<86>Feb 8 08:08:42 userdel[82913]: delete user 'rooter' <86>Feb 8 08:08:42 userdel[82913]: removed group 'rooter' owned by 'rooter' <86>Feb 8 08:08:42 userdel[82913]: removed shadow group 'rooter' owned by 'rooter' <86>Feb 8 08:08:42 groupadd[83048]: group added to /etc/group: name=rooter, GID=579 <86>Feb 8 08:08:42 groupadd[83048]: group added to /etc/gshadow: name=rooter <86>Feb 8 08:08:42 groupadd[83048]: new group: name=rooter, GID=579 <86>Feb 8 08:08:43 useradd[83186]: new user: name=rooter, UID=579, GID=579, home=/root, shell=/bin/bash <86>Feb 8 08:08:43 userdel[83445]: delete user 'builder' <86>Feb 8 08:08:43 userdel[83445]: removed group 'builder' owned by 'builder' <86>Feb 8 08:08:43 userdel[83445]: removed shadow group 'builder' owned by 'builder' <86>Feb 8 08:08:43 groupadd[83669]: group added to /etc/group: name=builder, GID=580 <86>Feb 8 08:08:43 groupadd[83669]: group added to /etc/gshadow: name=builder <86>Feb 8 08:08:43 groupadd[83669]: new group: name=builder, GID=580 <86>Feb 8 08:08:43 useradd[83731]: new user: name=builder, UID=580, GID=580, home=/usr/src, shell=/bin/bash <13>Feb 8 08:08:46 rpmi: sgml-common-0.6.3-alt15 1423664786 installed <13>Feb 8 08:08:46 rpmi: xml-utils-1:2.9.4.0.12.e905-alt1.1 1525115767 installed <13>Feb 8 08:08:46 rpmi: glib-1.2.10-alt21 sisyphus+220899.100.1.1 1549487365 installed <13>Feb 8 08:08:46 rpmi: libOpenSP-1.5.2-alt3.qa1 1365943435 installed <13>Feb 8 08:08:47 rpmi: OpenSP-1.5.2-alt3.qa1 1365943435 installed <13>Feb 8 08:08:47 rpmi: glib-devel-1.2.10-alt21 sisyphus+220899.100.1.1 1549487365 installed <13>Feb 8 08:08:47 rpmi: docbook-dtds-4.5-alt1 1223476557 installed <13>Feb 8 08:08:47 rpmi: w3c-markup-validator-libs-1.2-alt2 1508078373 installed <13>Feb 8 08:08:47 rpmi: docbook-to-man-2.0.0-alt1.qa1 1366113342 installed Building target platforms: i586 Building for target i586 Wrote: /usr/src/in/nosrpm/wise-2.4.1-alt1.qa1.nosrc.rpm Installing wise-2.4.1-alt1.qa1.src.rpm Building target platforms: i586 Building for target i586 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.51683 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf wise2.4.1 + echo 'Source #0 (wise2.4.1.tar.gz):' Source #0 (wise2.4.1.tar.gz): + /bin/gzip -dc /usr/src/RPM/SOURCES/wise2.4.1.tar.gz + /bin/tar -xf - + cd wise2.4.1 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #1 (01_welcome-csh.dpatch):' Patch #1 (01_welcome-csh.dpatch): + /usr/bin/patch -p1 patching file src/makefile patching file src/welcome.csh + echo 'Patch #2 (02_isnumber.dpatch):' Patch #2 (02_isnumber.dpatch): + /usr/bin/patch -p1 patching file src/models/phasemodel.c + tar xf /usr/src/RPM/SOURCES/manpages.tar + exit 0 Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.59115 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd wise2.4.1 ++ glib-config --cflags + make -j8 'CFLAGS=-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89' 'EXTRALIBS=-lm -lglib' -C src all (cd base ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" libwisebase.a ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiseconfig.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisememman.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiseoverlay.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiserandom.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 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; ^~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisetime.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisestreaminterface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 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); ~~~~^~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 linesubs.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 commandline.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/base' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/base' (cd HMMer2 ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" libhmmer.a ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c mathsupport.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c emit.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c masks.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c debug.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c emulation.c In file included from emulation.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c misc.c In file included from misc.c:25: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c plan9.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c tophits.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 */ ^~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c plan7.c plan7.c: In function 'Plan7ESTConfig': plan7.c:816:20: warning: 'tripnull' may be used uninitialized in this function [-Wmaybe-uninitialized] hmm->dnam[x][k] = Prob2Score(p, tripnull[x]); ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 */ ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ~~~~~~~~~~~^~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c histogram.c histogram.c: In function 'PrintASCIIHistogram': histogram.c:227:43: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] if (++num == emptybins) { lowbound += emptybins; break; } /* stop */ ~~~~~~~~~^~~~~~~~~~~~ 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)); ~^~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c aligneval.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c file.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ~~~~~~~~~~~~~^~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c iupac.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c revcomp.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c msf.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sqerror.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_ctype.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c trace.c In file included from trace.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_string.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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]; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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]; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c stack.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c translate.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_math.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c types.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c selex.c selex.c: In function 'ReadSELEX': selex.c:445:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] free(blocks); ^~~~~~~~~~~~ selex.c:231:15: warning: 'num' may be used uninitialized in this function [-Wmaybe-uninitialized] ainfo->nseq = num; ~~~~~~~~~~~~^~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 */ ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sqio.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c gnuregex.c 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: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: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: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: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: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: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); ^~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' (cd dynlibsrc ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" libdyna.a ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ shattermatrix.c shattermatrix.dy: In function 'Wise2_new_ShatterMatrixComponent': shattermatrix.dy:124:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ probability.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ basematrix.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ alnrange.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dprunimpl.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexevalset.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dbsearchimpl.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ alnconvert.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dnamatrix.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexconsensi.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ sequencestream.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexsequence.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ codon.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ codonmatrix.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genericindexresult.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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]; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hitlist.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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++) { ~~~~~~^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsp.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ searchstatlookup.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ linkedlist_lookpos.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hscore.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ searchstatinterface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ singlenumberspace.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ protein.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ sequencedb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteindb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ pairbaseseq.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ cdna.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genomic.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dna.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ randommodel.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genomicdb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ histogram.c histogram.dy: In function 'Wise2_PrintASCIIHistogram': histogram.dy:303:43: warning: 'lowbound' may be used uninitialized in this function [-Wmaybe-uninitialized] if (++num == emptybins) { lowbound += emptybins; break; } /* stop */ ~~~~~~~~~^~~~~~~~~~~~ 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)); ~^~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ cdnadb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ translation.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ btcanvas.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ embl.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ randomdb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dynlibcross.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ asciibtcanvas.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" libdyna_glib.a ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ subseqhash.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ shadowseq.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ intallocator.c intallocator.dy: In function 'Wise2_show_allocator_status_IntAllocator': intallocator.dy:216:15: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=] fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteinstreamedindex.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspscanruntime.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 'unsigned int' [-Wformat=] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspscaninterface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteinindexcons.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ staticseq.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 '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 '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 '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 '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 '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 '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 '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 '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; ^~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dnaindexcons.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" all ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/external' (cd mott; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" all) make[2]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/external/mott' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[2]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/external/mott' make[2]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/external/mott' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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:5:1: +#include mott_api.c:64:3: free(freq0); ^~~~ 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' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c -o gaplib.o gaplib.c cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 '/usr/src/RPM/BUILD/wise2.4.1/src/external/mott' make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/external' (cd socket ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" libwisesocket.a ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ directsocketwrite.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ transferinterface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ anonobj.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:24: warning: passing argument 2 of 'connect' from incompatible pointer type [-Wincompatible-pointer-types] connect(out->socket, &server, sizeof(server)); ^~~~~~~ In file included from functionclient.c:7: /usr/include/sys/socket.h:126:52: note: expected 'const struct sockaddr *' but argument is of type 'struct sockaddr_in *' extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/socket' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/socket' (cd dnaindex ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" all ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_glib_index.dy: In function 'Wise2_retrieve_by_kmer_KmerGlibIndex': kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); ^ kmer_glib_index.dy: In function 'Wise2_insert_by_kmer_KmerGlibIndex': kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); ^ kmer_glib_index.dy: In function 'Wise2_retrieve_active_kmer_KmerGlibIndex': kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models dnamapping.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models kmer_count.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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]); ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: returning 'void *' from a function with return type 'boolean' {aka 'int'} makes integer from pointer without a cast [-Wint-conversion] return NULL; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c 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: kmer_assembly_untangler.h:174:116: 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: 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; ^~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ -I../models assembly.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' (cd network ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" all ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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 '/usr/src/RPM/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' cc -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 -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` -lpthread make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/network' (cd models ; make CC="cc" CFLAGS="-c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89" EXTRALIBS="-lm -lglib" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ dnal.c dnal.c: In function 'main': dnal.c:78:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ seqaligndisplay.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ psw.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ pswdb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ dbac.c 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:259:38: warning: 'currMatch' may be used uninitialized in this function [-Wmaybe-uninitialized] *( ((1-currMatch)/3)/0.25 )))/log(2); ~~^~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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)); ~~~~~~~^~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ geneparser21.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ geneoutput.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ splicesitemodeler.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ genewisehsp.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ genefrequency.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ threestatemodel.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ gwlitemodel.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ matchsum.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ cdparser.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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, 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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); ^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ threestatedb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ pfamhmmer1db.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ pwmdna.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ standardout.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ genewisemodeldb.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ geneparser4.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ seqhit.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 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; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/dyna.h:53, from threestatemodel.h:7, from wise2xhmmer2.h:24, from genewisedb.c:4: genewisedb.c: In function 'show_output': ../dynlibsrc/genomicregion.h:453:35: warning: 'cgr' may be used uninitialized in this function [-Wmaybe-uninitialized] #define add_Gene_to_GenomicRegion Wise2_add_Gene_to_GenomicRegion ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genewisedb.c:216:19: note: 'cgr' was declared here GenomicRegion * cgr; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/seqalign.h:6, from wise2xhmmer2.h:23, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized in this function [-Wmaybe-uninitialized] #define add_SequenceSet Wise2_add_SequenceSet ^~~~~~~~~~~~~~~~~~~~~ estwisedb.c:183:17: note: 'set' was declared here SequenceSet * set; ^~~ In file included from estwisedb.c:16: 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; ^~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] } ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^ In file included from sywise.c:1: sywise20.h:328:46: warning: 'pal' may be used uninitialized in this function [-Wmaybe-uninitialized] #define convert_PackAln_to_AlnBlock_SyWise20 Wise2_convert_PackAln_to_AlnBlock_SyWise20 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sywise.c:196:13: note: 'pal' was declared here PackAln * pal; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ syexonmodel.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ `glib-config --cflags` promoterwise.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment to 'int (*)(void *)' from incompatible pointer type 'Wise2_EstEvidence * (*)(Wise2_EstEvidence *)' {aka 'struct Wise2_EstEvidence * (*)(struct Wise2_EstEvidence *)'} [-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; ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ localcispara.c make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ `glib-config --cflags` 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; ^~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment to 'char' from 'void *' makes integer from pointer without a cast [-Wint-conversion] for(i=0;iseed = temp; ~~~~~~~~~~^~~~~~ transfactor.dy: In function 'Wise2_read_ben_IUPAC_TransFactorSet': transfactor.dy:680:21: warning: '%s' directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=] sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:862, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: /usr/include/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 9 and 529 bytes into a destination of size 512 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ transfactor.dy: In function 'Wise2_calculate_TransFactorMatchSet': transfactor.dy:437:9: warning: 'cutoff' may be used uninitialized in this function [-Wmaybe-uninitialized] if( rev_prob > cutoff ) { ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' 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 '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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; ^~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ `glib-config --cflags` 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 || ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lglib -lpthread make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ motifmatrixdp.c motifmatrixdp.c: In function 'Wise2_calculate_shatter_LocalMotifMatrix': motifmatrixdp.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^~~ motifmatrixdp.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^~~ motifmatrixdp.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^~ motifmatrixdp.c: In function 'Wise2_serial_search_LocalMotifMatrix': motifmatrixdp.c:371:9: warning: unused variable 'db_status' [-Wunused-variable] Search_Return_Type serial_search_LocalMotifMatrix(Hscore * out,ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms) ^~~~~~~~~ motifmatrixdp.c: In function 'Wise2_PackAln_bestmemory_LocalMotifMatrix': motifmatrixdp.c:611:19: warning: unused variable 'de' [-Wunused-variable] LocalMotifMatrix * mat; ^~ motifmatrixdp.c: In function 'Wise2_max_special_strip_LocalMotifMatrix': motifmatrixdp.c:1551:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] { ^ motifmatrixdp.c:1550:9: warning: unused variable 'temp' [-Wunused-variable] int max_special_strip_LocalMotifMatrix(LocalMotifMatrix * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) ^~~~ motifmatrixdp.c: In function 'Wise2_PackAln_bestmemory_LocalMotifMatrix': motifmatrixdp.c:672:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib `glib-config --libs` -lpthread make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -c -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -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] ^ make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' cc -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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -lglib make[1]: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/src/models' make bin make[1]: Entering directory '/usr/src/RPM/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 /usr/src/RPM/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 '/usr/src/RPM/BUILD/wise2.4.1/src' + make -C manpages make: Entering directory '/usr/src/RPM/BUILD/wise2.4.1/manpages' docbook-to-man dba.sgml > dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make: Leaving directory '/usr/src/RPM/BUILD/wise2.4.1/manpages' + exit 0 Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.36678 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + /bin/chmod -Rf u+rwX -- /usr/src/tmp/wise-buildroot + : + /bin/rm -rf -- /usr/src/tmp/wise-buildroot + cd wise2.4.1 + install -d -m 755 /usr/src/tmp/wise-buildroot/usr/bin + install -m 755 src/models/pswdb src/models/psw src/models/genewisedb src/models/estwisedb src/models/estwise src/models/genewise src/models/dba src/models/dnal src/models/genomewise /usr/src/tmp/wise-buildroot/usr/bin + install -d -m 755 /usr/src/tmp/wise-buildroot/usr/share/wise + install -m 644 wisecfg/BLOSUM30.bla wisecfg/BLOSUM45.bla wisecfg/BLOSUM62.bla wisecfg/BLOSUM80.bla wisecfg/aa.rnd wisecfg/cb.tmf wisecfg/codon.martian wisecfg/codon.table wisecfg/gene.stat wisecfg/gon120.bla wisecfg/gon160.bla wisecfg/gon200.bla wisecfg/gon250.bla wisecfg/gon350.bla wisecfg/human.gf wisecfg/human.gp wisecfg/human.stats wisecfg/idenity.bla wisecfg/methods wisecfg/pb.gf wisecfg/pombe.gf wisecfg/tm.pri wisecfg/wag55 wisecfg/wag65 wisecfg/wag75 wisecfg/wag85 wisecfg/wise.2 wisecfg/wise.per wisecfg/worm.gf /usr/src/tmp/wise-buildroot/usr/share/wise + install -d -m 755 /usr/src/tmp/wise-buildroot/usr/share/man/man1 + cp manpages/dba.1 manpages/dnal.1 manpages/estwise.1 manpages/estwisedb.1 manpages/genewise.1 manpages/genewisedb.1 manpages/genomewise.1 manpages/promoterwise.1 manpages/psw.1 manpages/pswdb.1 manpages/scanwise.1 manpages/scanwise_server.1 /usr/src/tmp/wise-buildroot/usr/share/man/man1 + install -d -m 755 /usr/src/tmp/wise-buildroot/etc/profile.d + echo 'export WISECONFIGDIR=/usr/share/wise' + echo 'setenv WISECONFIGDIR /usr/share/wise' + /usr/lib/rpm/brp-alt Cleaning files in /usr/src/tmp/wise-buildroot (auto) Verifying and fixing files in /usr/src/tmp/wise-buildroot (binconfig,pkgconfig,libtool,desktop) Checking contents of files in /usr/src/tmp/wise-buildroot/ (default) Compressing files in /usr/src/tmp/wise-buildroot (auto) Verifying ELF objects in /usr/src/tmp/wise-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal) verify-elf: WARNING: ./usr/bin/genomewise: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/dnal: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/dba: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/genewise: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/estwise: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/estwisedb: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/genewisedb: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/psw: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/bin/pswdb: uses non-LFS functions: fopen Hardlinking identical .pyc and .pyo files Processing files: wise-2.4.1-alt1.qa1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.78689 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd wise2.4.1 + DOCDIR=/usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + export DOCDIR + rm -rf /usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + /bin/mkdir -p /usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + cp -prL README LICENSE docs /usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + chmod -R go-w /usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + chmod -R a+rX /usr/src/tmp/wise-buildroot/usr/share/doc/wise-2.4.1 + exit 0 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.KRiKRN find-provides: running scripts (debuginfo,lib,pam,perl,pkgconfig,python,shell) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.3gQl0U find-requires: running scripts (cpp,debuginfo,files,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks) Requires: /lib/ld-linux.so.2, libc.so.6(GLIBC_2.0), libc.so.6(GLIBC_2.1), libc.so.6(GLIBC_2.3), libc.so.6(GLIBC_2.3.4), libc.so.6(GLIBC_2.4), libc.so.6(GLIBC_2.7), libglib-1.2.so.0 >= set:midh12qlCZ6Z8gaRgR1ZqmKSnq, libm.so.6(GLIBC_2.0), libpthread.so.0(GLIBC_2.0), libpthread.so.0(GLIBC_2.1), rtld(GNU_HASH) Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.UxRyxv Creating wise-debuginfo package Processing files: wise-debuginfo-2.4.1-alt1.qa1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.9dFSRy find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.5oH7m4 find-requires: running scripts (debuginfo) Requires: wise = 2.4.1-alt1.qa1, /usr/lib/debug/lib/ld-linux.so.2.debug, debug(libc.so.6), debug(libglib-1.2.so.0), debug(libm.so.6), debug(libpthread.so.0) Wrote: /usr/src/RPM/RPMS/i586/wise-2.4.1-alt1.qa1.i586.rpm Wrote: /usr/src/RPM/RPMS/i586/wise-debuginfo-2.4.1-alt1.qa1.i586.rpm 128.81user 5.21system 1:14.28elapsed 180%CPU (0avgtext+0avgdata 144408maxresident)k 0inputs+0outputs (0major+2426079minor)pagefaults 0swaps 138.72user 7.78system 1:32.25elapsed 158%CPU (0avgtext+0avgdata 144408maxresident)k 0inputs+0outputs (0major+2873948minor)pagefaults 0swaps --- wise-2.4.1-alt1.qa1.i586.rpm.repo 2013-04-16 07:05:37.000000000 +0000 +++ wise-2.4.1-alt1.qa1.i586.rpm.hasher 2019-02-08 08:10:06.382908497 +0000 @@ -29,14 +29,14 @@ /usr/share/doc/wise-2.4.1/docs/wise3arch.tex 100644 -/usr/share/man/man1/dba.1.gz 100644 -/usr/share/man/man1/dnal.1.gz 100644 -/usr/share/man/man1/estwise.1.gz 100644 -/usr/share/man/man1/estwisedb.1.gz 100644 -/usr/share/man/man1/genewise.1.gz 100644 -/usr/share/man/man1/genewisedb.1.gz 100644 -/usr/share/man/man1/genomewise.1.gz 100644 -/usr/share/man/man1/promoterwise.1.gz 100644 -/usr/share/man/man1/psw.1.gz 100644 -/usr/share/man/man1/pswdb.1.gz 100644 -/usr/share/man/man1/scanwise.1.gz 100644 -/usr/share/man/man1/scanwise_server.1.gz 100644 +/usr/share/man/man1/dba.1.xz 100644 +/usr/share/man/man1/dnal.1.xz 100644 +/usr/share/man/man1/estwise.1.xz 100644 +/usr/share/man/man1/estwisedb.1.xz 100644 +/usr/share/man/man1/genewise.1.xz 100644 +/usr/share/man/man1/genewisedb.1.xz 100644 +/usr/share/man/man1/genomewise.1.xz 100644 +/usr/share/man/man1/promoterwise.1.xz 100644 +/usr/share/man/man1/psw.1.xz 100644 +/usr/share/man/man1/pswdb.1.xz 100644 +/usr/share/man/man1/scanwise.1.xz 100644 +/usr/share/man/man1/scanwise_server.1.xz 100644 /usr/share/wise 40755