Commits for galt

v301_preview2 to v301_base (2014-06-02 to 2014-06-09) v301

• closing vm 1.9 to new features so we can get it released
  • src/hg/encode3/validateManifest/VERSION.TXT - lines changed 1, context: html, text, full: html, text
• Inside an errCatch block warnings which are not followed by an errAbort just get swallowed up and ignored. I added a flag to the structure that remembers that warnings have occurred.
  • src/inc/errCatch.h - lines changed 5, context: html, text, full: html, text
  • src/lib/errCatch.c - lines changed 13, context: html, text, full: html, text
  • src/lib/errabort.c - lines changed 4, context: html, text, full: html, text
• Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
  • src/ai/paraFlow/compiler/pfToken.c - lines changed 1, context: html, text, full: html, text
  • src/ai/paraFlow/runtime/argsEnv.c - lines changed 1, context: html, text, full: html, text
  • src/ai/paraFlow/runtime/runErr.c - lines changed 1, context: html, text, full: html, text
  • src/ameme/ameme.c - lines changed 1, context: html, text, full: html, text
  • src/blatz/client.c - lines changed 1, context: html, text, full: html, text
  • src/blatz/server.c - lines changed 1, context: html, text, full: html, text
  • src/blatz/standalone.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/aliGlue/aliGlue.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/c2gCheck/g2cCheck.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/exonAli/exonAli.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/g2cCheck/g2cCheck.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/patSpace/findHits.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/patSpace/glueBacs.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/patSpace/patSpace.c - lines changed 1, context: html, text, full: html, text
  • src/cdnaAli/refineAli/refineAli.c - lines changed 1, context: html, text, full: html, text
  • src/fuzzyFind/ffapp.c - lines changed 1, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altPaths.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altSplice.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/exonWalk/exonWalk.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/autoSql.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/tests/jsonTest.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ctgToChromFa/ctgToChromFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/lib/encodePatchTdb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 1, context: html, text, full: html, text
  • src/hg/extractPslForLfs/extractPslForLfs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fqToQa/fqToQa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fqToQac/fqToQac.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToMrna/genePredToMrna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/cmParse/cmParse.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/gapper/gapper.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/mendMap/mendMap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/mm/mm/mm.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/ooGreedy/bak/ooGreedy.39.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/ooGreedy/bak/ooGreedy.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/ooGreedy/ooGreedy.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/psLayout/psLayout.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgConvert/hgConvert.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgCoordConv/hgCoordConv.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPcr/hgPcr.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/renderMain.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgUserSuggestion/hgUserSuggestion.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/lowelab.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/cart.h - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hPrint.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/customTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/findKGAlias.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/findKGProtAlias.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hCommon.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/jksql.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/loweutils.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbAlignData.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/metaData.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbAligned.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbFileOps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbPipeline.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbProcessed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbStatusTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbVerb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/sqlUpdater.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/process/gbProcess.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/selectWithPsl/selectWithPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/tests/subset/gbGetTestSubset.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTraceInfo/hgTraceInfo.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/testCart/cart.c - lines changed 1, context: html, text, full: html, text
  • src/hg/phyloGif/phyloGif.c - lines changed 2, context: html, text, full: html, text
  • src/hg/ratStuff/mafAddIRows/mafAddIRows.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/mafFilter/mafFilter.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/mafOrder/mafOrder.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/mafToAnc/mafToAnc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/stageMultiz/stageMultiz.c - lines changed 1, context: html, text, full: html, text
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 1, context: html, text, full: html, text
  • src/hg/rtdbWebUpdate/rtdbWebUpdate.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/details/dbSnp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/tajD/tajD.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snpException/snpException.c - lines changed 1, context: html, text, full: html, text
  • src/hg/spideyToPsl/spideyToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/splignToPsl/splignToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbQuery.c - lines changed 1, context: html, text, full: html, text
  • src/hg/visiGene/vgPrepImage/jp2Dec.c - lines changed 1, context: html, text, full: html, text
  • src/hg/zfishBacClonesandSts/zfishBacClonesandSts.c - lines changed 1, context: html, text, full: html, text
  • src/idbQuery/idbQuery.c - lines changed 1, context: html, text, full: html, text
  • src/inc/errAbort.h - lines changed 93, context: html, text, full: html, text
  • src/inc/errabort.h - lines changed 93, context: html, text, full: html, text
  • src/isPcr/webPcr/webPcr.c - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/fuzzyFind.c - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/gfInternal.c - lines changed 1, context: html, text, full: html, text
  • src/kehayden/linearSat/linearSat.c - lines changed 1, context: html, text, full: html, text
  • src/lib/annoGratorQuery.c - lines changed 1, context: html, text, full: html, text
  • src/lib/annoStreamer.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bwgCreate.c - lines changed 1, context: html, text, full: html, text
  • src/lib/cheapcgi.c - lines changed 1, context: html, text, full: html, text
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
  • src/lib/errAbort.c - lines changed 374, context: html, text, full: html, text
  • src/lib/errCatch.c - lines changed 1, context: html, text, full: html, text
  • src/lib/errabort.c - lines changed 374, context: html, text, full: html, text
  • src/lib/fa.c - lines changed 1, context: html, text, full: html, text
  • src/lib/gfNet.c - lines changed 1, context: html, text, full: html, text
  • src/lib/gff3.c - lines changed 1, context: html, text, full: html, text
  • src/lib/hmac.c - lines changed 1, context: html, text, full: html, text
  • src/lib/hmmPfamParse.c - lines changed 1, context: html, text, full: html, text
  • src/lib/htmlPage.c - lines changed 1, context: html, text, full: html, text
  • src/lib/htmshell.c - lines changed 1, context: html, text, full: html, text
  • src/lib/https.c - lines changed 2, context: html, text, full: html, text
  • src/lib/jointalign.c - lines changed 1, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 1, context: html, text, full: html, text
  • src/lib/log.c - lines changed 1, context: html, text, full: html, text
  • src/lib/maf.c - lines changed 1, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/meta.c - lines changed 1, context: html, text, full: html, text
  • src/lib/mime.c - lines changed 1, context: html, text, full: html, text
  • src/lib/net.c - lines changed 1, context: html, text, full: html, text
  • src/lib/paraFetch.c - lines changed 1, context: html, text, full: html, text
  • src/lib/pipeline.c - lines changed 1, context: html, text, full: html, text
  • src/lib/pthreadWrap.c - lines changed 1, context: html, text, full: html, text
  • src/lib/qa.c - lines changed 1, context: html, text, full: html, text
  • src/lib/rudp.c - lines changed 1, context: html, text, full: html, text
  • src/lib/seg.c - lines changed 1, context: html, text, full: html, text
  • src/lib/snofmake.c - lines changed 1, context: html, text, full: html, text
  • src/lib/tests/mimeDecodeTest.c - lines changed 1, context: html, text, full: html, text
  • src/lib/tests/udcTest.c - lines changed 1, context: html, text, full: html, text
  • src/lib/textOut.c - lines changed 1, context: html, text, full: html, text
  • src/lib/tokenizer.c - lines changed 1, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text
  • src/lib/vcfBits.c - lines changed 1, context: html, text, full: html, text
  • src/lib/xap.c - lines changed 1, context: html, text, full: html, text
  • src/lib/xp.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/lib/paraLib.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHub/heartbeat.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHub/paraHub.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNode/paraNode.c - lines changed 1, context: html, text, full: html, text
  • src/parasol/parasol/parasol.c - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/bigWigCat.c - lines changed 1, context: html, text, full: html, text
  • src/utils/catDir/catDir.c - lines changed 1, context: html, text, full: html, text
  • src/utils/est2genomeToPsl/est2genomeToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/utils/fastaToPsl/fastaToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/utils/git-reports/git-reports.c - lines changed 1, context: html, text, full: html, text
  • src/utils/htmlCheck/htmlCheck.c - lines changed 1, context: html, text, full: html, text
  • src/utils/verticalSplitSqlTable/verticalSplitSqlTable.c - lines changed 1, context: html, text, full: html, text
  • src/webBlat/webBlat.c - lines changed 1, context: html, text, full: html, text