File Changes for max

v460_base to v461_preview (2024-01-29 to 2024-02-06) v461

• src/README
  • lines changed 14, context: html, text, full: html, text
    40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e Tue Feb 6 07:05:20 2024 -0800
    documenting the online/offline and dev options in GBIC, no ticket
• src/hg/hgBeacon/makefile
  • lines changed 1, context: html, text, full: html, text
    84b6a4eed4c7e32abe9e33c246ad54c0b450a7c0 Tue Feb 6 05:47:32 2024 -0800
    removing testBeacon on cgi build, not needed in bin directory, no redmine
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 4, context: html, text, full: html, text
    f76022a8ee809aa35882a2808b67a45756dd0d1f Wed Jan 31 08:25:28 2024 -0800
    trying to get rid of a warning message that appears only on the RR due to some fontconfig issue, refs #32691
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    b3fa58bc96f662c6b997ee8003e2cb15a16b68ab Wed Jan 31 08:05:52 2024 -0800
    reload hgTracksif the pix variable is not set, refs #32925
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/htdocs/goldenPath/noPageHere.html
  • lines changed 15, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/htdocs/noPage.html
  • lines changed 15, context: html, text, full: html, text
    eebe3d904194d8e4fbf7575fd518d91ec4c314cd Mon Jan 29 11:38:05 2024 -0800
    committing empty page to trap web robots, no redmine, suggestion at team meeting by Hiram and others
  • lines changed 15, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/js/utils.js
  • lines changed 14, context: html, text, full: html, text
    b3fa58bc96f662c6b997ee8003e2cb15a16b68ab Wed Jan 31 08:05:52 2024 -0800
    reload hgTracksif the pix variable is not set, refs #32925
  • lines changed 1, context: html, text, full: html, text
    171c52177527ae126d3186ff4c1e225dfcd7526d Mon Feb 5 07:52:29 2024 -0800
    fixing dumb bug in previous commit, refs #32925
• src/hg/makeDb/trackDb/TOGAannotation.html
  • lines changed 8, context: html, text, full: html, text
    6d7150d4b11cf16b7b58d4c1eae3dbf6d240dffd Wed Jan 31 09:25:51 2024 -0800
    fixing track refs, email from M Hiller
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 12, context: html, text, full: html, text
    b1f12063e33feb9427afa17f0f50b18a0b2eb143 Tue Jan 30 04:45:08 2024 -0800
    the gnomad paper came out, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    b1f12063e33feb9427afa17f0f50b18a0b2eb143 Tue Jan 30 04:45:08 2024 -0800
    the gnomad paper came out, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 18, context: html, text, full: html, text
    b44200085524ad29f244699a5ce06fcda4e9af16 Tue Jan 30 05:01:28 2024 -0800
    realized too late that gnomad.html is not actually shown anywhere, strange, no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 9, context: html, text, full: html, text
    6361ad1b494f51fe3d761b1cefacc1f8c12be1c9 Wed Jan 31 07:09:14 2024 -0800
    adding linebreaks to clinvar mouseover and review status, #32915
• src/inc/common.mk
  • lines changed 208, context: html, text, full: html, text
    c4e215c27ac760c75d100338703a99009e33125c Tue Feb 6 05:28:53 2024 -0800
    We got various reports that the source tree is not building on Ubuntu anymore. Also, we got reports that there are strange issues with binaries built on Rocky8. To get the tree to build again on Ubuntu, and to narrow down problems on Rocky8, I'm removing a lot of the library auto-detection code in common.mk. The code was looking for hardcoded paths to .a files, which caused the strange linking errors on Ubuntu: even when the correct mysql lib version was installed, the makefile picked up an unrelated .a file and whatever was done to the mysql config, the dynamic libs were not picked up. This change removes most of these special cases. Most of the removals affect only the build on very old macports versions. I left untouched the IS_HGWDEV parts. SSL support is not optional anymore with this change, which hopefully affects not even builds on smartwatches and thermostats. Most users who want to use special library versions need to set their PATHs such that mysql_config and similar x_config programs return the right directories. Macports users probably need to do something like this (HT to Markd): export CFLAGS=-I/opt/local/include export LDFLAGs=-L/opt/local/lib
• src/product/installer/browserSetup.sh
  • lines changed 2, context: html, text, full: html, text
    8229e76fc318e703dda4fbd5557b22112ee627af Mon Feb 5 06:52:54 2024 -0800
    fixing typo in browserSetup.sh that lead to corrupted script
  • lines changed 36, context: html, text, full: html, text
    54195fff8bba3952c7fe45c9a228cbe7ab4855cc Mon Feb 5 08:05:54 2024 -0800
    adding development mode to GBIC script, refs #32762
  • lines changed 7, context: html, text, full: html, text
    74bbf1d81bdc64b42d6397eb8fb95d8403ed7ad5 Tue Feb 6 02:44:24 2024 -0800
    fix for GBIC for Ubuntu 21 and later, email from Glenn
  • lines changed 3, context: html, text, full: html, text
    a50fb85605c0248d9236aac95af75cfc2a31653a Tue Feb 6 06:11:19 2024 -0800
    making gbic dev mode work on debian distros
  • lines changed 16, context: html, text, full: html, text
    40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e Tue Feb 6 07:05:20 2024 -0800
    documenting the online/offline and dev options in GBIC, no ticket