Commits for galt

v476_preview to v476_preview2 (2024-12-16 to 2025-01-06) v476

4289758601bbabfbe7f19370470fa9a30831fb38 Fri Dec 20 22:18:24 2024 -0800

• Update browserSetup.sh after running it on Rocky 9.5 in vm on hgwdev.
  • src/product/installer/browserSetup.sh - lines changed 7, context: html, text, full: html, text

902e6b3728a6003f4de94c1a4a2893ac2a713d65 Sat Dec 21 17:06:32 2024 -0800

• fix for compiler warning on hgwdev-new.
  • src/lib/cheapcgi.c - lines changed 1, context: html, text, full: html, text

642b015b684a57d9e42b0a867ed4dc1e516c7897 Sat Dec 21 23:26:22 2024 -0800

• fixing more warnings on R9.
  • src/lib/common.c - lines changed 2, context: html, text, full: html, text

20d2f29ca6491f11c70c95e041220fe72c37a2dd Sun Dec 22 15:06:45 2024 -0800

• fix compiler warning about about restrict keywords in pthread_create.
  • src/hg/hgBlat/hgBlat.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 9, context: html, text, full: html, text

bc6bf7b8c9b952dd6434acbb09b99f25b46a9ab3 Mon Dec 30 21:07:43 2024 -0800

• Fixing compiler warngins compiling on hgwdev-new with Rocky 9
  • src/hg/lib/qaSeq.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 1, context: html, text, full: html, text
  • src/lib/wormdna.c - lines changed 2, context: html, text, full: html, text

8c4b84f67d26cc242ead927a758e19314ce22d24 Mon Dec 30 21:38:38 2024 -0800

• _REENTRANT is now set in common.h
  • src/parasol/inc/paraCommon.h - lines changed 1, context: html, text, full: html, text

cde73cd256f16555d283a8e7539e946e63151ede Mon Dec 30 22:47:21 2024 -0800

• fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new.
  • src/htslib/hts.c - lines changed 1, context: html, text, full: html, text
  • src/htslib/sam.c - lines changed 3, context: html, text, full: html, text

3dbf0d3c66fadf0e2b0c3ce76fb3f73f7a146434 Mon Dec 30 23:09:34 2024 -0800

• fixing compiler warnings for cgilib compiling Rocky 9 hgwdev-new.
  • src/hg/cgilib/hgSeq.c - lines changed 6, context: html, text, full: html, text

b1ba2b3e4d06262be97fcce62ae422cbf6c181cb Tue Dec 31 20:01:15 2024 -0800

• fix compiler warning on hgwdev-new with Rocky 9.
  • src/hg/hgHubConnect/hooks/pre-create.c - lines changed 1, context: html, text, full: html, text

d50328647c385edc3130e6df5159548dfc8a8336 Tue Dec 31 20:03:59 2024 -0800

• fix compiler warning on hgwdev-new with Rocky 9.
  • src/hg/hgIntegrator/hgIntegrator.c - lines changed 1, context: html, text, full: html, text

8f28719057af0f5971729c85d7e821f58d737f84 Tue Dec 31 20:15:01 2024 -0800

• fix compiler warning on hgwdev-new with Rocky 9.
  • src/hg/hgTables/wiggle.c - lines changed 1, context: html, text, full: html, text

aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800

• fix compiler warning in hgc on hgwdev-new with Rocky 9.
  • src/hg/hgc/barChartClick.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hgc/gencodeClick.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgc/hgdpClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

b51de84be3c8b388916f05772c42979170331ea0 Tue Dec 31 21:11:42 2024 -0800

• fix compiler warning in hgVisiGene on hgwdev-new with Rocky 9.
  • src/hg/visiGene/hgVisiGene/hgVisiGene.c - lines changed 6, context: html, text, full: html, text

f0bfd566e04f657b8ec144f504616067a5255b5c Tue Dec 31 21:27:20 2024 -0800

• fix hgEncodDataVersions bug found by Rocky 9 compiler on hgwdev-new
  • src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c - lines changed 2, context: html, text, full: html, text

b2747f670ec8572868679259f88196674ca6e32a Tue Dec 31 21:32:32 2024 -0800

• fix hgLoadMaf found by Rocky 9 compiler on hgwdev-new
  • src/hg/makeDb/hgLoadMaf/hgLoadMaf.c - lines changed 3, context: html, text, full: html, text

e323c52d6da91a50d484da6ff11dbbf0c706a29c Tue Dec 31 22:17:30 2024 -0800

• fix faSplit found by Rocky 9 compiler on hgwdev-new
  • src/utils/faSplit/faSplit.c - lines changed 6, context: html, text, full: html, text

1b32cf0583db4331765a056c45ff4fc98c36b649 Tue Dec 31 22:39:16 2024 -0800

• minor fix in clarity for safecpy in lib.
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text

22a69e4fe63f977e217b1aabfc0ad41df2990334 Tue Dec 31 23:34:43 2024 -0800

• minor compilter fix for pslSpliceJunctions.
  • src/utils/pslSpliceJunctions/pslSpliceJunctions.c - lines changed 2, context: html, text, full: html, text

967b1ecc11ceda965dc043f2bf607b8ffce4ac2d Tue Dec 31 23:39:34 2024 -0800

• minor compilter fix for ccCCp util.
  • src/utils/ccCp/ccCp.c - lines changed 1, context: html, text, full: html, text

7371ef06216ade7c7e1bc85b99c2043ac4220efa Tue Dec 31 23:42:58 2024 -0800

• minor compilter fix for fixCr.
  • src/utils/fixCr/fixCr.c - lines changed 2, context: html, text, full: html, text

7642d8f313d523d2bc7f054928a82969d2e745f8 Tue Dec 31 23:45:26 2024 -0800

• minor compilter fix for agpToFa.
  • src/hg/agpToFa/agpToFa.c - lines changed 1, context: html, text, full: html, text

eb6002e80a43afcbfb3fabfd7d9412887c7d3b3c Tue Dec 31 23:47:44 2024 -0800

• minor compilter fix for fakeFinContigs.
  • src/hg/fakeFinContigs/fakeFinContigs.c - lines changed 1, context: html, text, full: html, text

b59d72e0511481a477b5a9d772c68b975bd585bc Tue Dec 31 23:51:55 2024 -0800

• minor compilter fix for gbToFaRa.
  • src/hg/gbToFaRa/gbToFaRa.c - lines changed 2, context: html, text, full: html, text

b3415b3e149e52942ef55b14077aec42fd450d1d Tue Dec 31 23:54:13 2024 -0800

• minor compilter fix for gsBig.
  • src/hg/gsBig/gsBig.c - lines changed 1, context: html, text, full: html, text

e505f514d7b741bb400ac03d81cd5ce4b778a00c Tue Dec 31 23:56:47 2024 -0800

• minor compiler fix for hgClonePos.
  • src/hg/makeDb/hgClonePos/hgClonePos.c - lines changed 1, context: html, text, full: html, text

c9ad13b92e344edb3df4cef62781b2c7ecff1de5 Tue Dec 31 23:59:02 2024 -0800

• minor compiler fix for hgNibSeq.
  • src/hg/makeDb/hgNibSeq/hgNibSeq.c - lines changed 1, context: html, text, full: html, text

f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800

• fix various errors for utils compiled on Rocky 9 hgwdev-new.
  • src/hg/autoSql/autoSql.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoXml/autoXml.c - lines changed 2, context: html, text, full: html, text
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 1, context: html, text, full: html, text
  • src/hg/featureBits/featureBits.c - lines changed 2, context: html, text, full: html, text
  • src/hg/liftUp/liftUp.c - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/hgGcPercent.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/hgGoldGapGl/hgLoadGap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadOut/hgLoadOut.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/knownVsBlat/kvsSummary.c - lines changed 13, context: html, text, full: html, text
  • src/hg/mouseStuff/phToPsl/phToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/nci60/findStanAlignments.c - lines changed 2, context: html, text, full: html, text
  • src/hg/pslGlue/pslGlue.c - lines changed 1, context: html, text, full: html, text
  • src/hg/pslSort/pslSort.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/mafSplit.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ratStuff/stageMultiz/stageMultiz.c - lines changed 2, context: html, text, full: html, text
  • src/hg/semiNorm/semiNorm.c - lines changed 3, context: html, text, full: html, text
  • src/hg/splitFaIntoContigs/splitFaIntoContigs.c - lines changed 4, context: html, text, full: html, text
  • src/hg/trfBig/trfBig.c - lines changed 3, context: html, text, full: html, text
  • src/hg/uniqSize/uniqSize.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/vcfToBed/vcfToBed.c - lines changed 2, context: html, text, full: html, text

d57ca4989c27c9ada4938b1a6c29c44a8398b17e Wed Jan 1 02:35:07 2025 -0800

• compiler fix found compiling CIRM on hgwdev-new
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 3, context: html, text, full: html, text

ad6fd12391f2b2c8ef95a161a5c90351da65256e Wed Jan 1 05:10:29 2025 -0800

• add pragma for the last compile issue not fixed yet.
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text

59a24235a4ba60e2f5767d05faefa89bb4ecf2db Wed Jan 1 05:12:19 2025 -0800

• fixes for common.mk to work with hgwdev and hgwdev-new. handles static compiling as much as possible.
  • src/inc/common.mk - lines changed 27, context: html, text, full: html, text

d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800

• Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/runUsher.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/liftOver.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 2, context: html, text, full: html, text
  • src/inc/common.h - lines changed 32, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text

a04990e1e2e9dfddb8213799731f88cef8fdc5d6 Sat Jan 4 22:02:22 2025 -0800

• Resolving merge.

1d02fe3264e9f1d78757a31540e33c17d05691d8 Sat Jan 4 22:56:49 2025 -0800

• added an explanatory note about using 0 not NULL to ArraySize macro.
  • src/inc/common.h - lines changed 2, context: html, text, full: html, text

72de391e0d76b4a71f9d4663af78dabbe08fdabd Sat Jan 4 23:00:06 2025 -0800

• added another explanatory note about using 0 not NULL to ArraySize macro.
  • src/inc/common.h - lines changed 2, context: html, text, full: html, text

ab198fbbb00ac11d304283667e18fff758d3f07e Sun Jan 5 01:41:49 2025 -0800

• fix compiler warning on home rocky 8 server.
  • src/lib/basicBed.c - lines changed 2, context: html, text, full: html, text

927af5b0b1e586bc82412794462ac4816c793a59 Sun Jan 5 02:55:53 2025 -0800

• minor optimization to use static curl with old hgwdev.
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text