Commits for hiram

v282_preview to v282_preview2 (2013-04-02 to 2013-04-09) v282

• minimalist makefile changes for kentUtils build refs #9104
  • src/aladdin/aladdin/makefile - lines changed 14, context: html, text, full: html, text
  • src/aladdin/makefile - lines changed 3, context: html, text, full: html, text
  • src/fuse/makefile - lines changed 15, context: html, text, full: html, text
  • src/fuse/udcFuse/makefile - lines changed 18, context: html, text, full: html, text
  • src/getgene/makefile - lines changed 15, context: html, text, full: html, text
  • src/inc/userApp.mk - lines changed 1, context: html, text, full: html, text
  • src/meta/makefile - lines changed 7, context: html, text, full: html, text
  • src/meta/metaFlatten/makefile - lines changed 15, context: html, text, full: html, text
  • src/meta/metaReformat/makefile - lines changed 15, context: html, text, full: html, text
  • src/primeMate/makefile - lines changed 15, context: html, text, full: html, text
  • src/wormAli/makefile - lines changed 15, context: html, text, full: html, text
• moving to minimal makefiles for kentUtils build refs #9104
  • src/aladdin/aladdin/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/addCols/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bedClip/makefile - lines changed 19, context: html, text, full: html, text
  • src/utils/bedCommonRegions/makefile - lines changed 20, context: html, text, full: html, text
  • src/utils/bedGeneParts/makefile - lines changed 20, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bedPileUps/makefile - lines changed 16, context: html, text, full: html, text
  • src/utils/bedRemoveOverlap/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/bedRestrictToPositions/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bedToBigBed/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bigBedInfo/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/bigBedNamedItems/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bigBedSummary/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/bigWigAverageOverBed/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bigWigInfo/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/bigWigMerge/makefile - lines changed 19, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/bigWigToWig/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/calc/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/catDir/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/catUncomment/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/ccCp/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/chopFaLines/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/colTransform/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/convolve/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/countChars/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/detab/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/endsInLf/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faAlign/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faCmp/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/faCount/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/faFilter/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faFilterN/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faFlyBaseToUcsc/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faFrag/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faGapLocs/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/faGapSizes/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/faNcbiToUcsc/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faNoise/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/faOneRecord/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faPolyASizes/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faRandomize/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/faRc/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faSimplify/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faSize/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faSomeRecords/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faSplit/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/faToFastq/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/faToNib/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faToTab/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/faToTwoBit/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/faTrans/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/faTrimPolyA/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/faTrimRead/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/fastqToFa/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/findMotif/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/fixCr/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/gapSplit/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/gffPeek/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/git-reports/makefile - lines changed 22, context: html, text, full: html, text
  • src/utils/headRest/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/htmlCheck/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/htmlPics/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/jkUniq/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/lineCount/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/nibFrag/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/nibSize/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/nt4Frag/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/paraFetch/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/paraSync/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/pslToPslx/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/pslToXa/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/raSqlQuery/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/raToTab/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/randomLines/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/rmFaDups/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/rowsToCols/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/makefile - lines changed 21, context: html, text, full: html, text
  • src/utils/scrambleFa/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/sizeof/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/spacedToTab/makefile - lines changed 12, context: html, text, full: html, text
  • src/utils/splitFile/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/splitFileByColumn/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/stringify/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/subChar/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/subColumn/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/subs/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/tableSum/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/tailLines/makefile - lines changed 16, context: html, text, full: html, text
  • src/utils/textHist2/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/textHistogram/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/tickToDate/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/toLower/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/toUpper/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/twoBitInfo/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/udcCleanup/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/undupFa/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/upper/makefile - lines changed 10, context: html, text, full: html, text
  • src/utils/venn/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/verticalSplitSqlTable/makefile - lines changed 15, context: html, text, full: html, text
  • src/utils/weedLines/makefile - lines changed 13, context: html, text, full: html, text
  • src/utils/wigCorrelate/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/wigTestMaker/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/wigToBigWig/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/wordLine/makefile - lines changed 11, context: html, text, full: html, text
• now using minimal makefile for kentUtils build refs #9104
  • src/utils/raToLines/linesToRa/linesToRa.c - lines changed 70, context: html, text, full: html, text
  • src/utils/raToLines/linesToRa/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/raToLines/makefile - lines changed 16, context: html, text, full: html, text
  • src/utils/raToLines/raToLines/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/raToLines/raToLines/raToLines.c - lines changed 68, context: html, text, full: html, text
• minimal makefile style for kentUtils build refs #9104
  • src/utils/timing/gmtime/gmtime.c - lines changed 33, context: html, text, full: html, text
  • src/utils/timing/gmtime/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/timing/localtime/localtime.c - lines changed 33, context: html, text, full: html, text
  • src/utils/timing/localtime/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/timing/makefile - lines changed 34, context: html, text, full: html, text
  • src/utils/timing/mktime/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/timing/mktime/mktime.c - lines changed 46, context: html, text, full: html, text
• add comment about preMyLibs
  • src/inc/userApp.mk - lines changed 9, context: html, text, full: html, text
• saving the existing awk script here so it can be removed from scripts directory refs #9104
  • src/hg/genePredToBed/genePredToBed.awk - lines changed 32, context: html, text, full: html, text
• minimal makefiles now in place for kentUtils build refs #9104
  • src/hg/affyTransciptome/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/agpAllToFaFile/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/agpCloneCheck/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/agpCloneList/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/agpToFa/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/agpToGl/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/autoDtd/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/autoSql/makefile - lines changed 22, context: html, text, full: html, text
  • src/hg/autoXml/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/bedIntersect/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/bedItemOverlapCount/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/bedOrBlocks/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/bedSort/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/bedSplitOnChrom/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/bedToGenePred/makefile - lines changed 23, context: html, text, full: html, text
  • src/hg/blastToPsl/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/borfBig/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/checkCoverageGaps/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/checkHgFindSpec/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/checkTableCoords/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/ctgFaToFa/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/ctgToChromFa/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/dbTrash/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/embossToPsl/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/encode3/validateManifest/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/estOrient/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/fakeFinContigs/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/fakeOut/makefile - lines changed 10, context: html, text, full: html, text
  • src/hg/ffaToFa/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/fishClones/makefile - lines changed 23, context: html, text, full: html, text
  • src/hg/fqToQa/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/fqToQac/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/fragPart/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/gbGetEntries/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/gbOneAcc/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/gbToFaRa/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/geneBounds/assessLibs/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/averagExp/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/axtForEst/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/bedCons/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/bedThickToCds/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/geneBounds/checkableBorf/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/geneBounds/clusterPsl/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/geneBounds/clusterRna/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/geneBounds/dnaMotifFind/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/eisenInput/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/emblMatrixToMotif/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/estLibStats/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/expToRna/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/iriToControlTable/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/geneBounds/iriToDnaMotif/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/geneBounds/lib/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/geneBounds/liftPromoHits/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/motifLogo/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/motifSig/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/geneBounds/orf/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/orfCompare/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/geneBounds/orfEnum/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/geneBounds/orfStats/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/polyInfo/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/promoSeqFromCluster/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/raToCds/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrf/makefile - lines changed 14, context: html, text, full: html, text
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  • src/hg/genePredCheck/makefile - lines changed 14, context: html, text, full: html, text
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  • src/hg/genePredSingleCover/makefile - lines changed 22, context: html, text, full: html, text
  • src/hg/genePredToBed/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/genePredToFakePsl/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/genePredToGtf/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/genePredToGtf/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToMafFrames/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/getFeatDna/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/getRna/makefile - lines changed 24, context: html, text, full: html, text
  • src/hg/getRnaPred/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/gigAssembler/checkAgpAndFa/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/gpStats/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/gpToGtf/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/gpcrParser/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/gsBig/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/hgChroms/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/hgGetAnn/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/hgKnownGeneList/makefile - lines changed 22, context: html, text, full: html, text
  • src/hg/hgSelect/makefile - lines changed 27, context: html, text, full: html, text
  • src/hg/hgSpeciesRna/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/hgTablesTest/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/hgsqlLocal/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/hgsqlSwapTables/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/hgsqlTableDate/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/hgsqladmin/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/hgsqldump/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/hgsqldumpLocal/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/hgsqlimport/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/intronEnds/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/lfsOverlap/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/liftAcross/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/liftAgp/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/liftFrags/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/liftUp/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/maskOutFa/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/mdToNcbiLift/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/mrnaToGene/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/near/hgCeOrfToGene/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgClusterGenes/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgEmblProtLinks/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgExpDistance/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgGoAssociation/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/near/hgKnownToSuper/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgMapToGene/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgMapViaSwissProt/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgNearTest/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/near/hgNetDist/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/near/hgProtIdToGenePred/makefile - lines changed 14, context: html, text, full: html, text
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• adding -lm to all binary build due to Brian's checkin for anti-aliased line drawing refs #9104
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• adding -lm to all binary build due to Brian's checkin for anti-aliased line drawing refs #9104
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• an extra blank has been removed from the asParse generator refs #9897
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• fixup broken 'make test' situation with the makefile changes refs #9104
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• makefile fixups refs #9104
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• blatSuite actually depends upon hgLib since it is trying to build hg/* programs refs #9104
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• cleaning up test target and adding that generic target in userApp.mk refs #9104
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• fixup dangerous test target refs #9104
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• fixup make test targets to function with userApp.sh refs #9104
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• fixup test references for userApp.sh refs #9104
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• fixup test references for userApp.sh refs #9104
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• fixup test references for userApp.sh refs #9104
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• eliminating compile errors and warnings refs #9104
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• implementing minimal makefile structure refs #9104
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  • src/hg/makeDb/schema/makeTableDescriptions/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/tfbsConsLoc/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/tfbsConsSort/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDbRaFormat/makefile - lines changed 16, context: html, text, full: html, text
• can not have different install rule for CGI loader commands refs #9104
  • src/hg/makeDb/hgLoadBed/makefile - lines changed 25, context: html, text, full: html, text