<86>Jan 13 07:01:00 userdel[20154]: delete user 'rooter' <86>Jan 13 07:01:00 userdel[20154]: removed group 'rooter' owned by 'rooter' <86>Jan 13 07:01:00 userdel[20154]: removed shadow group 'rooter' owned by 'rooter' <86>Jan 13 07:01:00 groupadd[20212]: group added to /etc/group: name=rooter, GID=615 <86>Jan 13 07:01:00 groupadd[20212]: group added to /etc/gshadow: name=rooter <86>Jan 13 07:01:00 groupadd[20212]: new group: name=rooter, GID=615 <86>Jan 13 07:01:00 useradd[20377]: new user: name=rooter, UID=615, GID=615, home=/root, shell=/bin/bash <86>Jan 13 07:01:00 userdel[20399]: delete user 'builder' <86>Jan 13 07:01:00 userdel[20399]: removed group 'builder' owned by 'builder' <86>Jan 13 07:01:00 userdel[20399]: removed shadow group 'builder' owned by 'builder' <86>Jan 13 07:01:00 groupadd[20420]: group added to /etc/group: name=builder, GID=616 <86>Jan 13 07:01:00 groupadd[20420]: group added to /etc/gshadow: name=builder <86>Jan 13 07:01:00 groupadd[20420]: new group: name=builder, GID=616 <86>Jan 13 07:01:00 useradd[20447]: new user: name=builder, UID=616, GID=616, home=/usr/src, shell=/bin/bash <13>Jan 13 07:01:02 rpmi: sgml-common-0.6.3-alt15 1423664786 installed <13>Jan 13 07:01:02 rpmi: xml-utils-1:2.9.4.0.12.e905-alt1 1488560707 installed <13>Jan 13 07:01:02 rpmi: glib-1.2.10-alt20 1461002535 installed <13>Jan 13 07:01:02 rpmi: libOpenSP-1.5.2-alt3.qa1 1365943435 installed <13>Jan 13 07:01:02 rpmi: OpenSP-1.5.2-alt3.qa1 1365943435 installed <13>Jan 13 07:01:02 rpmi: docbook-to-man-2.0.0-alt1.qa1 1366113342 installed <13>Jan 13 07:01:02 rpmi: glib-devel-1.2.10-alt20 1461002535 installed <13>Jan 13 07:01:02 rpmi: docbook-dtds-4.5-alt1 1223476557 installed <13>Jan 13 07:01:03 rpmi: w3c-markup-validator-libs-1.2-alt1 1316525214 installed 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.49988 + 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/tar -xf - + /bin/gzip -dc /usr/src/RPM/SOURCES/wise2.4.1.tar.gz + 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.49988 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd wise2.4.1 + '[' -n '' ']' + NPROCS=8 ++ glib-config --cflags + make -j8 'CFLAGS=-c -pipe -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 make: Entering directory `/usr/src/RPM/BUILD/wise2.4.1/src' (cd base ; make CC="cc" CFLAGS="-c -pipe -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 -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiseconfig.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisestring.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiseerror.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisememman.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisefile.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiserandom.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisetime.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wiseoverlay.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 wisestreaminterface.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 commandline.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 linesubs.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; ^ wisestring.dy: In function 'Wise2_show_text': wisestring.dy:757:9: warning: 'pushpoi' may be used uninitialized in this function [-Wmaybe-uninitialized] push=(*pushpoi); ^ 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 -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 -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c alphabet.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c core_algorithms.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c debug.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c emit.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c emulation.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c histogram.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c hmmio.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c mathsupport.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; ^ In file included from emulation.c:26:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c masks.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c misc.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c modelmakers.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c plan7.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 */ ^ modelmakers.c: At top level: modelmakers.c:850:1: warning: 'print_matassign' defined but not used [-Wunused-function] print_matassign(int *matassign, int alen) ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c plan9.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 */ ^ In file included from misc.c:25:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c prior.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c tophits.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; ^ 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 */ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c trace.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c aligneval.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]); ^ In file included from trace.c:26:0: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] static char *copyright = "\ ^ 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) */ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c alignio.c 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)); ^ alignio.c: In function 'ReadAlignedFASTA': alignio.c:143:16: warning: 'aseq' may be used uninitialized in this function [-Wmaybe-uninitialized] *ret_aseq = aseq; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c cluster.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c dayhoff.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c file.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c getopt.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c gnuregex.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c interleaved.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c iupac.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c msf.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]; ^ gnuregex.c: In function 'regex_compile': gnuregex.c:1613:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if (COMPILE_STACK_EMPTY) ^ gnuregex.c:1633:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] 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); ^ getopt.c: In function 'Getopt': getopt.c:62:7: warning: 'opti' may be used uninitialized in this function [-Wmaybe-uninitialized] int opti; ^ 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 */ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c revcomp.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c selex.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sqerror.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sqio.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_ctype.c 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; ^ selex.c: In function 'ReadSELEX': cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_math.c selex.c:445:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] free(blocks); ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c sre_string.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c stack.c interleaved.c: In function 'ReadInterleaved': interleaved.c:427:3: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] free(blocks); ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c translate.c 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]; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -c types.c cc -c -pipe -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:71:21: warning: 'rwt' may be used uninitialized in this function [-Wmaybe-uninitialized] lwt[i] = rwt[i] = 0.0; ^ weight.c: In function 'VoronoiWeights': weight.c:163:11: warning: 'best' may be used uninitialized in this function [-Wmaybe-uninitialized] int best; /* index of nearest real sequence */ ^ ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[1]: Leaving directory `/usr/src/RPM/BUILD/wise2.4.1/src/HMMer2' (cd dynlibsrc ; make CC="cc" CFLAGS="-c -pipe -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 -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ packaln.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ aln.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dnamatrix.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ probability.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ alnrange.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ alnconvert.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ basematrix.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ shattermatrix.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); ^ 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; ^ shattermatrix.dy: In function 'Wise2_new_ShatterMatrixComponent': shattermatrix.dy:124:7: warning: unused variable 'j' [-Wunused-variable] int j; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ matrixdebug.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dpenvelope.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dbsearchimpl.c 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); ^ 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] } ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dprunimpl.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexsequence.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexevalset.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ complexconsensi.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ sequence.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ sequencestream.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ seqalign.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hitlist.c sequence.dy: In function 'Wise2_read_fasta_Sequence': sequence.dy:767:11: warning: unused variable 'seen_weight' [-Wunused-variable] boolean seen_weight = 0; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsp.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspstream.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ codon.c hspstream.dy: In function 'Wise2_typed_LinearHSPmanager_from_Stream': hspstream.dy:109:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ compmat.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ codonmatrix.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++) { ^ cc -c -pipe -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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ sequencedb.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hscore.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ seqlookup.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ arrayseqlookup.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]; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genericindexresult.c cc -c -pipe -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 arrayseqlookup.dy: In function 'Wise2_add_ArraySeqHead': cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ singlenumberspace.c arrayseqlookup.dy:294:24: warning: variable 'temp' set but not used [-Wunused-but-set-variable] ArraySeqLookupUnit * temp; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ histogram.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ searchstatinterface.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ searchstatlookup.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 */ ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteindb.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ protein.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ pairbase.c 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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ pairbaseseq.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genomicdb.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ randommodel.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ randomdb.c 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)); ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genomic.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ cdna.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ cdnadb.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dna.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ embl.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ genomicregion.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ gene.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ transcript.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ translation.c 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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ btcanvas.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; ^ 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; ^ 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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ asciibtcanvas.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dynlibcross.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); ^ 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 -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 -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ subseqhash.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ intallocator.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteinstreamedindex.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ shadowseq.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ shadowseqindex.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsphandler.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspscaninterface.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsp2hitscan.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; ^ 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); ^ 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", ^ 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", ^ 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", ^ 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", ^ 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; ^ 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); ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsplookupscan.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsplookupthreaded.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspthreadeddb.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hspscanruntime.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] } ^ 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); ^ 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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ hsptwohitscan.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ proteinindexcons.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ dnaindexcons.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; ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory `/usr/src/RPM/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; make CC="cc" CFLAGS="-c -pipe -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 -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. cc -c -pipe -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: 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 -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 -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 -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 -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ functionserver.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ functionclient.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ anonobj.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ transferinterface.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ directsocketwrite.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); ^ 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:7:0: /usr/include/sys/socket.h:137:12: 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); ^ 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 -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 -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 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); ^ cc -c -pipe -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 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]); ^ 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; ^ cc -c -pipe -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 cc -c -pipe -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_untangler.dy: In function 'Wise2_untangle_KmerAssembly': kmer_assembly_untangler.dy:120:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ^ kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ^ kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t {aka long long int}' [-Wformat=] kmer_assembly_untangler.dy:157:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ^ kmer_assembly_untangler.dy:159:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ^ kmer_assembly_untangler.dy:101:22: warning: variable 'link_set' set but not used [-Wunused-but-set-variable] KmerAssemblyLink * link_set[1024]; ^ kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:444:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); ^ kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^ In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.h:174:6: note: expected 'int *' but argument is of type 'long int *' void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ kmer_assembly_untangler.dy: In function 'Wise2_lift_forward_tangled_KmerAssemblyPath': kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'kmer_t {aka long long int}' [-Wformat=] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ^ kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t {aka long long int}' [-Wformat=] cc -c -pipe -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 cc -c -pipe -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 kmer_assembly_contig.dy: In function 'Wise2_KmerAssemblyContigSet_from_KmerAssemblyIndex': kmer_assembly_contig.dy:66:27: warning: unused variable 'final' [-Wunused-variable] KmerAssemblyContigSet * final; ^ cc -c -pipe -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 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); ^ cc -c -pipe -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 cc -c -pipe -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 In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.dy: In function 'Wise2_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.h:102:31: warning: 'newpath' may be used uninitialized in this function [-Wmaybe-uninitialized] #define free_KmerAssemblyPath Wise2_free_KmerAssemblyPath ^ kmer_assembly_untangler.dy:363:22: note: 'newpath' was declared here KmerAssemblyPath * newpath; ^ cc -c -pipe -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 cc -c -pipe -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: return makes integer from pointer without a cast [-Wint-conversion] return NULL; ^ make[1]: Leaving directory `/usr/src/RPM/BUILD/wise2.4.1/src/dnaindex' (cd network ; make CC="cc" CFLAGS="-c -pipe -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 -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 cc -c -pipe -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 cc -c -pipe -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] } ^ 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; ^ 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 -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 -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 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] 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] dnal.c: In function 'main': dnal.c:78:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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) ^ cc -c -pipe -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 cc -c -pipe -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 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; ^ 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': 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; ^ proteinsw.c:824:19: warning: unused variable 'de' [-Wunused-variable] ProteinSW * mat; ^ 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; ^ 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) ^ 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) ^ 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; ^ cc -c -pipe -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 dbac.c: In function 'showPFF': dbac.c:250:43: warning: 'currMatch' may be used uninitialized in this function [-Wmaybe-uninitialized] *(currMatch/0.25)))/log(2); ^ cc -c -pipe -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 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) ^ 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) ^ cc -c -pipe -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 cc -c -pipe -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 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; ^ 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; ^ 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) ^ 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)); ^ cc -c -pipe -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. cc -c -pipe -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 dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:961:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] } ^ cc -c -pipe -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 cc -c -pipe -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; ^ 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; ^ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:649:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:883:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:885:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 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; ^ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:862:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 genewise4.c: In function 'Wise2_calculate_shatter_GeneWise4': 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; ^ 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) ^ cc -c -pipe -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 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) ^ cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ genewise21.c cc -c -pipe -Wall -g -O2 -march=i586 -mtune=generic -I/usr/include/glib-1.2 -I/usr/lib/glib/include -std=gnu89 -I../base/ -I../dynlibsrc/ geneloop21.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; ^ cc -c -pipe -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 genestretch6.c: In function 'Wise2_PackAln_calculate_Small_GeneStretch6': genestretch6.c:1839:19: warning: unused variable 'pau' [-Wunused-variable] genewise21.c: In function 'Wise2_calculate_shatter_GeneWise21': genewise21.c:154:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^ genewise21.c:153:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^ genewise21.c:151:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2606:19: warning: unused variable 'de' [-Wunused-variable] GeneWise21 * mat; ^ 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] geneloop21.c: In function 'Wise2_calculate_shatter_GeneLoop21': geneloop21.c:147:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] int lenj; ^ geneloop21.c:146:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] int leni; ^ geneloop21.c:144:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] int k; ^ genewise21.c: In function 'Wise2_PackAln_calculate_Small_GeneWise21': genewise21.c:3507:19: warning: unused variable 'pau' [-Wunused-variable] geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2280:19: warning: unused variable 'de' [-Wunused-variable] GeneLoop21 * mat; ^ geneloop21.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop21': geneloop21.c:3093:19: warning: unused variable 'pau' [-Wunused-variable] pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:990:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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] genephase6.c: In function 'Wise2_thread_loop_GenePhase6': genephase6.c:873:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:941:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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) ^ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1129:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1178:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1241:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 gwrap.dy: In function 'Wise2_Hscore_from_TSM_genewise': gwrap.dy:527:25: warning: unused variable 'tempcse' [-Wunused-variable] ComplexSequenceEval * tempcse; ^ 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; ^ cc -c -pipe -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 geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1329:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 genewisemodel.c: In function 'Wise2_pack_GeneWiseScore': genewisemodel.dy:114:10: warning: 'out' is used uninitialized in this function [-Wuninitialized] return out; ^ 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); ^ cc -c -pipe -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 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); ^ In file included from /usr/include/stdio.h:936:0, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function 'fgets', inlined from 'Wise2_read_fasta_PhasedProtein' at phasemodel.dy:241:3: /usr/include/bits/stdio2.h:261:9: 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); ^ 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) ^ cc -c -pipe -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 cc -c -pipe -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 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) ^ 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] genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1400:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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] 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) ^ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1553:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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] } ^ cc -c -pipe -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 estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:997:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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 cc -c -pipe -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) ^ cc -c -pipe -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. estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1175:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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/ genewise.c: In function 'build_objects': genewise.c:446:10: warning: unused variable 'ifp' [-Wunused-variable] FILE * ifp; ^ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1373:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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/dyna.h:53:0, from threestatemodel.h:7, from wise2xhmmer2.h:24, from genewisedb.c:4: genewisedb.c: In function 'show_output': ../dynlibsrc/genomicregion.h: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; ^ In file included from ../dynlibsrc/seqalign.h:6:0, from wise2xhmmer2.h:23, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized in this function [-Wmaybe-uninitialized] #define add_SequenceSet Wise2_add_SequenceSet ^ estwisedb.c:183:17: note: 'set' was declared here SequenceSet * set; ^ In file included from estwisedb.c:16:0: estwrap.h:166:36: warning: 'anchored' may be used uninitialized in this function [-Wmaybe-uninitialized] #define write_mul_estwise_AlnBlock Wise2_write_mul_estwise_AlnBlock ^ estwisedb.c:182:14: note: 'anchored' was declared here AlnBlock * anchored; ^ cc -c -pipe -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 estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1205:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] cc -c -pipe -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 cc -c -pipe -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 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; ^ cc -c -pipe -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 genome_evidence.dy: In function 'Wise2_free_GenomeEvidenceUnit': genome_evidence.dy:61:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ cc -c -pipe -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 est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] in->geu_free = free_EstEvidence; ^ est_evidence.dy: In function 'Wise2_est_start_pot': est_evidence.dy:183:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ est_evidence.dy: In function 'Wise2_est_stop_pot': est_evidence.dy:203:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ cc -c -pipe -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] sywise20.c: In function 'Wise2_thread_loop_SyWise20': sywise20.c:764:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ cc -c -pipe -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 geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2341:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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; ^ cc -c -pipe -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 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] 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; ^ genomewise9.c: In function 'Wise2_thread_loop_GenomeWise9': genomewise9.c:745:1: warning: control reaches end of non-void function [-Wreturn-type] { ^ cc -c -pipe -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) ^ cc -c -pipe -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 cc -c -pipe -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 sywise.c:318:7: warning: 'pal' may be used uninitialized in this function [-Wmaybe-uninitialized] alb = convert_PackAln_to_AlnBlock_SyWise20(pal); ^ 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) ^ cc -c -pipe -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; ^ cc -c -pipe -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 cc -c -pipe -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 makes integer from pointer without a cast [-Wint-conversion] for(i=0;icurrent_pos >= tm->input->len || tm->para->no_hitalns > 0 && tm->current_pos > tm->para->no_hitalns || ^ 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 transfactor.dy: In function 'Wise2_read_TransFactor': transfactor.dy:888:13: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized] out->seed = temp; ^ 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 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 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 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 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 ) { ^ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1392:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 motifmatrixdp.c: In function 'Wise2_PackAln_bestmemory_LocalMotifMatrix': motifmatrixdp.c:672:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2667:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 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 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 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 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 sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1416:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1268:12: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] 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: 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.79259 + 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) 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.1321 + 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.svxrTe find-provides: running scripts (alternatives,debuginfo,lib,pam,perl,pkgconfig,python,shell) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.I2lL0f 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.qLZexo 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.HCFtsG find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.rTAHiZ 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 99.59user 5.30system 0:43.97elapsed 238%CPU (0avgtext+0avgdata 133220maxresident)k 0inputs+0outputs (0major+2146120minor)pagefaults 0swaps 107.31user 7.64system 0:56.92elapsed 201%CPU (0avgtext+0avgdata 133220maxresident)k 0inputs+0outputs (0major+2531726minor)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 2019-01-13 07:01:49.621545721 +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