File Changes for hiram

v292_preview2 to v292_base (2013-11-04 to 2013-11-11) v292

• src/hg/genePredCheck/genePredCheck.c
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    compare chrom names case dependent refs #11907
• src/hg/inc/versionInfo.h
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    New version number v292
• src/hg/makeDb/doc/falPer1.txt
  • lines changed 70, context: html, text, full: html, text
    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/doc/galGal4.txt
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    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 106, context: html, text, full: html, text
    running up refGene and knownCanonical alignments files for 100-way refs #11808
  • lines changed 114, context: html, text, full: html, text
    cleaning up keys in the oreganno track to clean up joiner checks
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    done with refGene and knownCanonical alignment files for 100-way refs #11808
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 125, context: html, text, full: html, text
    running up Ostrich and Falcon lastz to Turkey refs #10272
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    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    add blank line between stanzas to fix brokeness
• src/hg/orthoMap/orthoEvaluate.c
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    new 5.0 gcc compiler on mac OSX identifies non-void function not returning a value refs #12106
• src/hg/utils/automation/ensGene/anaPla1.ensGene.ra
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    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/cioSav2.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/echTel1.ensGene.ra
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    update to current copies refs #11675
• src/hg/utils/automation/ensGene/eriEur1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/ficAlb1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/gadMor1.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/galGal4.ensGene.ra
  • lines changed 7, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/gorGor3.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    correct chrom names case translation refs #11907
• src/hg/utils/automation/ensGene/musFur1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/ochPri2.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/pelSin1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/petMar2.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/proCap1.ensGene.ra
  • lines changed 4, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/tarSyr1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/tupBel1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/turTru1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/vicPac1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/xenTro3.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/xipMac1.ensGene.ra
  • lines changed 6, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/makefile
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    do not build refreshNamedSessionCustomTracks on Mac OSX will not work refs #12106
• src/hg/utils/mysqlSecurityCheck/makefile
  • lines changed 14, context: html, text, full: html, text
    update makefile to userApps specifications refs #12106
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    correct path names to libcrypto and libssl refs #12005
  • lines changed 4, context: html, text, full: html, text
    trying different order for crypto ssl mysql static libs refs @12005
  • lines changed 3, context: html, text, full: html, text
    need duplicate entries for ssl and crypto static libs refs #12005
  • lines changed 4, context: html, text, full: html, text
    can use static libstdc++.a and librt.a when on hgwdev refs #12005
  • lines changed 2, context: html, text, full: html, text
    eliminate useless -L/lib directive on Mac OSX refs #12106
• src/lib/cirTree.c
  • lines changed 1, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/elmTree.c
  • lines changed 2, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/utils/bigWigCorrelate/bigWigCorrelate.c
  • lines changed 4, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX has the word restrict as a reserved word can not use as a variable refs #12106
• src/utils/qa/weeklybld/buildEnv.csh
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    v292 final build