angie: changes by file

review to branch (2009-09-22 to 2009-09-29) v216

• src/cdnaAli/findCdna/findCdna.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/gfServer/gfServer.c
  • 1.55 lines changed: 10, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/borfBig/borfBig.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/encode/validateFiles/validateFiles.c
  • 1.27 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/gsBig/gsBig.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgCustom/hgCustom.c
  • 1.132 lines changed: 2, context: html, text, full: html, text
    Initialize orgForm.clade to empty string instead of NULL (oops!) which causes segfault on solaris. orgForm.clade is overwritten w/selected value when mainForm select is changed, and ignored if genome or db is changed, so initializing to stub value is fine.
• src/hg/hgGene/rnaStructure.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgGene/wikiTrack.c
  • 1.24 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgGenome/mainPage.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgPcr/hgPcr.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgSession/hgSession.c
  • 1.52 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTables/identifiers.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.503 lines changed: 1, context: html, text, full: html, text
    snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent?
• src/hg/hgTracks/config.c
  • 1.84 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/hgTracks.c
  • 1.1600 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/rnaPLFoldTrack.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/simpleTracks.c
  • 1.106 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgc/bamClick.c
  • 1.10 lines changed: 10, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.9 lines changed: 10, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/hgc/hgc.c
  • 1.1576 lines changed: 11, context: html, text, full: html, text
    snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent?
  • 1.1573 lines changed: 39, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgc/hgdpClick.c
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/inc/bamFile.h
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/lib/bamFile.c
  • 1.9 lines changed: 17, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.8 lines changed: 35, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/lib/customFactory.c
  • 1.104 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/hgFind.c
  • 1.222 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/hui.c
  • 1.238 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/jksql.c
  • 1.136 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/web.c
  • 1.171 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/liftOver/liftOver.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/doc/hg18.txt
  • 1.384 lines changed: 107, context: html, text, full: html, text
    Genome Variants: added Korean (SJK). Added base counts to 1000 Genomes SNPs.
• src/hg/makeDb/hgCountAlign/hgCountAlign.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
  • 1.27 lines changed: 14, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgCGAP/hgCGAP.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg/hgKegg.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg2/hgKegg2.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg3/hgKegg3.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/samHit/samHit.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/trackDb/snp130.html
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Added description of repetitive sequence highlighting in re-alignment of flanking sequences.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.8 lines changed: 79, context: html, text, full: html, text
    pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.420 lines changed: 17, context: html, text, full: html, text
    pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp.
• src/hg/mouseStuff/chainSplit/chainSplit.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/mouseStuff/netSplit/netSplit.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/near/hgClusterGenes/hgClusterGenes.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/phyloGif/phyloGif.c
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasKgXref/kgAliasKgXref.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasM/kgAliasM.c
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasRefseq/kgAliasRefseq.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgPepMrna/kgPepMrna.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgPick/kgPick.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgProtAlias/kgProtAlias.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgXref/kgXref.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgXref2/kgXref2.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • 1.11 lines changed: 8, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pbHgnc/pbHgnc.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pfamXref/pfamXref.c
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spOrganism/spOrganism.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spToProteins/spToProteins.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm3/spm3.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm6/spm6.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm7/spm7.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/qa/apacheMonitor.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/sim4big/sim4big.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/trfBig/trfBig.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/makefile
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFiles.csh
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Move aside tmp output after failure; keep a lastLog file with most recent successful log.
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Adding uptime command after error/warning messages so we can see whether load is high.
  • 1.1 lines changed: 58, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/inc/common.h
  • 1.154 lines changed: 12, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/isPcr/webPcr/webPcr.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/jkOwnLib/gfBlatLib.c
  • 1.28 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/jkOwnLib/gfPcrLib.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/common.c
  • 1.132 lines changed: 32, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/fa.c
  • 1.38 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/htmlPage.c
  • 1.38 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/net.c
  • 1.72 lines changed: 7, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/obscure.c
  • 1.48 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/options.c
  • 1.27 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/snof.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/twoBit.c
  • 1.28 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/wormdna.c
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/reformat/gbtofa/gbtofa.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/utils/ccCp/ccCp.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/weblet/counter/counter.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/weblet/hitreport/hitreport.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.