlite.c: In function 'Wise2_calculate_shatter_GeneLiteModel': gwlite.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ gwlite.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ gwlite.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1117:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ gwlite.c:2293:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_GeneLiteModel(GeneLiteModel * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1178:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlitemodel.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwrap.c gwrap.dy: In function 'Wise2_Hscore_from_TSM_genewise': gwrap.dy:527:25: warning: unused variable 'tempcse' [-Wunused-variable] ComplexSequenceEval * tempcse; ^~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ matchsum.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwrap.c estwrap.dy: In function 'Wise2_Hscore_from_TSM_estwise': estwrap.dy:269:22: warning: variable 'ret' set but not used [-Wunused-but-set-variable] Search_Return_Type ret; ^~~ estwrap.dy: In function 'Wise2_AlnBlock_from_TSM_estwise_wrap': estwrap.dy:138:14: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] AlnBlock * out; ^~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodel.c genewisemodel.c: In function 'Wise2_pack_GeneWiseScore': genewisemodel.dy:114:10: warning: 'out' is used uninitialized in this function [-Wuninitialized] return out; ^~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_ProteinIntronList': phasemodel.dy:65:10: warning: unused variable 'run2' [-Wunused-variable] char * run2; ^~~~ phasemodel.dy:64:10: warning: unused variable 'run1' [-Wunused-variable] char * run1; ^~~~ phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:233:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ phasemodel.dy:231:14: warning: unused variable 'input' [-Wunused-variable] Sequence * input; ^~~~~ phasemodel.dy:241:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(name,10000,ifp); ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, 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:260:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ cdparser.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function 'Wise2_write_intron_desc': genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] sprintf(buffer," Intron ??? ",in_number); ^~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwise3.c estwise3.c: In function 'Wise2_calculate_shatter_EstWise3': estwise3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estwise3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estwise3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1144:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ estwise3.c:2401:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_EstWise3(EstWise3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1205:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslim3.c estslim3.c: In function 'Wise2_calculate_shatter_EstSlim3': estslim3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estslim3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estslim3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:936:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ estslim3.c:1893:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_EstSlim3(EstSlim3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:997:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estloop3.c estloop3.c: In function 'Wise2_calculate_shatter_EstLoop3': estloop3.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estloop3.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estloop3.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1312:19: warning: unused variable 'de' [-Wunused-variable] EstLoop3 * mat; ^ estloop3.c: In function 'Wise2_PackAln_calculate_Small_EstLoop3': estloop3.c:1809:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1373:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estfrag3.c estfrag3.c: In function 'Wise2_calculate_shatter_EstFrag3': estfrag3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estfrag3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estfrag3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:965:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ estfrag3.c:2241:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_EstFrag3(EstFrag3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:1026:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslimloop.c estslimloop.c: In function 'Wise2_calculate_shatter_EstSlimLoop3': estslimloop.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estslimloop.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estslimloop.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1114:19: warning: unused variable 'de' [-Wunused-variable] EstSlimLoop3 * mat; ^~ estslimloop.c: In function 'Wise2_PackAln_calculate_Small_EstSlimLoop3': estslimloop.c:1535:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1175:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwquickdb.c gwquickdb.dy: In function 'Wise2_init_GeneWiseQuickDB': gwquickdb.dy:46:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gwquickdb.dy: In function 'Wise2_reload_GeneWiseQuickDB': gwquickdb.dy:65:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatedb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pfamhmmer1db.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pwmdna.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodeldb.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqhit.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ standardout.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser4.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estquick3.c estquick3.c: In function 'Wise2_calculate_shatter_EstQuick3': estquick3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ estquick3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ estquick3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:860:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ estquick3.c:1765:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_EstQuick3(EstQuick3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:921:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function 'build_objects': genewise.c:446:10: warning: unused variable 'ifp' [-Wunused-variable] 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/dyna.h:53:0, from threestatemodel.h:7, from wise2xhmmer2.h:24, from genewisedb.c:4: genewisedb.c: In function 'show_output': ../dynlibsrc/genomicregion.h:532:37: warning: 'cgr' may be used uninitialized in this function [-Wmaybe-uninitialized] #define show_halfwise_GenomicRegion Wise2_show_halfwise_GenomicRegion ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genewisedb.c:216:19: note: 'cgr' was declared here 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/seqalign.h:6:0, from wise2xhmmer2.h:23, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized in this function [-Wmaybe-uninitialized] #define add_SequenceSet Wise2_add_SequenceSet ^~~~~~~~~~~~~~~~~~~~~ estwisedb.c:183:17: note: 'set' was declared here SequenceSet * set; ^~~ In file included from estwisedb.c:16:0: estwrap.h:166:36: warning: 'anchored' may be used uninitialized in this function [-Wmaybe-uninitialized] #define write_mul_estwise_AlnBlock Wise2_write_mul_estwise_AlnBlock ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ estwisedb.c:182:14: note: 'anchored' was declared here AlnBlock * anchored; ^~~~~~~~ gcc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function 'main': genomewise.c:95:10: warning: unused variable 'divide_string' [-Wunused-variable] char * divide_string = "//"; ^~~~~~~~~~~~~ genomewise.c:81:7: warning: unused variable 'kbyte' [-Wunused-variable] int kbyte = 10000; ^~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise9.c genomewise9.c: In function 'Wise2_calculate_shatter_GenomeWise9': genomewise9.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ genomewise9.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ genomewise9.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1331:19: warning: unused variable 'de' [-Wunused-variable] GenomeWise9 * mat; ^~ genomewise9.c: In function 'Wise2_PackAln_calculate_Small_GenomeWise9': genomewise9.c:1895:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ genomewise9.c: In function 'Wise2_thread_loop_GenomeWise9': genomewise9.c:745:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1392:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genome_evidence.c genome_evidence.dy: In function 'Wise2_free_GenomeEvidenceUnit': genome_evidence.dy:61:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] 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] int i; ^ est_evidence.dy: In function 'Wise2_est_stop_pot': est_evidence.dy:203:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ gcc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function 'make_PairBaseCodonModelScore': sywise.c:64:10: warning: unused variable 'ifp' [-Wunused-variable] FILE * ifp; ^~~ sywise.c: In function 'show_score_sequence': sywise.c:117:28: warning: array subscript has type 'char' [-Wchar-subscripts] match_score = m->base[pbs->seq[alc->alu[1]->start+1]]; ^ sywise.c:118:29: warning: array subscript has type 'char' [-Wchar-subscripts] match_score += m->base[pbs->seq[alc->alu[1]->start+2]]; ^ sywise.c:119:29: warning: array subscript has type 'char' [-Wchar-subscripts] 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] boolean show_gene_raw = 0; ^~~~~~~~~~~~~ sywise.c:211:11: warning: unused variable 'show_trans' [-Wunused-variable] boolean show_trans = 1; ^~~~~~~~~~ sywise.c:204:27: warning: variable 'std_opt' set but not used [-Wunused-but-set-variable] StandardOutputOptions * std_opt; ^~~~~~~ sywise.c:202:13: warning: unused variable 'trans' [-Wunused-variable] Protein * trans; ^~~~~ sywise.c:201:19: warning: variable 'gr2' set but not used [-Wunused-but-set-variable] GenomicRegion * gr2; ^~~ sywise.c:183:13: warning: unused variable 'score_mat' [-Wunused-variable] CompMat * score_mat; ^~~~~~~~~ sywise.c:168:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ sywise.c:318:7: warning: 'pal' may be used uninitialized in this function [-Wmaybe-uninitialized] alb = convert_PackAln_to_AlnBlock_SyWise20(pal); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise20.c sywise20.c: In function 'Wise2_calculate_shatter_SyWise20': sywise20.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ sywise20.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ sywise20.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ sywise20.c: In function 'Wise2_serial_search_SyWise20': sywise20.c:789:9: warning: unused variable 'db_status' [-Wunused-variable] 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] SyWise20 * mat; ^ sywise20.c: In function 'Wise2_PackAln_calculate_Small_SyWise20': sywise20.c:1943:19: warning: unused variable 'pau' [-Wunused-variable] int score; ^ sywise20.c: In function 'Wise2_thread_loop_SyWise20': sywise20.c:764:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1416:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ syexonmodel.c gcc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function 'pseudo_gene_assessment': pseudowise.c:99:23: warning: array subscript has type 'char' [-Wchar-subscripts] if( protein->comp[aa][pep->seq[pep_pos]] < 0 ) { ^ pseudowise.c:57:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ pseudowise.c:57:7: warning: unused variable 'i' [-Wunused-variable] int i,j; ^ pseudowise.c: In function 'main': pseudowise.c:180:7: warning: variable 'offset' set but not used [-Wunused-but-set-variable] int offset; ^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise7.c pseudowise7.c: In function 'Wise2_calculate_shatter_PseudoWise7': pseudowise7.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ pseudowise7.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ pseudowise7.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1207:19: warning: unused variable 'de' [-Wunused-variable] 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] { ^ pseudowise7.c:2470:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_PseudoWise7(PseudoWise7 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1268:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localdba.c localdba.c: In function 'Wise2_calculate_shatter_LocalDnaMatchBlock': localdba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ localdba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ localdba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ localdba.c: In function 'Wise2_serial_search_LocalDnaMatchBlock': localdba.c:487:9: warning: unused variable 'db_status' [-Wunused-variable] 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] 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] { ^ localdba.c:1983:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ localdba.c: In function 'Wise2_PackAln_bestmemory_LocalDnaMatchBlock': localdba.c:902:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c localcishit.dy: In function 'Wise2_expand_to_subhits_LocalCisHitSet': localcishit.dy:91:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] int score; ^~~~~ localcishit.dy:90:7: warning: unused variable 'score_start' [-Wunused-variable] int score_start; ^~~~~~~~~~~ localcishit.dy:89:7: warning: unused variable 'tend' [-Wunused-variable] int tend; ^~~~ localcishit.dy:88:7: warning: unused variable 'qend' [-Wunused-variable] int qend; ^~~~ localcishit.dy:87:7: warning: variable 'tstart' set but not used [-Wunused-but-set-variable] int tstart; ^~~~~~ localcishit.dy:86:7: warning: variable 'qstart' set but not used [-Wunused-but-set-variable] int qstart; ^~~~~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localcispara.c gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment makes integer from pointer without a cast [-Wint-conversion] for(i=0;iseed = temp; ~~~~~~~~~~^~~~~~ transfactor.dy: In function 'Wise2_calculate_TransFactorMatchSet': transfactor.dy:437:9: warning: 'cutoff' may be used uninitialized in this function [-Wmaybe-uninitialized] if( rev_prob > cutoff ) { ^ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pairwiseshortdna.c pairwiseshortdna.dy: In function 'Wise2_query_to_reverse_target': pairwiseshortdna.dy:56:11: warning: variable 'reverse_tree' set but not used [-Wunused-but-set-variable] GTree * reverse_tree; ^~~~~~~~~~~~ pairwiseshortdna.dy:55:11: warning: variable 'forward_tree' set but not used [-Wunused-but-set-variable] 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:73:7: warning: unused variable 'c' [-Wunused-variable] int c; ^ scanwisep.c:72:7: warning: unused variable 'ret' [-Wunused-variable] int ret; ^~~ scanwisep.c:70:14: warning: unused variable 'seq' [-Wunused-variable] Sequence * seq; ^~~ scanwisep.c: In function 'HitPair_from_HSPset_sw': scanwisep.c:305:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ scanwisep.c: In function 'HitList_from_LinearHSPmanager_sw': scanwisep.c:326:30: warning: unused variable 'conv' [-Wunused-variable] 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] SearchStatInterface * ssl; ^~~ scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:144:10: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] return out; ^~~ gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c hsp2aln_sw.dy: In function 'Wise2_worker_thread_LM2HitList': hsp2aln_sw.dy:119:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: creating libmodel.a make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/models' make bin make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /builddir/build/BUILD/wise2.4.1/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' make: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.2iLOtN + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 ++ dirname /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 + cd wise2.4.1 + pushd src/bin ~/build/BUILD/wise2.4.1/src/bin ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.riscv64/usr/bin + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.riscv64/usr/share/wise2 + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.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/wise2-2.4.1-1.fc28.riscv64/usr/share/wise2/examples + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/etc/profile.d + echo 'export WISECONFIGDIR=/usr/share/wise2/' + echo 'setenv WISECONFIGDIR /usr/share/wise2/' + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: wise2-2.4.1-1.fc28.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.lDyMo7 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2 + cp -pr README /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2 + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gz7xZO + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.base /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dynlibsrc /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.dyc /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + cp -pr LICENSE.GPL /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2 + exit 0 Provides: config(wise2) = 2.4.1-1.fc28 wise2 = 2.4.1-1.fc28 wise2(riscv-64) = 2.4.1-1.fc28 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) rtld(GNU_HASH) Processing files: wise2-doc-2.4.1-1.fc28.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.aIQHZO + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-doc + cp -pr docs /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-doc + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.ZT4Px6 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2-doc + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/licenses/wise2-doc + exit 0 Provides: wise2-doc = 2.4.1-1.fc28 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-examples-2.4.1-1.fc28.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4UN0Uo + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-examples + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-examples + cp -pr test_data/README /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64/usr/share/doc/wise2-examples + exit 0 Provides: wise2-examples = 2.4.1-1.fc28 wise2-examples(riscv-64) = 2.4.1-1.fc28 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 Wrote: /builddir/build/SRPMS/wise2-2.4.1-1.fc28.src.rpm Wrote: /builddir/build/RPMS/riscv64/wise2-2.4.1-1.fc28.riscv64.rpm Wrote: /builddir/build/RPMS/noarch/wise2-doc-2.4.1-1.fc28.noarch.rpm Wrote: /builddir/build/RPMS/riscv64/wise2-examples-2.4.1-1.fc28.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.BFUIOp + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-1.fc28.riscv64 + exit 0 + touch /buildok + cleanup + set +e + sync + sleep 5 + sync + poweroff Terminated ++ cleanup ++ set +e ++ sync Terminated +++ cleanup +++ set +e +++ sync +++ sleep 5 +++ sync +++ poweroff