All File Changes

v478_preview2 to v478_base (2025-02-17 to 2025-02-24) v478

• src/hg/cirm/cdw/lib/cdwPageFooter.h
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    82851bc32cde8075939406e40b6bd97e7b8664d2 Wed Feb 19 15:06:51 2025 -0800
    Adding to internal SSPsyGene footer a link to shared drive for ease of finding for consortium members
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 2, context: html, text, full: html, text
    82851bc32cde8075939406e40b6bd97e7b8664d2 Wed Feb 19 15:06:51 2025 -0800
    Adding to internal SSPsyGene footer a link to shared drive for ease of finding for consortium members
• src/hg/hgConvert/hgConvert.c
  • lines changed 11, context: html, text, full: html, text
    65d2977c726c1639d4a463f8178e43c08704f173 Fri Feb 21 15:33:35 2025 -0800
    hgConvert should errAbort when it can't find a chain file instead of crashing, refs #35271
• src/hg/hgSession/backup.c
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    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/hgTables/hgTables.c
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    49eb00a2d0f47737a528e3ca0d8dc5ac2ff09229 Thu Feb 20 16:37:56 2025 -0800
    Updating the big* data schema tools and table browser text, refs #35223
• src/hg/hgTables/rangeHistogram.c
  • lines changed 9, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    49eb00a2d0f47737a528e3ca0d8dc5ac2ff09229 Thu Feb 20 16:37:56 2025 -0800
    Updating the big* data schema tools and table browser text, refs #35223
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/hgText/hgText.c
  • lines changed 2, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/hgTracks/factorSource.c
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    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    46fa9fa9710504c701e286ed9908aea277304729 Fri Feb 21 16:53:34 2025 -0800
    hgTracks imageV2 Only do it for the case where we are drawing center labels. fixes #31541
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 10, context: html, text, full: html, text
    3491d223c8596113721f630745bd9ec0c55e1833 Mon Feb 24 08:03:19 2025 -0800
    adding note about duplicate IDs in ensemb/gencode, refs #35222
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    99aa2466dea4cf74a4a226debfcbbcf388637c3a Mon Feb 24 09:56:52 2025 -0800
    Updating the duplicate IDs in ensemb/gencod FAQ entry, refs #35222
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 11, context: html, text, full: html, text
    be21b178a0bedc251d7cbcd22d914e05d8a9cf3a Wed Feb 19 15:01:31 2025 -0800
    Expanding the section that explains to users how to load settings via file on the URL, refs #25277
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 45, context: html, text, full: html, text
    d1480f47eaefcb26436f4818ea85befb187f1958 Mon Feb 24 09:17:11 2025 -0800
    Announcing the release of the enGenome VarChat track, refs #35081
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    d1480f47eaefcb26436f4818ea85befb187f1958 Mon Feb 24 09:17:11 2025 -0800
    Announcing the release of the enGenome VarChat track, refs #35081
• src/hg/inc/jksql.h
  • lines changed 2, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    3933038e366f5c27945dcbb18862c91c756c2e5c Mon Feb 24 11:20:14 2025 -0800
    New version number v478
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    58572f970097a2a8d39b57e81ccc3700c1f30527 Wed Feb 19 11:35:03 2025 -0800
    Fix unintentional call to dragReorder when clicking on a grey bar, fixes #34750
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/lib/jksql.c
  • lines changed 4, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/liftOver/makefile
  • lines changed 22, context: html, text, full: html, text
    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/hg/makeDb/doc/asmHubs/README.txt
  • lines changed 3, context: html, text, full: html, text
    87586a71c52ad59bc437786485e7e900cae367ee Mon Feb 24 07:19:52 2025 -0800
    up to date error checking refs #35201
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 12, context: html, text, full: html, text
    f57df65b77591fb1aad3208fac9ce2442f658234 Tue Feb 18 15:30:46 2025 -0800
    adding 12 assemblies per user request refs #29545
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    5d7d739e101f89f82ef7c4ce1fdc9a1c413cdef1 Tue Feb 18 19:53:43 2025 -0800
    adding GCA_034509865.1_ASM3450986v1 chicken (Silkie 2023) per user request refs #29545
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    045f9d50d5be5de9489a7c1e044757aef3469142 Wed Feb 19 09:04:30 2025 -0800
    adding GCA_037788925.1_MytGallo_primary_0.1 Mediterranean mussel (MGYT20220701 primary hap 2024) per user request refs #29545
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    a256e54c8778078498ea06d7447e0d1591090a12 Thu Feb 20 10:03:20 2025 -0800
    added two birds per user request refs #29545
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    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/asmHubs/reRunTrackDb.sh
  • lines changed 54, context: html, text, full: html, text
    89f7e9cc7e39854c535c49875835fa1b54bacaa4 Wed Feb 19 13:43:45 2025 -0800
    script to re-run a trackDb build refs #35201
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    e82cf3f6e6233075340fa340802429e1f037d7c0 Wed Feb 19 13:53:06 2025 -0800
    using a cut on the file will allow using the order.tsv files refs #35201
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    5d7d739e101f89f82ef7c4ce1fdc9a1c413cdef1 Tue Feb 18 19:53:43 2025 -0800
    adding GCA_034509865.1_ASM3450986v1 chicken (Silkie 2023) per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    a256e54c8778078498ea06d7447e0d1591090a12 Thu Feb 20 10:03:20 2025 -0800
    added two birds per user request refs #29545
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    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    f57df65b77591fb1aad3208fac9ce2442f658234 Tue Feb 18 15:30:46 2025 -0800
    adding 12 assemblies per user request refs #29545
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    045f9d50d5be5de9489a7c1e044757aef3469142 Wed Feb 19 09:04:30 2025 -0800
    adding GCA_037788925.1_MytGallo_primary_0.1 Mediterranean mussel (MGYT20220701 primary hap 2024) per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800
    VGP update refs #29545
• src/hg/makeDb/hgGoldGapGl/makefile
  • lines changed 23, context: html, text, full: html, text
    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/hg/makeDb/hgLoadMaf/makefile
  • lines changed 28, context: html, text, full: html, text
    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/hg/makeDb/hgLoadWiggle/makefile
  • lines changed 29, context: html, text, full: html, text
    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/hg/makeDb/scripts/enigma/BRCAmla.py
  • lines changed 2, context: html, text, full: html, text
    ace0c6866e5b9b793c4cf3bd6f79515e575884a9 Tue Feb 18 15:19:03 2025 -0800
    Fixing a bug in the ENIGMA MLA generation where scores present on different datasets were not getting combined properly.
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
  • lines changed 2, context: html, text, full: html, text
    97338dbf71b671d85cedc20b099f360e0ec06785 Tue Feb 18 16:48:53 2025 -0800
    Code review edits, refs #35243
• src/hg/makeDb/trackDb/human/trackDb.ra
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    52d89c6d3d4b84de8e344bdc727f6d8263edc7c8 Mon Feb 24 09:30:54 2025 -0800
    Updating pennantIcons for the release of the enGenome VarChat track, refs #35081
• src/hg/makeDb/trackDb/human/varChat.html
  • lines changed 1, context: html, text, full: html, text
    97338dbf71b671d85cedc20b099f360e0ec06785 Tue Feb 18 16:48:53 2025 -0800
    Code review edits, refs #35243
• src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/oneShot/testSqlDbDotTable/testSqlDbDotTable.c
  • lines changed 2, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/pslCDnaFilter/makefile
  • lines changed 1, context: html, text, full: html, text
    d4926daf233227dc632c2af1fd93bfbebed1eebf Fri Feb 21 12:21:16 2025 -0800
    userApps need extraHeaders targets to be satisfied _before_ building the primary object, refs #35269
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    60d5a650d17e1798f010eb688956b26069bb6673 Fri Feb 21 15:40:30 2025 -0800
    Revert "userApps need extraHeaders targets to be satisfied _before_ building the primary object, refs #35269" This reverts commit d4926daf233227dc632c2af1fd93bfbebed1eebf.
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    62e3355c6aff5308aa632661258c2ced872fa1b4 Fri Feb 21 15:47:45 2025 -0800
    fixed build order issue with generated hearder files in userApps
• src/hg/qa/checkCardinality.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/qa/reviewIndexes.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/test/otest/test1.c
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    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
• src/hg/utils/automation/asmHubCpG.pl
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    ac0b61420ab00d96616349e7ea289406b9054932 Thu Feb 20 13:01:15 2025 -0800
    tolerant of missing CpG bbi files refs #29545
• src/hg/utils/automation/asmHubTrackDb.sh
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    5dcb723fb12fbac15ffdd0c3464fce6f722e2e7e Wed Feb 19 13:40:18 2025 -0800
    readjust default visibilities refs #35201
• src/hg/utils/blatServersCheck/blatServersCheck.c
  • lines changed 1, context: html, text, full: html, text
    d983323cd2570af1cf3971763d14ef2d88c06fe4 Wed Feb 19 17:00:19 2025 -0800
    sqlTableSize needs to support tables with more than 2B rows (rarely, but it does), refs #35262
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    d616e51d6f1576fc2e78fab2563cf5e251fdf8be Thu Feb 20 08:50:18 2025 -0800
    Whoops, missed one swap from int to long for sqlTableSize, refs #35262
• src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    30271e358055c61f7b60f1f5532939ca5756b5c2 Tue Feb 18 16:53:22 2025 -0800
    Adding the specific file that is different so the message is a little more descriptive.
• src/hg/utils/otto/mtb/R00000039_repregions.bed
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    be36a20a1828c3d22d24ed63988e5cd5a8024a09 Fri Feb 21 11:55:13 2025 -0800
    Fixing MS-DOS CRLF line terminators (\r\n --> \n) that caused build error.
• src/inc/cgiLoader.mk
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    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/inc/common.mk
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    34e8448fb29e6fd0bf3e6c48e00d53aa8ffdc4ed Thu Feb 20 10:38:04 2025 -0800
    a couple of updates for building on Mac OSX no redmine
• src/inc/srcVersion.h
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    3933038e366f5c27945dcbb18862c91c756c2e5c Mon Feb 24 11:20:14 2025 -0800
    New version number v478
• src/inc/userApp.mk
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    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
  • lines changed 1, context: html, text, full: html, text
    d4926daf233227dc632c2af1fd93bfbebed1eebf Fri Feb 21 12:21:16 2025 -0800
    userApps need extraHeaders targets to be satisfied _before_ building the primary object, refs #35269
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    60d5a650d17e1798f010eb688956b26069bb6673 Fri Feb 21 15:40:30 2025 -0800
    Revert "userApps need extraHeaders targets to be satisfied _before_ building the primary object, refs #35269" This reverts commit d4926daf233227dc632c2af1fd93bfbebed1eebf.
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    62e3355c6aff5308aa632661258c2ced872fa1b4 Fri Feb 21 15:47:45 2025 -0800
    fixed build order issue with generated hearder files in userApps
• src/lib/bbiWrite.c
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    8a7fe87bf9ffd7fc1038c9d85984955afb82f0dc Thu Feb 20 17:06:31 2025 -0800
    Updating the bedToBigBed help message and error output for the new sort option, refs #29104
• src/tagStorm/makefile
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    34770b218ef5c3100da392a3119a3b0d50d99bfb Thu Feb 20 17:56:46 2025 -0800
    Implement old make behavior were programs will be remade after a make clean removing the .o, even though actually program is not out of date with respect to the .c
• src/utils/bedToBigBed/bedToBigBed.c
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    aee5cb870a32c26ba410232a896e5dda0e92fb5c Wed Feb 19 17:50:40 2025 -0800
    add sort option to bedToBigBed refs #29104
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    e4f7eda5f5bb015ddc38f592869339263909854a Thu Feb 20 10:03:46 2025 -0800
    tweak bedToBigBed to come up with its own temp file name
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    8a7fe87bf9ffd7fc1038c9d85984955afb82f0dc Thu Feb 20 17:06:31 2025 -0800
    Updating the bedToBigBed help message and error output for the new sort option, refs #29104
• src/utils/bedToBigBed/tests/expected/notSorted.bed
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    aee5cb870a32c26ba410232a896e5dda0e92fb5c Wed Feb 19 17:50:40 2025 -0800
    add sort option to bedToBigBed refs #29104
• src/utils/bedToBigBed/tests/makefile
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    aee5cb870a32c26ba410232a896e5dda0e92fb5c Wed Feb 19 17:50:40 2025 -0800
    add sort option to bedToBigBed refs #29104
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    e4f7eda5f5bb015ddc38f592869339263909854a Thu Feb 20 10:03:46 2025 -0800
    tweak bedToBigBed to come up with its own temp file name
• src/utils/qa/errorLogKeywordSearch.py
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    00290c3ab85e01370f80f4e23caf6309072ad908 Wed Feb 19 15:33:53 2025 -0800
    Tweaking a few things in the keyword search, notably making the search term a raw string so it doesn't give a warning and fixing the log file fetch to try and match euro + asia, also I needed to update the year which was stuck in 2024. No RM.
• src/utils/qa/makeDownloadFileList.sh
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    fc304da842594644ab8d05375d153be32d1e251e Fri Feb 21 11:16:30 2025 -0800
    Short cron to keep track of the file lists on hgdownload and hgdownload2, refs #34321
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    9d44445a77c9481b087864904bfbe189955af554 Fri Feb 21 11:25:58 2025 -0800
    I forgot to remove a troubleshooting stanza. Oops. Refs #34321
• src/utils/qa/weeklybld/buildEnv.csh
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    82048679ae0d16b221e0150cb9726527575be741 Mon Feb 24 11:18:20 2025 -0800
    v478 final build, refs #35217
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    a05f20222fff4594fa2f427eca7bb48521ee8eb9 Fri Feb 21 10:04:28 2025 -0800
    Removing mariadb sandbox mode lines from hgcentral dumps, no ticket
• src/utils/userApps/mkREADME.sh
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    557bc870081c38719069925583655e530ca56920 Wed Feb 19 11:40:10 2025 -0800
    new program tabFmt needs special handling no redmine

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• files changed: 84