pkgsrc-WIP-changes by thread

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• rna-seq: Add rna-start dep, Jason W. Bacon
• rna-star: Remove useless -pthread, Jason Bacon
• pkgchkxx: Update to 0.1.2, PHO
• opensmtpd: fix directory permissions., Paolo Vincenzo Olivo
• wip/opensmtpd: update to opensmtpd-7.3.0p1, Paolo Vincenzo Olivo
• py-htseq: Clean up, test on Darwin, Jason Bacon
• py-htseq: Clean up, test on Alma 8, Jason W. Bacon
• py-pysam: Fix build on Darwin, Jason Bacon
• py-pysam: Fix rpath to find libs under site-packag, Jason W. Bacon
• ppsspp: Build with Clang, Charlotte Koch
• cloudflared: update to 2023.7.3, Iku Iwasa
• task: update to 3.28.0, Iku Iwasa
• iosevka-*: update to 25.1.1, Iku Iwasa
• fasda: Update to 0.1.3.26, Jason W. Bacon
• kallisto: MAKE_JOBS_SAFE=no for Mac M1 8-core, Jason Bacon
• py-pysam/TODO: Add more debug info, Jason W. Bacon
• fasda: Update to 0.1.3.25, Jason W. Bacon
• py-pysam: not for Python 2, Thomas Klausner
• *: remove users of wip/grass/* which does not exis, Thomas Klausner
• py-htseq: set allowed python versions, Thomas Klausner
• py-carbon: fix paths, update distinfo, Thomas Klausner
• py-pysam: Test on Alma8, same errors and NetBSD, Jason W. Bacon
• py-pysam: Add cython dep and TODO for rpath errors, Jason W. Bacon
• py-htseq: Successful build, generate PLIST, Jason W. Bacon
• py-pysam: Work toward update to 0.16.0, Jason W. Bacon
• fbsd2pkg: Update to 0.6.0.5, Jason W. Bacon
• py-htseq: Begin work on update to 2.0.3, Jason W. Bacon
• vis-editor: fixed dependency of curses and ncurses, Manuel Kuklinski
• ppsspp: Add a message about potential conflicts wi, Charlotte Koch
• py-qtawesome: fix Python versions, Adam Ciarciński
• atac-seq: Add curl to simplify pipeline scripts, Jason W. Bacon
• atac-seq: Bump version for curl addition, Jason W. Bacon
• rna-seq: Add curl to simplify pipeline scripts, Jason W. Bacon
• suxus: import suxus-1.5 as wip/suxus, Paolo Vincenzo Olivo
• u-boot-rock5b: Add support for Radxa Rock5B SBC, Johann Rudloff
• desktop-installer: Update auto-admin dep to latest, Jason W. Bacon
• desktop-installer: Update to 0.8.1.24, Jason W. Bacon
• perl-devel: update to 5.39.1, Thomas Klausner
• django4: Add version 4.2.3, Frédéric Fauberteau
• gpick: add upgrade candidate, Thomas Klausner
• kallisto: Clean up build options and patches, Jason W. Bacon
• py-spydrnet: initial release, mayuresh
• kallisto: Begin work on 0.50.0 update, Jason W. Bacon
• rna-star: Clean up patches, Jason Bacon
• rna-star: Fix build on Alma8, clean up Makefile, Jason W. Bacon
• rna-star: Successful compile on Darwin, Jason Bacon
• rna-star: Clean up, Jason Bacon
• rna-star: Successful build on NetBSD, Jason W. Bacon
• rna-star: Spliced Transcripts Alignment to a Refer, Jason W. Bacon
• cyclone: add a patch to workaround a bug in let-va, Yorick Hardy
• fastq-trim: Update to 0.1.2.10, Jason W. Bacon
• rust: fix the name of patches., Havard Eidnes
• wip/pkgchkxx: Update to 0.1.1, PHO
• kubectl: update to 1.27.4, Iku Iwasa
• iosevka-*: update to 25.1.0, Iku Iwasa
• cloudflared: update to 2023.7.1, Iku Iwasa
• bats-core: update to 1.10.0, Iku Iwasa
• py-identify: update to 2.5.26, Iku Iwasa
• fallout{1,2}-ce: download third party libraries on, Yorick Hardy
• jfsw-git: update patches to make jfsw build again, Yorick Hardy
• gzdoom: fix distinfo and PLIST, Yorick Hardy
• serious-engine-tse-git: fix distinfo, Yorick Hardy
• exult-snapshot: fix PLIST, Yorick Hardy
• cyclone: order Makefile variables as suggested by , Yorick Hardy
• rust: reverse the change in LLVM which created the, Havard Eidnes
• atac-seq: Sync PYTHON_VERSIONS_INCOMPATIBLE from c, Jason W. Bacon
• rna-seq, atac-seq: Bump version to flag multiqc ad, Jason W. Bacon
• py-multiqc: Clean up includes, Jason W. Bacon
• py-multiqc: Switch to committed py-coloredlogs dep, Jason W. Bacon
• py-coloredlogs: Fix DESCR formatting, Jason W. Bacon
• py-coloredlogs: Clean up, add TEST_DEPENDS, Jason W. Bacon
• py-verboselogs: Extend Python logging module to ad, Jason W. Bacon
• py-capturer: Clean up, Jason W. Bacon
• py-humanfriendly, py-capturer, py-coloredlogs: Use, Jason W. Bacon
• py-humanfriendly, py-capturer, py-coloredlogs: Ado, Jason W. Bacon
• py-humanfriendly: Fix TEST_DEPENDS, Jason W. Bacon
• wip/pkgchkxx: Import 0.1, PHO
• py-coloredlogs: comms -> devel, Jason W. Bacon
• py-humanfriendly: devel -> textproc, Jason W. Bacon
• py-humanfriendly: Clean up, Jason W. Bacon
• py-m2r2: import version 0.3.3.post2, Pierre Pronchery
• (math/R) As an interim fix --disable-nls, as the s, Makoto Fujiwara
• libflame: Update to newer git commit and enable op, Matthew Danielson
• blis: Update to newer git commit, Matthew Danielson
• vaultwarden-web-vault: Add to TODO, Greg Troxel
• vaultwarden-web-vault: pkg rename, Daniel Ziltener
• (math/R) dirty hack completed, hope clean up many , Makoto Fujiwara
• cmvnd-fonts: improve package DESCR, Paolo Vincenzo Olivo
• elvish-dev: sync HEAD, pin
  • <Possible follow-ups>
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin
  • elvish-dev: sync HEAD, pin (via pkgsrc-wip)
  • elvish-dev: sync HEAD, pin (via pkgsrc-wip)
• fasda: Update to 0.1.3.23, Jason W. Bacon
• py-coloredlogs: Update to 15.0.1 and clean up, Jason W. Bacon
• py-multiqc: Update deps to committed packages, Jason W. Bacon
• py-humanfriendly: Note possible circular dep, Jason W. Bacon
• py-capturer: Fix MASTER_SITES and DEPENDS, Jason W. Bacon
• atac-seq: Add py-multiqc dep, Jason W. Bacon
• rna-seq: Add py-multiqc dep, Jason W. Bacon
• py-multiqc: Add py-lzstring dep, Jason W. Bacon
• py-colormath: Update to latest release and adopt, Jason W. Bacon
• py-spectra: Add py-colormath dep, Jason W. Bacon
• py-lzstring: LZ-based in-memory string compression, Jason W. Bacon
• py-multiqc: Add py-spectra dep, Jason W. Bacon
• py-spectra: Color scales and color conversion made, Jason W. Bacon
• py-multiqc: Add py-rich-click dep and PLIST, Jason W. Bacon
• py-rich-click: Format click help output nicely wit, Jason W. Bacon
• (math/R) reduce warning from pkglint, Makoto Fujiwara
• (math/R) add patch for gettext-0.22 API change for, Makoto Fujiwara
• (math/R) fix unresolved gettext on src/extra/tre/r, Makoto Fujiwara
• (math/R) rename patch filename to follow the rule, Makoto Fujiwara
• (math/R) reduce unresolved reference on gettext, s, Makoto Fujiwara
• vaultwarden-web_vault: Initial creation of the pac, Daniel Ziltener
• py-multiqc: Clean up Makefile and document patch, Jason W. Bacon
• py-multiqc: Aggregate bioinformatics analysis repo, Jason W. Bacon
• gl2ps: remove, graphics/gl2ps is newer, Thomas Klausner
• fastq-trim: Update to 0.1.2.9, Jason W. Bacon
• py-shodan: Take MAINTAINERship, Leonardo Taccari
• fastq-trim: Update to 0.1.2.8, Jason W. Bacon
• fasda: Update to 0.1.3.21, Jason W. Bacon
• stringtie: Fix TEST_DEPENDS, add zlib dep for Linu, Jason W. Bacon
• fasda: Update to 0.1.3.20, Jason W. Bacon
• stringtie: Enable test target, Jason W. Bacon
• fasda: Update to 0.1.3.10, Jason W. Bacon
• fasda: Add stringtie dep for computing abundances, Jason W. Bacon
• stringtie: Transcript assembly and quantification , Jason W. Bacon
• py-referencing: add incomplete package, Thomas Klausner
• cmvnd-fonts: import fonts/cmvnd-fonts as wip/cmvnd, Paolo Vincenzo Olivo
• libpthread-stubs: update to 0.5., Thomas Klausner
• TODO: remove one that was done, Thomas Klausner
• cmvnd-fonts: fix distfile handling., Paolo Vincenzo Olivo
• + cmvnd-fonts, Paolo Vincenzo Olivo
• remove SUBDIR+ for previously imported packages., Paolo Vincenzo Olivo
• php-basercms: Update to 5.0.2, Atsushi Toyokura
• fasda: Update to 0.1.3.9, Jason W. Bacon
• wip: Add py-shodan, Leonardo Taccari
• py-shodan: Import py-shodan-1.29.1 as wip/py-shoda, Leonardo Taccari
• alacritty-dev & elvish-dev: sync to latest commit, pin
• (math/R) add patch trying to fix unrsolved libintl, Makoto Fujiwara
• apache-arrow: Update to 12.0.1, Matthew Danielson
• py-apache-arrow: address most pkglint warnings., Matthew Danielson
• py-apache-arrow: Update to 12.0.1, Matthew Danielson
• kubeconform: Update to 0.6.3, Leonardo Taccari
• py-dask: Update to 2023.7.0, Matthew Danielson
• py-distributed: Update to 2023.7.0, Matthew Danielson
• py-fastparquet: Update to 2023.7.0, Matthew Danielson
• Finalize protobuf update to 23.4.0., Benny Siegert
• protobuf: add my half-finished, half-baked update, Benny Siegert
• Copy devel/protobuf to wip/protobuf., Benny Siegert
• go121: update to 1.21rc3, Benny Siegert
• q-dns: update to 0.11.4, Iku Iwasa
• cloudflared: update to 2023.7.0, Iku Iwasa
• iosevka-*: update to 25.0.1, Iku Iwasa
• fastq-trim: Update to 0.1.2.7, Jason W. Bacon
• fastq-trim: Update to 0.1.2.6, Jason W. Bacon
• rust: fix bootstrap.py to again recognize earmv7hf, Havard Eidnes
• rust: add a required CHECK_INTERPRETER_SKIP+= file, Havard Eidnes
• rust: update to version 1.71.0., Havard Eidnes
• cvs2hg: restore '-m' lost in conversion to Python, Thomas Klausner
• rslack: remove, pin
• spotifyd: remove, soon in main, pin
• gdb: Move to gdb8, Frédéric Fauberteau
• *: switch to py-django3, Thomas Klausner
• cvs2hg: convert from sh(1) to python, Thomas Klausner
• cvs2fossil: avoid quoting problem, Thomas Klausner
• cvs2fossil: update patch comment, remove unused pa, Thomas Klausner
• mirmake: also rename mirmake's `install' binary., Paolo Vincenzo Olivo
• mirmake: finish package., Paolo Vincenzo Olivo