All File Changes

v476_preview2 to v476_base (2025-01-06 to 2025-01-13) v476

• confs/hgwdev.hg.conf
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    3df7629e6b020ab3a92657b76e1e1bc151a5eb5f Sun Jan 12 01:11:17 2025 -0800
    Installing updated hg.conf files from UCSC servers
• src/ameme/makefile
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    12cbc1fdde9c30c87616b8bb86dbbad764a55129 Mon Jan 13 09:19:55 2025 -0800
    clean up the duplicated -lm and use static zlib and bz2lib when available refs #35048
• src/hg/affyTransciptome/makefile
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    153a91e0067b0c2ccc9988dfb2a82507a8c8589f Mon Jan 13 10:27:33 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/affySplice/makefile
  • lines changed 2, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/agxToXml/makefile
  • lines changed 1, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/altSplice/makefile
  • lines changed 1, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/axtCountBeds/makefile
  • lines changed 2, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/exonWalk/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/filterEdges/makefile
  • lines changed 2, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/altSplice/spliceWalk/makefile
  • lines changed 2, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/cirm/cdw/cdwWebBrowse/makefile
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    b94a10b41cdcff72ffc131c5873895e35489a961 Mon Jan 13 10:08:36 2025 -0800
    missed a call to stringify and error in install rule
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
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    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
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    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/makefile
  • lines changed 1, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/hgBlat/hgBlat.c
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    5c3c3701e278cac3d79ab818baeb952cc5df3d10 Fri Jan 10 00:29:14 2025 -0800
    fixing minor void * declare from code review feedback.
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    048d0dcf99a55daf4dbec3c9f39decafe81b2c5c Fri Jan 10 12:47:51 2025 -0800
    fix compiler complaint of nightly util build.
• src/hg/hgGateway/hgGateway.html
  • lines changed 9, context: html, text, full: html, text
    065c73c0daab740c4307262044e3c6dc3cb1e4ee Thu Jan 9 16:41:50 2025 -0800
    Adding an image and mouseOver to the assemblySearch.html link on the hgGateway page, refs #35040
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    e9a3e487007cfbc88d465800ba82db2a99202a7b Fri Jan 10 15:33:47 2025 -0800
    Require both storeUserFiles and showHubApiKey to be true in hg.conf before printing the hubtools api key generation section on the hub development tab of hgHubConnect
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    ee28d7177e4cf3d6eae7bbf636e3ddc7f429adda Fri Jan 10 15:47:26 2025 -0800
    Make sure jquery is explicitly included in iframes, refs #35018
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    fe5394322e0471624edee88d695531934b2a27dd Sat Jan 11 19:05:44 2025 -0800
    Put hgHubConnect async check behind hubSpace hg.conf control, refs Jonathan email
• src/hg/hgPhyloPlace/phyloPlace.c
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    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
  • lines changed 2, context: html, text, full: html, text
    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 1, context: html, text, full: html, text
    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
  • lines changed 1, context: html, text, full: html, text
    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    5c3c3701e278cac3d79ab818baeb952cc5df3d10 Fri Jan 10 00:29:14 2025 -0800
    fixing minor void * declare from code review feedback.
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    048d0dcf99a55daf4dbec3c9f39decafe81b2c5c Fri Jan 10 12:47:51 2025 -0800
    fix compiler complaint of nightly util build.
• src/hg/hgTracks/searchTracks.c
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    5c3c3701e278cac3d79ab818baeb952cc5df3d10 Fri Jan 10 00:29:14 2025 -0800
    fixing minor void * declare from code review feedback.
  • lines changed 1, context: html, text, full: html, text
    048d0dcf99a55daf4dbec3c9f39decafe81b2c5c Fri Jan 10 12:47:51 2025 -0800
    fix compiler complaint of nightly util build.
• src/hg/hgc/gencodeClick.c
  • lines changed 13, context: html, text, full: html, text
    2e9a42eb1791472834ee9e90467eab183e8586fc Fri Jan 10 01:30:43 2025 -0800
    code review feedback. fixed compiler warning in hgc gencodeClick.
• src/hg/hgc/hgc.c
  • lines changed 18, context: html, text, full: html, text
    7cf33ee882ae64d20b55f50698bf6d0da1c28a3a Fri Jan 10 01:53:04 2025 -0800
    fixes based on Braneys helpful feedback.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 37, context: html, text, full: html, text
    ab9e4c7bf0b20c84cae8c0c144e97ac5046f8313 Wed Jan 8 08:37:26 2025 -0800
    Updated the FAQreleases.html#release13 entry and added a link to assemblySearch.html, refs #32596
• src/hg/htdocs/cite.html
  • lines changed 4, context: html, text, full: html, text
    8ec683722a9d39602f3ed003f8fc1e08e601dc7c Thu Jan 9 14:03:59 2025 -0800
    Updating the most recent UCSC Genome Browser publication in cite.html, refs #35051
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    22c8f329a95abd54770fbf6cc8d8d70c8c5149ee Mon Jan 6 13:49:01 2025 -0800
    adding note about chromAlias, refs #26360
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    e2b98fea1d49086c830b2b3b2f39ff8dc6db5ca6 Mon Jan 6 14:09:20 2025 -0800
    fixing link typo
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    976f3d791bdf8009fa1fb1f85dc11aa7b443af49 Tue Jan 7 15:44:25 2025 -0800
    Adding a link to the track hub definitions page from the Genome Browser user guide, no Redmine.
• src/hg/htdocs/staff.html
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    bcaf2ff4815c1ede8686b3c17507958a22f546f9 Fri Jan 10 17:41:05 2025 -0800
    Moving Parisa to the alumni section.
• src/hg/inc/versionInfo.h
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    6fdc309d2cb5c4e8a209f9a0064df807662a46de Mon Jan 13 11:57:00 2025 -0800
    New version number v476
• src/hg/js/hgMyData.js
  • lines changed 28, context: html, text, full: html, text
    690b7e4b9c74d17ea3fc17c70435f5984f4c2f04 Mon Jan 6 16:43:13 2025 -0800
    Fix links to hub.txt files to work correctly. Fix order of files returned from the server to sort on location first then uploadTime. Still working on making newly uploaded files sort to the right place in UI
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    04e19b4c5a3d76b31a21f068fc8ba4d86744dc2a Tue Jan 7 15:16:07 2025 -0800
    Fix row ordering when adding a new row
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    02c03e4dfbe6b6d89a457daf75cf231d36477e76 Wed Jan 8 11:29:13 2025 -0800
    Remove some dead template code and TODO comments, refs #31058
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    a7a5949636596841e4dcef2e7682e976de84addf Wed Jan 8 12:24:26 2025 -0800
    Make back button work when doing an upload, clicking to view a file and then immediately hitting web browser back button, refs #31058
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    a727404f38d39890a83e81426cfe24ea940eaac6 Thu Jan 9 15:02:35 2025 -0800
    Make tracks with period, and other 'forbidden' characters turn on when selecting them from the hubspace UI
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    3d572367254cbf4644b0e8793ac7bdf42bb192c5 Fri Jan 10 02:16:48 2025 -0800
    fixing case that Gerardo found: user hides a few tracks without reloading the page in between these clicks, refs #34959
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    cf8d4ff57d9b734f42d0afd66df6b8e6fb64a50a Fri Jan 10 02:21:52 2025 -0800
    just comments
• src/hg/js/utils.js
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    aa0d552ae6d3f9eef21dd6697c7f1e27bbe070cd Wed Jan 8 03:10:23 2025 -0800
    fixing the nested case for right-click hide, refs #34959
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    b997597b9acbcea5754cd3808181ea88825ba28e Thu Jan 9 15:55:20 2025 -0800
    Fix hub_id_ strip function to correctly join back together the stuff after the first two underscores, refs #35406
• src/hg/lib/customFactory.c
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    ecbcec2757f571e370e32145d3ac02b448629a21 Wed Jan 8 10:06:59 2025 -0800
    used char** instead of char*[] to avoid stringop-overflow warning
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    5c3c3701e278cac3d79ab818baeb952cc5df3d10 Fri Jan 10 00:29:14 2025 -0800
    fixing minor void * declare from code review feedback.
  • lines changed 1, context: html, text, full: html, text
    048d0dcf99a55daf4dbec3c9f39decafe81b2c5c Fri Jan 10 12:47:51 2025 -0800
    fix compiler complaint of nightly util build.
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
  • lines changed 1, context: html, text, full: html, text
    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/hg/lib/userdata.c
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    690b7e4b9c74d17ea3fc17c70435f5984f4c2f04 Mon Jan 6 16:43:13 2025 -0800
    Fix links to hub.txt files to work correctly. Fix order of files returned from the server to sort on location first then uploadTime. Still working on making newly uploaded files sort to the right place in UI
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    4111981ad81cc75933fab5f9c7d44221e3c2dc49 Tue Jan 7 15:47:23 2025 -0800
    Infer bigBed type from bbi header, refs #31058
• src/hg/makeDb/doc/asmHubs/master.run.list
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    eab384506ebd6032e9bdb874ff1007449f1e7cf4 Thu Jan 9 16:02:50 2025 -0800
    adding a couple per user request refs #29545
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    d3eeae30481c6834f1b1505f6220f2ac07d40fa1 Sun Jan 12 11:56:00 2025 -0800
    adding per user request and testing new hgwdev for building assemblies refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    eab384506ebd6032e9bdb874ff1007449f1e7cf4 Thu Jan 9 16:02:50 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/felCat8/cactus241way.txt
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    fac69064e72ae464ea9f34d137cd0a7bc38a0ee2 Tue Jan 7 13:15:53 2025 -0800
    adding phyloP for 241-way data refs #35032
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d3eeae30481c6834f1b1505f6220f2ac07d40fa1 Sun Jan 12 11:56:00 2025 -0800
    adding per user request and testing new hgwdev for building assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d3eeae30481c6834f1b1505f6220f2ac07d40fa1 Sun Jan 12 11:56:00 2025 -0800
    adding per user request and testing new hgwdev for building assemblies refs #29545
• src/hg/makeDb/doc/repeatBrowser2020.txt
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    407074a45a95f68e42f746f306c6b5e7d765096e Wed Jan 8 15:09:31 2025 -0800
    added repeatBrowser build document to source so it doesn't get lost
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    eab384506ebd6032e9bdb874ff1007449f1e7cf4 Thu Jan 9 16:02:50 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.241way.ra
  • lines changed 15, context: html, text, full: html, text
    4e20c4ec97228975702e46227080f1a7ea14a1e7 Tue Jan 7 13:08:52 2025 -0800
    adding phyloP for 241-way data refs #35032add
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    ff6a56bb89e1bdb95a639ba1e89c8a917c0e7cc8 Tue Jan 7 13:09:17 2025 -0800
    adding phyloP for 241-way data refs #35032
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 9, context: html, text, full: html, text
    b0c17e134726b4a4111fef680ae14c563220f998 Tue Jan 7 20:56:04 2025 -0800
    Code review edits for the NCBI Gene Orthologs track description, refs #35020
• src/hg/makeDb/trackDb/mouse/mm39/cytoBand.ra
  • lines changed 9, context: html, text, full: html, text
    f45a165caef28c169ed0d775e9a3e4c5dea6cc86 Wed Jan 8 13:57:06 2025 -0800
    release updated mm39 cytoBand data, refs #35007
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
  • lines changed 9, context: html, text, full: html, text
    b0c17e134726b4a4111fef680ae14c563220f998 Tue Jan 7 20:56:04 2025 -0800
    Code review edits for the NCBI Gene Orthologs track description, refs #35020
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f45a165caef28c169ed0d775e9a3e4c5dea6cc86 Wed Jan 8 13:57:06 2025 -0800
    release updated mm39 cytoBand data, refs #35007
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 9, context: html, text, full: html, text
    b0c17e134726b4a4111fef680ae14c563220f998 Tue Jan 7 20:56:04 2025 -0800
    Code review edits for the NCBI Gene Orthologs track description, refs #35020
• src/hg/orthoMap/makefile
  • lines changed 2, context: html, text, full: html, text
    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
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    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
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    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/hg/utils/automation/HgAutomate.pm
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    18db2d3611d35ea9df50bd5773fda2925299a2a4 Sat Jan 11 14:44:58 2025 -0800
    adding hgwdev-new temporarily for testing on the new hgwdev machine refs #34990
• src/hg/utils/otto/civic/civicToBed.py
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    cb31fb5a2ebbbb167b7f07c19f3af9e3e724068c Tue Jan 7 13:48:52 2025 -0800
    civic: remove certifi package hgwdev-new no longer needs the PyPI certificate bundle
• src/hg/utils/otto/civic/pyproject.toml
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    cb31fb5a2ebbbb167b7f07c19f3af9e3e724068c Tue Jan 7 13:48:52 2025 -0800
    civic: remove certifi package hgwdev-new no longer needs the PyPI certificate bundle
• src/hg/utils/otto/civic/uv.lock
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    cb31fb5a2ebbbb167b7f07c19f3af9e3e724068c Tue Jan 7 13:48:52 2025 -0800
    civic: remove certifi package hgwdev-new no longer needs the PyPI certificate bundle
• src/hg/utils/raSqlQuery/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/tdbQuery/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/htslib/hts.c
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    fda94da6315d3cbcd541a8580870dad45697b2bc Fri Jan 10 00:57:53 2025 -0800
    Revert "fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new." This reverts commit cde73cd256f16555d283a8e7539e946e63151ede.
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    7ec42d4b6eb8a815b95b7af131150b7e4a5569cd Fri Jan 10 01:02:32 2025 -0800
    Reapply "fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new." This reverts commit fda94da6315d3cbcd541a8580870dad45697b2bc.
• src/htslib/sam.c
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    fda94da6315d3cbcd541a8580870dad45697b2bc Fri Jan 10 00:57:53 2025 -0800
    Revert "fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new." This reverts commit cde73cd256f16555d283a8e7539e946e63151ede.
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    7ec42d4b6eb8a815b95b7af131150b7e4a5569cd Fri Jan 10 01:02:32 2025 -0800
    Reapply "fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new." This reverts commit fda94da6315d3cbcd541a8580870dad45697b2bc.
• src/inc/common.h
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    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
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    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/inc/common.mk
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    37e6df88ac99518cc699a378d3ca405af19fbb68 Thu Jan 9 23:34:36 2025 -0800
    One final bit allows -static compile now on hgwdev-new. Sadly, it had some issues still.
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    614bfb99ad0bd183574f839e1fb2d589b004c81c Fri Jan 10 01:20:12 2025 -0800
    Brian in code review asked me to reverse these changes on hgwdev, however they were working just fine. May restore them soon.
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    5d3f8e7077604794f7eef4181971e7ab1f901216 Fri Jan 10 15:20:01 2025 -0800
    broken build extra space sonLib .a no redmine
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    46558d202e8e7978e90e920441879fb2f2d99897 Fri Jan 10 17:40:06 2025 -0800
    Revert "broken build extra space sonLib .a no redmine" This reverts commit 5d3f8e7077604794f7eef4181971e7ab1f901216.
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    86ea800458384a01b483a3c1587641883b901510 Fri Jan 10 17:40:24 2025 -0800
    Revert "Brian in code review asked me to reverse these changes on hgwdev, however they were working just fine. May restore them soon." This reverts commit 614bfb99ad0bd183574f839e1fb2d589b004c81c.
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    1f0f06ed4995b90bd4336fc87cb8beda20ca39b7 Fri Jan 10 18:20:48 2025 -0800
    fix for hgwdev-new to use /cluster/software/r9 for specially compiled R9 libs instead of /culster/sofware which has been correctly recompield for R7 libs. So now both hggwdev and hgwdev-new are correct and not mixed up for compiling.
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    bc0daa57e76433e7fde5e352df577d5120e3bcc1 Mon Jan 13 01:11:31 2025 -0800
    Add an version of stringify that is in interperted langauges so it does not have to be built first and in the path. Useful if building just parts of the tree
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    12cbc1fdde9c30c87616b8bb86dbbad764a55129 Mon Jan 13 09:19:55 2025 -0800
    clean up the duplicated -lm and use static zlib and bz2lib when available refs #35048
• src/inc/srcVersion.h
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    6fdc309d2cb5c4e8a209f9a0064df807662a46de Mon Jan 13 11:57:00 2025 -0800
    New version number v476
• src/lib/makefile
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    b94a10b41cdcff72ffc131c5873895e35489a961 Mon Jan 13 10:08:36 2025 -0800
    missed a call to stringify and error in install rule
• src/lib/vcf.c
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    af856e8ae4df16b4a41609d7ac6e649244682dec Tue Jan 7 17:16:27 2025 -0800
    Revert "Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga." This reverts commit d61df7dc771a130c58e59709121e41b9ec85b4c8.
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    1b20a1774021cdcb07303801d55b7ca3fa6cff09 Wed Jan 8 05:54:20 2025 -0800
    fix up chop functions so they don't call ArraySize with NULL
• src/makefile
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    bc0daa57e76433e7fde5e352df577d5120e3bcc1 Mon Jan 13 01:11:31 2025 -0800
    Add an version of stringify that is in interperted langauges so it does not have to be built first and in the path. Useful if building just parts of the tree
• src/parasol/lib/paraMessage.c
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    f727e7c1325f863157c57d88ba0a1c3cf65b1478 Sat Jan 11 16:19:08 2025 -0800
    fix for overflowing packet issue when paraHub restarts but most jobs are run on just one node.
• src/parasol/paraNode/paraNode.c
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    f727e7c1325f863157c57d88ba0a1c3cf65b1478 Sat Jan 11 16:19:08 2025 -0800
    fix for overflowing packet issue when paraHub restarts but most jobs are run on just one node.
• src/utils/bedClip/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bedGraphToBigWig/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bedPileUps/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bedToBigBed/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigBedInfo/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigBedNamedItems/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigBedSummary/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigBedToBed/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigAverageOverBed/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigInfo/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigMerge/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigSummary/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigToBedGraph/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/bigWigToWig/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/qa/hubPublicAutoUpdate
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    ba44900e4c5c8364c27120e499a7872711a3b4ef Mon Jan 6 14:27:06 2025 -0800
    Editing the script to have /usr/bin/curl instead of /cluster/software/bin/curl.bad due to an error regarding libssl.so.3, no RM
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    985687c2e3ba9ac8ff822c7d53371f369cd4a974 Tue Jan 7 11:37:27 2025 -0800
    Updating the script using Jonathan's suggestion for 'curl'. NO RM
• src/utils/qa/weeklybld/buildEnv.csh
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    822518b257a98b9341d4f1f8a2fe5ede0da1f2cf Mon Jan 13 11:56:12 2025 -0800
    v476 final build, refs #34963
• src/utils/stringify/makefile
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    bc0daa57e76433e7fde5e352df577d5120e3bcc1 Mon Jan 13 01:11:31 2025 -0800
    Add an version of stringify that is in interperted langauges so it does not have to be built first and in the path. Useful if building just parts of the tree
  • lines changed 1, context: html, text, full: html, text
    b94a10b41cdcff72ffc131c5873895e35489a961 Mon Jan 13 10:08:36 2025 -0800
    missed a call to stringify and error in install rule
• src/utils/stringify/stringifyEz
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    bc0daa57e76433e7fde5e352df577d5120e3bcc1 Mon Jan 13 01:11:31 2025 -0800
    Add an version of stringify that is in interperted langauges so it does not have to be built first and in the path. Useful if building just parts of the tree
  • lines changed 1, context: html, text, full: html, text
    308fd2c5d198f1531c648d9d1e2dcf090533b9a4 Mon Jan 13 10:12:16 2025 -0800
    fixed case where stringifyEz encoding different from stringify and would break some cases
• src/utils/twoBitDup/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/wigCorrelate/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/wigToBigWig/makefile
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    714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800
    eliminate the duplication of the -lm library refs #35048

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• files changed: 123