* Package: sci-biology/blat-34-r2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking blatSrc34.zip to /var/tmp/portage/sci-biology/blat-34-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/blat-34-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc ... * Applying blat-34-fix-build-system.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc ... make -j1 make -C lib make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/lib' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o aliType.o -c aliType.c aliType.c:5:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 5 | static char const rcsid[] = "$Id: aliType.c,v 1.4 2003/05/06 07:33:41 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o apacheLog.o -c apacheLog.c apacheLog.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: apacheLog.c,v 1.1 2005/09/03 02:07:40 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o asParse.o -c asParse.c asParse.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: asParse.c,v 1.6 2007/02/11 21:43:15 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o axt.o -c axt.c axt.c:23:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 23 | static char const rcsid[] = "$Id: axt.c,v 1.47 2006/06/18 23:11:58 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o axtAffine.o -c axtAffine.c axtAffine.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: axtAffine.c,v 1.7 2005/04/10 14:41:20 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o base64.o -c base64.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bits.o -c bits.c bits.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: bits.c,v 1.19 2006/02/28 05:40:46 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o binRange.o -c binRange.c binRange.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: binRange.c,v 1.20 2006/07/01 05:01:25 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o blastOut.o -c blastOut.c blastOut.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: blastOut.c,v 1.26 2006/03/10 17:43:36 angie Exp $"; | ^~~~~ In file included from /usr/include/string.h:494, from ../inc/common.h:33, from blastOut.c:2: In function ‘strncpy’, inlined from ‘tabBlastOut’ at blastOut.c:731:5: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated copying 10 bytes from a string of length 21 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o blastParse.o -c blastParse.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o boxClump.o -c boxClump.c boxClump.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: boxClump.c,v 1.5 2005/01/10 00:11:34 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o boxLump.o -c boxLump.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o browserGfx.o -c browserGfx.c browserGfx.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: browserGfx.c,v 1.8 2006/05/08 09:43:31 aamp Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o cda.o -c cda.c cda.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 14 | static char const rcsid[] = "$Id: cda.c,v 1.6 2003/05/06 07:33:41 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chain.o -c chain.c chain.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: chain.c,v 1.25 2007/02/19 18:29:32 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainBlock.o -c chainBlock.c chainBlock.c: In function ‘findBestPredecessors’: chainBlock.c:290:16: warning: variable ‘bestLeaf’ set but not used [-Wunused-but-set-variable] 290 | struct kdLeaf *bestLeaf = NULL; | ^~~~~~~~ At top level: chainBlock.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: chainBlock.c,v 1.17 2005/04/10 14:41:21 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainConnect.o -c chainConnect.c chainConnect.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: chainConnect.c,v 1.3 2005/08/07 23:25:26 baertsch Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainToAxt.o -c chainToAxt.c chainToAxt.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: chainToAxt.c,v 1.4 2005/04/10 14:41:21 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainToPsl.o -c chainToPsl.c chainToPsl.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: chainToPsl.c,v 1.5 2005/04/10 14:41:21 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o cheapcgi.o -c cheapcgi.c cheapcgi.c: In function ‘cgiParseMultipart’: cheapcgi.c:172:75: warning: variable ‘ct’ set but not used [-Wunused-but-set-variable] 172 | har *cd = NULL, *cdMain = NULL, *cdName = NULL, *cdFileName = NULL, *ct = NULL; | ^~ At top level: cheapcgi.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: cheapcgi.c,v 1.85 2006/12/19 18:49:52 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o codebias.o -c codebias.c codebias.c: In function ‘codonFindFrame’: codebias.c:105:8: warning: variable ‘logProbs’ set but not used [-Wunused-but-set-variable] 105 | double logProbs[3]; | ^~~~~~~~ At top level: codebias.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: codebias.c,v 1.6 2005/04/10 14:41:21 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o colHash.o -c colHash.c colHash.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: colHash.c,v 1.3 2003/05/06 07:33:41 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o common.o -c common.c common.c: In function ‘firstWordInFile’: common.c:1695:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1695 | fgets(wordBuf, wordBufSize, f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: common.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: common.c,v 1.108 2007/03/30 00:12:11 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o correlate.o -c correlate.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dgRange.o -c dgRange.c dgRange.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: dgRange.c,v 1.3 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o diGraph.o -c diGraph.c diGraph.c:7:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 7 | static char const rcsid[] = "$Id: diGraph.c,v 1.9 2005/08/17 03:01:29 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dlist.o -c dlist.c dlist.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: dlist.c,v 1.11 2005/07/04 18:44:09 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaLoad.o -c dnaLoad.c dnaLoad.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: dnaLoad.c,v 1.8 2005/03/28 17:21:28 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaMarkov.o -c dnaMarkov.c dnaMarkov.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: dnaMarkov.c,v 1.4 2005/04/10 14:41:22 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaseq.o -c dnaseq.c dnaseq.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: dnaseq.c,v 1.19 2005/11/10 03:40:34 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnautil.o -c dnautil.c dnautil.c: In function ‘findHeadPolyTMaybeMask’: dnautil.c:913:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable] 913 | int pastPoly = 0; | ^~~~~~~~ At top level: dnautil.c:18:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 18 | static char const rcsid[] = "$Id: dnautil.c,v 1.49 2007/03/14 04:54:55 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaMotif.o -c dnaMotif.c dnaMotif.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: dnaMotif.c,v 1.4 2006/09/14 21:08:24 braney Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dtdParse.o -c dtdParse.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dystring.o -c dystring.c dystring.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: dystring.c,v 1.22 2006/02/02 16:24:24 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o emblParse.o -c emblParse.c emblParse.c:52:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 52 | static char const rcsid[] = "$Id: emblParse.c,v 1.3 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errabort.o -c errabort.c errabort.c:18:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 18 | static char const rcsid[] = "$Id: errabort.c,v 1.13 2004/11/10 00:10:50 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errCatch.o -c errCatch.c errCatch.c:22:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 22 | static char const rcsid[] = "$Id: errCatch.c,v 1.2 2006/08/10 01:02:47 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fa.o -c fa.c fa.c: In function ‘faReadSeq’: fa.c:278:1: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 278 | read(fd, s, maxSize); | ^~~~~~~~~~~~~~~~~~~~ At top level: fa.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: fa.c,v 1.37 2007/02/20 18:50:21 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffAli.o -c ffAli.c ffAli.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: ffAli.c,v 1.9 2004/02/13 09:33:32 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffScore.o -c ffScore.c ffScore.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: ffScore.c,v 1.5 2003/10/21 22:06:32 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o filePath.o -c filePath.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fixColor.o -c fixColor.c fixColor.c:5:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 5 | static char const rcsid[] = "$Id: fixColor.c,v 1.3 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o flydna.o -c flydna.c flydna.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: flydna.c,v 1.4 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fof.o -c fof.c fof.c: In function ‘fofMake’: fof.c:481:16: warning: variable ‘itemSize’ set but not used [-Wunused-but-set-variable] 481 | int i, fileIx, itemSize; | ^~~~~~~~ At top level: fof.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: fof.c,v 1.7 2006/03/10 17:43:36 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fuzzyShow.o -c fuzzyShow.c fuzzyShow.c: In function ‘ffShAliPart’: fuzzyShow.c:101:5: warning: variable ‘charsInLine’ set but not used [-Wunused-but-set-variable] 101 | int charsInLine; | ^~~~~~~~~~~ At top level: fuzzyShow.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: fuzzyShow.c,v 1.23 2007/03/27 23:21:25 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gapCalc.o -c gapCalc.c gapCalc.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: gapCalc.c,v 1.4 2006/06/18 23:09:36 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gdf.o -c gdf.c gdf.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: gdf.c,v 1.4 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gemfont.o -c gemfont.c gemfont.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: gemfont.c,v 1.9 2006/06/20 18:17:38 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfNet.o -c gfNet.c gfNet.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: gfNet.c,v 1.8 2004/06/01 16:49:03 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gff.o -c gff.c gff.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: gff.c,v 1.21 2007/02/01 00:43:16 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfxPoly.o -c gfxPoly.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifcomp.o -c gifcomp.c gifcomp.c:59:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 59 | static char const rcsid[] = "$Id: gifcomp.c,v 1.7 2003/05/21 21:03:22 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifdecomp.o -c gifdecomp.c gifdecomp.c:22:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 22 | static char const rcsid[] = "$Id: gifdecomp.c,v 1.3 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifLabel.o -c gifLabel.c gifLabel.c:7:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 7 | static char const rcsid[] = "$Id: gifLabel.c,v 1.7 2005/06/06 20:20:10 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifread.o -c gifread.c gifread.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: gifread.c,v 1.4 2005/04/10 14:41:23 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifwrite.o -c gifwrite.c gifwrite.c:7:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 7 | static char const rcsid[] = "$Id: gifwrite.c,v 1.6 2003/05/21 21:02:22 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hash.o -c hash.c hash.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: hash.c,v 1.36 2007/04/14 17:07:27 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o histogram.o -c histogram.c histogram.c:6:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 6 | static char const rcsid[] = "$Id: histogram.c,v 1.4 2004/09/14 23:43:58 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hmmPfamParse.o -c hmmPfamParse.c hmmPfamParse.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: hmmPfamParse.c,v 1.3 2007/03/23 16:38:40 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hmmstats.o -c hmmstats.c hmmstats.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: hmmstats.c,v 1.4 2003/05/06 07:33:42 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o htmlPage.o -c htmlPage.c htmlPage.c: In function ‘htmlSlurpWithCookies’: htmlPage.c:903:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 903 | write(sd, dyHeader->string, dyHeader->stringSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htmlPage.c: In function ‘htmlPageFromForm’: htmlPage.c:1380:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 1380 | write(sd, dyHeader->string, dyHeader->stringSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htmlPage.c:1390:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 1390 | write(sd, dyHeader->string, dyHeader->stringSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htmlPage.c:1391:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 1391 | write(sd, cgiVars, contentLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: htmlPage.c:26:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 26 | static char const rcsid[] = "$Id: htmlPage.c,v 1.32 2006/07/29 00:17:28 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o htmshell.o -c htmshell.c htmshell.c:20:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 20 | static char const rcsid[] = "$Id: htmshell.c,v 1.32 2006/12/13 18:17:55 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o internet.o -c internet.c internet.c:6:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 6 | static char const rcsid[] = "$Id: internet.c,v 1.10 2005/04/10 14:41:23 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o intExp.o -c intExp.c intExp.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: intExp.c,v 1.6 2003/05/06 07:33:43 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o jointalign.o -c jointalign.c jointalign.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: jointalign.c,v 1.11 2003/05/06 07:33:43 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o jpegSize.o -c jpegSize.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o keys.o -c keys.c keys.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: keys.c,v 1.10 2005/04/10 14:41:23 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o kxTok.o -c kxTok.c kxTok.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: kxTok.c,v 1.10 2004/11/05 23:08:58 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o linefile.o -c linefile.c linefile.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: linefile.c,v 1.54 2007/03/23 08:12:42 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o localmem.o -c localmem.c localmem.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 14 | static char const rcsid[] = "$Id: localmem.c,v 1.10 2005/04/11 07:20:03 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o log.o -c log.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o maf.o -c maf.c maf.c: In function ‘mafFlipStrand’: maf.c:672:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 672 | if (mc->text != NULL) | ^~ maf.c:674:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 674 | if (mc->quality != NULL) | ^~ At top level: maf.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: maf.c,v 1.34 2007/04/12 18:54:23 rico Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mafFromAxt.o -c mafFromAxt.c mafFromAxt.c:6:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 6 | static char const rcsid[] = "$Id: mafFromAxt.c,v 1.4 2003/05/17 23:47:15 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mafScore.o -c mafScore.c mafScore.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: mafScore.c,v 1.9 2005/11/23 17:20:50 braney Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o md5.o -c md5.c md5.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: md5.c,v 1.4 2003/05/06 07:33:43 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgTinyFont.o -c mgTinyFont.c mgTinyFont.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: mgTinyFont.c,v 1.4 2005/12/15 20:33:55 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgSmallFont.o -c mgSmallFont.c mgSmallFont.c:6:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 6 | static char const rcsid[] = "$Id: mgSmallFont.c,v 1.4 2005/12/15 20:33:55 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgMediumFont.o -c mgMediumFont.c mgMediumFont.c:3:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 3 | static char const rcsid[] = "$Id: mgMediumFont.c,v 1.5 2005/12/15 20:33:55 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgLargeFont.o -c mgLargeFont.c mgLargeFont.c:3:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 3 | static char const rcsid[] = "$Id: mgLargeFont.c,v 1.5 2005/12/15 20:33:55 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgHugeFont.o -c mgHugeFont.c mgHugeFont.c:3:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 3 | static char const rcsid[] = "$Id: mgHugeFont.c,v 1.5 2005/12/15 20:18:30 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memalloc.o -c memalloc.c memalloc.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: memalloc.c,v 1.30 2007/03/07 01:46:43 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memgfx.o -c memgfx.c memgfx.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: memgfx.c,v 1.47 2007/04/15 00:33:35 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgCircle.o -c mgCircle.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgPolygon.o -c mgPolygon.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mime.o -c mime.c mime.c: In function ‘parseMultiParts’: mime.c:601:13: warning: variable ‘toobig’ set but not used [-Wunused-but-set-variable] 601 | boolean toobig=FALSE; | ^~~~~~ At top level: mime.c:19:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 19 | static char const rcsid[] = "$Id: mime.c,v 1.13 2006/06/20 18:31:24 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o net.o -c net.c net.c: In function ‘netSkipHttpHeaderLinesCatch’: net.c:699:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 699 | char *version, *code; | ^~~~~~~ net.c:673:7: warning: variable ‘headerVal’ set but not used [-Wunused-but-set-variable] 673 | char *headerVal = NULL; | ^~~~~~~~~ net.c:672:7: warning: variable ‘headerName’ set but not used [-Wunused-but-set-variable] 672 | char *headerName = NULL; | ^~~~~~~~~~ net.c: In function ‘netSkipHttpHeaderLines’: net.c:775:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 775 | char *version, *code; | ^~~~~~~ net.c: In function ‘sendFtpCommand’: net.c:391:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 391 | write(sd, cmd, strlen(cmd)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ net.c: In function ‘netHttpConnect’: net.c:555:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 555 | write(sd, dy->string, dy->stringSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ net.c: In function ‘netOpenHttpExt’: net.c:569:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 569 | write(sd, "\r\n", 2); | ^~~~~~~~~~~~~~~~~~~~ net.c: In function ‘netHttpGet’: net.c:1153:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 1153 | write(lf->fd, dy->string, dy->stringSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: net.c:17:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 17 | static char const rcsid[] = "$Id: net.c,v 1.55 2006/10/06 22:17:38 hiram Exp $"; | ^~~~~ In file included from /usr/include/string.h:494, from ../inc/common.h:33, from net.c:6: In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:268:5: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:314:7: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 128 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:315:7: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:308:7: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 128 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:335:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 16 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘netParseUrl’ at net.c:339:1: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 128 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nib.o -c nib.c nib.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: nib.c,v 1.24 2007/03/13 20:43:05 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nibTwo.o -c nibTwo.c nibTwo.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: nibTwo.c,v 1.5 2006/03/10 17:43:37 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nt4.o -c nt4.c nt4.c: In function ‘newNt4’: nt4.c:36:6: warning: variable ‘unpacked’ set but not used [-Wunused-but-set-variable] 36 | DNA *unpacked; | ^~~~~~~~ At top level: nt4.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: nt4.c,v 1.5 2005/04/10 14:41:24 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o obscure.o -c obscure.c obscure.c: In function ‘incCounterFile’: obscure.c:24:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 24 | fread(&val, sizeof(val), 1, f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ obscure.c: In function ‘cpFile’: obscure.c:235:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 235 | write(d, buf, readSize); | ^~~~~~~~~~~~~~~~~~~~~~~ At top level: obscure.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 14 | static char const rcsid[] = "$Id: obscure.c,v 1.44 2007/03/02 00:45:01 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o oldGff.o -c oldGff.c oldGff.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: oldGff.c,v 1.6 2005/04/10 14:41:24 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o oligoTm.o -c oligoTm.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o options.o -c options.c options.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: options.c,v 1.24 2005/12/12 04:03:40 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o osunix.o -c osunix.c osunix.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: osunix.c,v 1.31 2007/01/30 19:43:46 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pairHmm.o -c pairHmm.c pairHmm.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: pairHmm.c,v 1.5 2005/04/11 06:43:58 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o phyloTree.o -c phyloTree.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pipeline.o -c pipeline.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o portimpl.o -c portimpl.c portimpl.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 14 | static char const rcsid[] = "$Id: portimpl.c,v 1.14 2006/06/23 21:44:04 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pscmGfx.o -c pscmGfx.c pscmGfx.c:18:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 18 | static char const rcsid[] = "$Id: pscmGfx.c,v 1.20 2007/04/15 00:43:41 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o psGfx.o -c psGfx.c psGfx.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: psGfx.c,v 1.30 2007/04/15 00:29:47 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o psl.o -c psl.c psl.c:22:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 22 | static char const rcsid[] = "$Id: psl.c,v 1.76 2007/03/04 20:24:19 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslGenoShow.o -c pslGenoShow.c pslGenoShow.c: In function ‘pslShowAlignmentStranded2’: pslGenoShow.c:31:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable] 31 | int qcfmStart, qcfmEnd, tcfmStart, tcfmEnd; | ^~~~~~~ pslGenoShow.c:31:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable] 31 | int qcfmStart, qcfmEnd, tcfmStart, tcfmEnd; | ^~~~~~~ pslGenoShow.c:30:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable] 30 | int qbafStart, qbafEnd, tbafStart, tbafEnd; | ^~~~~~~ pslGenoShow.c:30:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable] 30 | int qbafStart, qbafEnd, tbafStart, tbafEnd; | ^~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslShow.o -c pslShow.c pslShow.c: In function ‘pslShowAlignmentStranded’: pslShow.c:26:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable] 26 | int qcfmStart, qcfmEnd, tcfmStart, tcfmEnd; | ^~~~~~~ pslShow.c:26:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable] 26 | int qcfmStart, qcfmEnd, tcfmStart, tcfmEnd; | ^~~~~~~ pslShow.c:25:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable] 25 | int qbafStart, qbafEnd, tbafStart, tbafEnd; | ^~~~~~~ pslShow.c:25:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable] 25 | int qbafStart, qbafEnd, tbafStart, tbafEnd; | ^~~~~~~ At top level: pslShow.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: pslShow.c,v 1.5 2005/10/05 19:07:43 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslTbl.o -c pslTbl.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslTransMap.o -c pslTransMap.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o psPoly.o -c psPoly.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pthreadWrap.o -c pthreadWrap.c pthreadWrap.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: pthreadWrap.c,v 1.3 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o qa.o -c qa.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o quickHeap.o -c quickHeap.c quickHeap.c:30:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 30 | static char const rcsid[] = "$Id: quickHeap.c,v 1.1 2005/10/21 05:36:08 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o quotedP.o -c quotedP.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ra.o -c ra.c ra.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: ra.c,v 1.11 2007/03/28 17:13:55 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o rangeTree.o -c rangeTree.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o rbTree.o -c rbTree.c rbTree.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: rbTree.c,v 1.10 2007/02/24 15:59:29 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o repMask.o -c repMask.c repMask.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: repMask.c,v 1.6 2005/04/10 14:41:25 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o rle.o -c rle.c rle.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: rle.c,v 1.6 2005/05/10 00:50:16 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o rnautil.o -c rnautil.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o rudp.o -c rudp.c rudp.c:58:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 58 | static char const rcsid[] = "$Id: rudp.c,v 1.14 2005/12/12 02:24:47 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o scoreWindow.o -c scoreWindow.c scoreWindow.c:4:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 4 | static char const rcsid[] = "$Id: scoreWindow.c,v 1.4 2004/07/16 22:42:55 baertsch Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o seqOut.o -c seqOut.c seqOut.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: seqOut.c,v 1.27 2007/03/26 18:11:48 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o seqStats.o -c seqStats.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servBrcMcw.o -c servBrcMcw.c servBrcMcw.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: servBrcMcw.c,v 1.3 2006/06/19 22:02:56 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servcis.o -c servcis.c servcis.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: servcis.c,v 1.10 2006/06/19 22:02:57 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servCrunx.o -c servCrunx.c servCrunx.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: servCrunx.c,v 1.7 2006/06/19 22:02:56 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servcl.o -c servcl.c servcl.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: servcl.c,v 1.7 2006/06/19 22:02:57 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servmsII.o -c servmsII.c servmsII.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: servmsII.c,v 1.6 2006/06/19 22:02:57 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o servpws.o -c servpws.c servpws.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: servpws.c,v 1.6 2006/06/19 22:02:57 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o shaRes.o -c shaRes.c shaRes.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: shaRes.c,v 1.4 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o slog.o -c slog.c slog.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: slog.c,v 1.4 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o snof.o -c snof.c snof.c: In function ‘snofNameAtIx’: snof.c:282:1: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 282 | fread(snof->mid, snof->itemSize, 1, snof->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: snof.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: snof.c,v 1.4 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o snofmake.o -c snofmake.c snofmake.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: snofmake.c,v 1.5 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o snofsig.o -c snofsig.c snofsig.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: snofsig.c,v 1.4 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o spacedColumn.o -c spacedColumn.c spacedColumn.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: spacedColumn.c,v 1.1 2007/03/23 06:29:51 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o spacedSeed.o -c spacedSeed.c spacedSeed.c:6:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 6 | static char const rcsid[] = "$Id: spacedSeed.c,v 1.1 2005/01/10 00:02:37 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o spaceSaver.o -c spaceSaver.c spaceSaver.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: spaceSaver.c,v 1.10 2004/09/02 20:08:44 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o sqlNum.o -c sqlNum.c sqlNum.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: sqlNum.c,v 1.16 2005/12/09 22:39:36 hiram Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o sqlList.o -c sqlList.c sqlList.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 14 | static char const rcsid[] = "$Id: sqlList.c,v 1.19 2006/07/17 19:35:30 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o subText.o -c subText.c subText.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: subText.c,v 1.11 2005/04/10 14:41:26 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o synQueue.o -c synQueue.c synQueue.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: synQueue.c,v 1.6 2006/03/11 23:07:02 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o tabRow.o -c tabRow.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o textOut.o -c textOut.c textOut.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: textOut.c,v 1.3 2006/08/04 06:00:20 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o tokenizer.o -c tokenizer.c tokenizer.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: tokenizer.c,v 1.3 2004/07/14 05:47:14 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o trix.o -c trix.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o twoBit.o -c twoBit.c twoBit.c: In function ‘readBlockCoords’: twoBit.c:388:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 388 | fread(nStarts, sizeof(nStarts[0]), blkCount, f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ twoBit.c:389:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 389 | fread(nSizes, sizeof(nSizes[0]), blkCount, f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ twoBit.c: In function ‘twoBitOutNBeds’: twoBit.c:952:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 952 | fread(nStarts, sizeof(nStarts[0]), nBlockCount, tbf->f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ twoBit.c:953:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 953 | fread(nSizes, sizeof(nSizes[0]), nBlockCount, tbf->f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ twoBit.c: In function ‘twoBitSeqSizeNoNs’: twoBit.c:994:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 994 | fread(nStarts, sizeof(nStarts[0]), nBlockCount, tbf->f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ twoBit.c:995:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 995 | fread(nSizes, sizeof(nSizes[0]), nBlockCount, tbf->f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: twoBit.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: twoBit.c,v 1.22 2006/07/31 22:18:22 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o verbose.o -c verbose.c verbose.c:7:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 7 | static char const rcsid[] = "$Id: verbose.c,v 1.5 2005/10/17 15:46:41 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o vGfx.o -c vGfx.c vGfx.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: vGfx.c,v 1.6 2006/06/23 23:45:02 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o vGif.o -c vGif.c vGif.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: vGif.c,v 1.4 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o wildcmp.o -c wildcmp.c wildcmp.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: wildcmp.c,v 1.5 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o wormdna.o -c wormdna.c wormdna.c: In function ‘wormGeneForOrf’: wormdna.c:606:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable] 606 | int wordCount; | ^~~~~~~~~ wormdna.c: In function ‘wormCdnaInfo’: wormdna.c:272:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 272 | fgets(commentBuf, sizeof(commentBuf), cdnaFa); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ wormdna.c: In function ‘wormGeneRange’: wormdna.c:1045:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1045 | fgets(lineBuf, sizeof(lineBuf), c2cFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ wormdna.c: In function ‘findAltSpliceRange’: wormdna.c:974:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 974 | fgets(lineBuf, sizeof(lineBuf), f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: wormdna.c:20:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 20 | static char const rcsid[] = "$Id: wormdna.c,v 1.10 2005/04/10 14:41:26 markd Exp $"; | ^~~~~ In file included from /usr/include/string.h:494, from ../inc/common.h:33, from wormdna.c:8: In function ‘strncpy’, inlined from ‘wormIsGeneName’ at wormdna.c:525:1: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘wormParseChromRange’ at wormdna.c:882:1: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xa.o -c xa.c xa.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: xa.c,v 1.5 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xAli.o -c xAli.c xAli.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 12 | static char const rcsid[] = "$Id: xAli.c,v 1.6 2005/04/10 14:41:26 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xap.o -c xap.c xap.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: xap.c,v 1.11 2005/12/19 05:18:26 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xenshow.o -c xenshow.c xenshow.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: xenshow.c,v 1.5 2003/05/06 07:33:44 kate Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xmlEscape.o -c xmlEscape.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xp.o -c xp.c xp.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: xp.c,v 1.15 2005/12/19 17:51:14 kent Exp $"; | ^~~~~ mkdir amd64 x86_64-pc-linux-gnu-ar rcus amd64/jkweb.a aliType.o apacheLog.o asParse.o axt.o axtAffine.o base64.o bits.o binRange.o blastOut.o blastParse.o boxClump.o boxLump.o browserGfx.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o codebias.o colHash.o common.o correlate.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaseq.o dnautil.o dnaMotif.o dtdParse.o dystring.o emblParse.o errabort.o errCatch.o fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o fuzzyShow.o gapCalc.o gdf.o gemfont.o gfNet.o gff.o gfxPoly.o gifcomp.o gifdecomp.o gifLabel.o gifread.o gifwrite.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o internet.o intExp.o jointalign.o jpegSize.o keys.o kxTok.o linefile.o localmem.o log.o maf.o mafFromAxt.o mafScore.o md5.o mgTinyFont.o mgSmallFont.o mgMediumFont.o mgLargeFont.o mgHugeFont.o memalloc.o memgfx.o mgCircle.o mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o phyloTree.o pipeline.o portimpl.o pscmGfx.o psGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o psPoly.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rangeTree.o rbTree.o repMask.o rle.o rnautil.o rudp.o scoreWindow.o seqOut.o seqStats.o servBrcMcw.o servcis.o servCrunx.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spacedColumn.o spacedSeed.o spaceSaver.o sqlNum.o sqlList.o subText.o synQueue.o tabRow.o textOut.o tokenizer.o trix.o twoBit.o verbose.o vGfx.o vGif.o wildcmp.o wormdna.o xa.o xAli.o xap.o xenshow.o xmlEscape.o xp.o make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/lib' make -C jkOwnLib make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/jkOwnLib' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bandExt.o -c bandExt.c bandExt.c:21:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 21 | static char const rcsid[] = "$Id: bandExt.c,v 1.13 2006/03/14 19:02:31 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o crudeali.o -c crudeali.c crudeali.c:17:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 17 | static char const rcsid[] = "$Id: crudeali.c,v 1.5 2006/05/09 01:05:55 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffAliHelp.o -c ffAliHelp.c ffAliHelp.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: ffAliHelp.c,v 1.10 2005/11/20 19:24:57 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffSeedExtend.o -c ffSeedExtend.c ffSeedExtend.c: In function ‘clumpToExactRange’: ffSeedExtend.c:218:57: warning: variable ‘lastTe’ set but not used [-Wunused-but-set-variable] 218 | BIOPOL *lastQs = NULL, *lastQe = NULL, *lastTs = NULL, *lastTe = NULL; | ^~~~~~ At top level: ffSeedExtend.c:15:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 15 | static char const rcsid[] = "$Id: ffSeedExtend.c,v 1.36 2006/06/22 16:24:43 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fuzzyFind.o -c fuzzyFind.c fuzzyFind.c: In function ‘rwFindTilesBetween’: fuzzyFind.c:1170:5: warning: variable ‘tileIx’ set but not used [-Wunused-but-set-variable] 1170 | int tileIx; | ^~~~~~ At top level: fuzzyFind.c:43:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 43 | static char const rcsid[] = "$Id: fuzzyFind.c,v 1.17 2006/05/09 01:05:55 markd Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o genoFind.o -c genoFind.c genoFind.c:20:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 20 | static char const rcsid[] = "$Id: genoFind.c,v 1.23 2007/02/04 05:09:02 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfBlatLib.o -c gfBlatLib.c gfBlatLib.c: In function ‘clumpToHspRange’: gfBlatLib.c:732:57: warning: variable ‘lastTe’ set but not used [-Wunused-but-set-variable] 732 | BIOPOL *lastQs = NULL, *lastQe = NULL, *lastTs = NULL, *lastTe = NULL; | ^~~~~~ gfBlatLib.c: In function ‘startSeqQuery’: gfBlatLib.c:114:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 114 | write(conn, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gfBlatLib.c:115:1: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 115 | read(conn, buf, 1); | ^~~~~~~~~~~~~~~~~~ gfBlatLib.c:118:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 118 | write(conn, seq->dna, seq->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: gfBlatLib.c:21:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 21 | static char const rcsid[] = "$Id: gfBlatLib.c,v 1.25 2007/04/20 22:44:11 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfClientLib.o -c gfClientLib.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfInternal.o -c gfInternal.c gfInternal.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 13 | static char const rcsid[] = "$Id: gfInternal.c,v 1.3 2006/06/22 16:24:44 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfOut.o -c gfOut.c gfOut.c:17:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 17 | static char const rcsid[] = "$Id: gfOut.c,v 1.16 2006/06/22 16:24:44 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfPcrLib.o -c gfPcrLib.c gfPcrLib.c: In function ‘pcrLocalStrand’: gfPcrLib.c:299:5: warning: variable ‘sizeLeft’ set but not used [-Wunused-but-set-variable] 299 | int sizeLeft; | ^~~~~~~~ gfPcrLib.c: In function ‘gfPcrGetRanges’: gfPcrLib.c:390:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 390 | write(conn, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: gfPcrLib.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: gfPcrLib.c,v 1.8 2006/03/15 18:36:16 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfWebLib.o -c gfWebLib.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ooc.o -c ooc.c ooc.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: ooc.c,v 1.2 2003/09/09 21:44:02 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o patSpace.o -c patSpace.c patSpace.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: patSpace.c,v 1.3 2006/03/15 18:36:16 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o supStitch.o -c supStitch.c supStitch.c:18:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 18 | static char const rcsid[] = "$Id: supStitch.c,v 1.38 2007/04/20 22:43:37 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o trans3.o -c trans3.c trans3.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 8 | static char const rcsid[] = "$Id: trans3.c,v 1.5 2007/04/20 22:43:37 kent Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xenbig.o -c xenbig.c xenbig.c: In function ‘xStitch’: xenbig.c:886:13: warning: variable ‘partCount’ set but not used [-Wunused-but-set-variable] 886 | int partCount; | ^~~~~~~~~ At top level: xenbig.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 16 | static char const rcsid[] = "$Id: xenbig.c,v 1.3 2006/03/15 18:36:16 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xensmall.o -c xensmall.c xensmall.c: In function ‘xenAlignSmall’: xensmall.c:224:5: warning: variable ‘matchOff’ set but not used [-Wunused-but-set-variable] 224 | int matchOff, qSlipOff, tSlipOff; | ^~~~~~~~ At top level: xensmall.c:11:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 11 | static char const rcsid[] = "$Id: xensmall.c,v 1.11 2006/03/15 18:36:16 angie Exp $"; | ^~~~~ x86_64-pc-linux-gnu-ar rcus ../lib/amd64/jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o supStitch.o trans3.o xenbig.o xensmall.o make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/jkOwnLib' make -C blat make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/blat' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o blat.o -c blat.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/blat blat.o ../lib/amd64/jkOwnLib.a ../lib/amd64/jkweb.a -lm true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/blat make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/blat' make -C gfClient make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/gfClient' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfClient.o -c gfClient.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/gfClient gfClient.o ../lib/amd64/jkOwnLib.a ../lib/amd64/jkweb.a -lm true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/gfClient make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/gfClient' make -C gfServer make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/gfServer' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfServer.o -c gfServer.c gfServer.c: In function ‘stopServer’: gfServer.c:741:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 741 | write(sd, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gfServer.c: In function ‘statusServer’: gfServer.c:756:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 756 | write(sd, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gfServer.c: In function ‘queryServer’: gfServer.c:787:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 787 | write(sd, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gfServer.c:789:1: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 789 | read(sd, buf, 1); | ^~~~~~~~~~~~~~~~ gfServer.c:792:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 792 | write(sd, seq->dna, seq->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gfServer.c: In function ‘pcrServer’: gfServer.c:840:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 840 | write(sd, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gfServer.c: In function ‘getFileList’: gfServer.c:874:1: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 874 | write(sd, buf, strlen(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/gfServer gfServer.o ../lib/amd64/jkOwnLib.a ../lib/amd64/jkweb.a -lm true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/gfServer make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/gfServer' make -C hg/pslPretty make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslPretty' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslPretty.o -c pslPretty.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/pslPretty pslPretty.o ../../lib/amd64/jkweb.a -lm make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslPretty' make -C hg/pslReps make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslReps' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslReps.o -c pslReps.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/pslReps pslReps.o ../../lib/amd64/jkweb.a -lm make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslReps' make -C hg/pslSort make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslSort' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pslSort.o -c pslSort.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/pslSort pslSort.o ../../lib/amd64/jkweb.a -lm make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/hg/pslSort' make -C utils/nibFrag make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/nibFrag' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nibFrag.o -c nibFrag.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/nibFrag nibFrag.o ../../lib/amd64/jkweb.a make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/nibFrag' make -C utils/faToNib make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/faToNib' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o faToNib.o -c faToNib.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/faToNib faToNib.o ../../lib/amd64/jkweb.a -lm make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/faToNib' make -C utils/faToTwoBit make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/faToTwoBit' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o faToTwoBit.o -c faToTwoBit.c x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/faToTwoBit faToTwoBit.o ../../lib/amd64/jkweb.a -lm true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/faToTwoBit make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/faToTwoBit' make -C utils/twoBitToFa make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/twoBitToFa' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DJK_WARN -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o twoBitToFa.o -c twoBitToFa.c twoBitToFa.c:10:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 10 | static char const rcsid[] = "$Id: twoBitToFa.c,v 1.11 2006/10/16 21:21:12 galt Exp $"; | ^~~~~ x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/twoBitToFa twoBitToFa.o ../../lib/amd64/jkweb.a -lm #true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/twoBitToFa make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/twoBitToFa' make -C utils/twoBitInfo make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/twoBitInfo' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o twoBitInfo.o -c twoBitInfo.c x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/twoBitInfo twoBitInfo.o ../../lib/amd64/jkweb.a -lm true /var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/bin/amd64/twoBitInfo make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/utils/twoBitInfo' make -C webBlat make[1]: Entering directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/webBlat' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o webBlat.o -c webBlat.c x86_64-pc-linux-gnu-gcc -o webBlat webBlat.o ../lib/amd64/jkOwnLib.a ../lib/amd64/jkweb.a -lm /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/amd64/jkweb.a(htmshell.o):(.bss+0x20): multiple definition of `htmlRecover'; webBlat.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/amd64/jkweb.a(portimpl.o):(.bss+0x0): multiple definition of `htmlRecover'; webBlat.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/amd64/jkweb.a(pslShow.o):(.bss+0x0): multiple definition of `htmlRecover'; webBlat.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/amd64/jkweb.a(seqOut.o):(.bss+0x0): multiple definition of `htmlRecover'; webBlat.o:(.bss+0x20): first defined here collect2: error: ld returned 1 exit status make[1]: *** [makefile:10: webBlat] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc/webBlat' make: *** [makefile:15: all] Error 2 * ERROR: sci-biology/blat-34-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/blat-34-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/blat-34-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:blat-34-r2:20200126-141522.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/blat-34-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/blat-34-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc' * S: '/var/tmp/portage/sci-biology/blat-34-r2/work/blatSrc'