Bulk #53091

aliciaaevans · 2025-01-07T22:42:02Z

Merging bulk back to master after most of the pinnings updates and Bioconductor 3.20 have been completed.

Build failures from this round of bulk are here: https://github.com/bioconda/bioconda-recipes/wiki/build-failures-bulk (this will not update as long as we don't commit to bulk.) After this PR is merged to master, the community is encouraged to fix these remaining issues. Live updated build failures: https://github.com/bioconda/bioconda-recipes/wiki/build-failures.

(Checks on this PR will not pass)

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bgruening

Just a few comments. Great work @aliciaaevans! Please feel free to merge as quickly as you like to not get stalled. We can work on the comments in new PRs.

bgruening · 2025-01-08T08:20:39Z

.github/workflows/Bulk.yml

@@ -58,7 +59,7 @@ jobs:
            --worker-offset ${{ matrix.runner }} --n-workers 6 \
            --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
            --lint --record-build-failures --skiplist-leafs \
-            --exclude bioconda-repodata-patches
+            --exclude bioconda-repodata-patches # --subdag-depth 5


should we include subdag again by default?

@daler and I discussed this a bit. It does help, but not quite as efficiently as we'd hoped. It might be good to leave --subdag-depth 0 as the default since otherwise the first run through generates a lot of dependency failures we have to clean up later. One down side is that if you fix something upstream, then you have to run through all the levels again to pick up the stragglers.

bgruening · 2025-01-08T13:32:50Z

recipes/bioconductor-a4/meta.yaml

@@ -1,47 +1,52 @@
-{% set version = "1.50.0" %}
+{% set version = "1.54.0" %}


I'm wondering in general why the ordering has changed. I remember that we fixed the ordering of YAML sections at some point to make the diffs easier.

bgruening · 2025-01-08T13:33:15Z

recipes/bioconductor-a4/meta.yaml

+about:
+  description: Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.
+  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
+  license: GPL-3


We should also use SPDX identifiers here in the next update.

recipes/bioconductor-pcaexplorer/build_failure.osx-64.yaml

recipes/bioconductor-pcaexplorer/build_failure.linux-64.yaml

corneliusroemer · 2025-01-30T21:33:07Z

It seems this PR didn't bump all the build numbers the way it should have, example: pyfastx was at number 0 before and is after.

https://github.com/bioconda/bioconda-recipes/blame/master/recipes/pyfastx/meta.yaml

corneliusroemer · 2025-01-30T21:51:52Z

Some git diff-tree magic yields the following list of recipes that didn't get a number bump despite meta.yaml changes:

recipes/biobb_mem/meta.yaml
recipes/chia-rep/meta.yaml
recipes/nwalign3/meta.yaml
recipes/pyfastx/meta.yaml
recipes/r-dimsum/meta.yaml
recipes/telescope/meta.yaml
recipes/umi_tools/meta.yaml
recipes/yahmm/meta.yaml

corneliusroemer · 2025-01-30T22:00:35Z

Possibly the list of files that should get build number bumped is much longer (2296 in total), I haven't verified this one:
should_be_bumped.txt

* [ci skip] add build failure record for recipe recipes/bioconductor-flowcore * [ci skip] add build failure record for recipe recipes/t-coffee * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.matrix * [ci skip] add build failure record for recipe recipes/bioconductor-bayesspace * [ci skip] add build failure record for recipe recipes/bioconductor-diffbind * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * r-pathwaytmb: add run exports * r-alakazam: annotate build failure and skip * bioconductor-mosdef: annotate build failure and skip * bioconductor-mosdef: skip for osx too * velocyto.py: annotate build failure and skip * r-alakazam: annotate build failure * bioconductor-genetonic: annotate build failure and skip * bioconductor-ideal: annotate build failure and skip * bioconductor-pcaexplorer: annotate build failure and skip * bioconductor-genetonic: annotate build failure and skip * bioconductor-ideal: annotate build failure and skip * bioconductor-pcaexplorer: annotate build failure and skip * t-coffee: annotate build failure * [ci run] Trigger Build * [ci skip] add build failure record for recipe recipes/bioconductor-gsva * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-rsbml * [ci skip] add build failure record for recipe recipes/bioconductor-flowcore * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.matrix * bioconductor-{chipseeker,reactomepa}: annotate build failures and skip * [ci skip] add build failure record for recipe recipes/bioconductor-bayesspace * [ci skip] add build failure record for recipe recipes/perl-bio-db-hts * [ci skip] remove build failure record for recipe recipes/perl-bio-bigfile * [ci skip] add build failure record for recipe recipes/bioconductor-diffbind * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * bioconductor-flowcore: patch for binary_function * increase osx workers * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-bambu * [ci skip] add build failure record for recipe recipes/bioconductor-segmenter * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * bioconductor-gsva: annotate build failure * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-rsbml * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-bayesspace * [ci skip] remove build failure record for recipe recipes/bioconductor-flowcore * bioconductor-bayesspace: annotate build failure * [ci skip] remove build failure record for recipe recipes/bioconductor-flowclust * [ci skip] remove build failure record for recipe recipes/bioconductor-ncdfflow * [ci skip] add build failure record for recipe recipes/bioconductor-flowworkspace * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.matrix * [ci skip] remove build failure record for recipe recipes/perl-bio-db-hts * [ci skip] add build failure record for recipe recipes/bioconductor-diffbind * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * bioconductor-flowworkspace: patch to enable binary_function * bioconductor-rsbml: annotate build failure * bioconductor-alabaster.matrix: annotate build failure * bioconductor-diffbind: annotate build failure * bioconductor-gmapr: annotate build failure * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-bambu * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-cytoml * cleanup patch file * rebuild alabaster.base * bioconductor-cytoml: try some stuff * rebuild downstream of flowcore * remove build failures for downstreams that can build now * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-beachmat.hdf5 * rebuild skipped recipes with built dependencies * rebuild skipped recipes with built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * rebuild skipped recipes with built dependencies * bioconductor-beachmat.hdf5: add zlib * bioconductor-alabaster.base: try setting version min * [ci skip] add build failure record for recipe recipes/bioconductor-cytoml * rebuild skipped recipes with built dependencies * bioconductor-cytoml: annotate build failure * [ci skip] add build failure record for recipe recipes/bioconductor-cytoml * bioconductor-cytoml: annotate and skip * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-cager * [ci skip] add build failure record for recipe recipes/bioconductor-diffhic * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * [ci skip] add build failure record for recipe recipes/bioconductor-elmer * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * rebuild skipped recipes with built dependencies * rebuild skipped recipes with built dependencies * rebuild bioconductor-enrichplot and downstream * [ci skip] add build failure record for recipe recipes/bioconductor-diffhic * rebuild downstream of biconductor-clusterprofiler * bioconductor-alabaster.base: try something else to fix osx * [ci skip] add build failure record for recipe recipes/bioconductor-beadarrayusecases * bioconductor-diffhic: add zlib * [ci skip] remove build failure record for recipe recipes/bioconductor-beachmat.hdf5 * rebuild skipped recipes with built dependencies * rebuild skipped recipes with built dependencies * rebuild skipped recipes with built dependencies * bioconductor-alabaster.base: try setting other values * rebuild skipped recipes with built dependencies * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-descan2 * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-bambu * [ci skip] add build failure record for recipe recipes/bioconductor-qckitfastq * [ci skip] add build failure record for recipe recipes/bioconductor-diffhic * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * [ci skip] add build failure record for recipe recipes/bioconductor-biocancer * [ci skip] add build failure record for recipe recipes/bioconductor-mosclip * [ci skip] add build failure record for recipe recipes/bioconductor-mirit * [ci skip] add build failure record for recipe recipes/bioconductor-mirit * bioconductor-bandle: fix dependency version * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-cetf * [ci skip] add build failure record for recipe recipes/bioconductor-h5vc * [ci skip] add build failure record for recipe recipes/bioconductor-scrapper * [ci skip] add build failure record for recipe recipes/bioconductor-sictools * [ci skip] add build failure record for recipe recipes/bioconductor-scatac.explorer * [ci skip] add build failure record for recipe recipes/bioconductor-diffhic * bioconductor-blacksheepr: update pasilla versions * bioconductor-{diffhic,h5vtfastq}: zlib and liblzma as host deps * bioconductor-{mirit,mosclip}: annotate build failures and skip * bump bioconductor-data-packages * bioconductor-scatac.explorer: bump version * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-bambu * [ci skip] remove build failure record for recipe recipes/bioconductor-diffhic * [ci skip] add build failure record for recipe recipes/bioconductor-bandle * [ci skip] remove build failure record for recipe recipes/bioconductor-qckitfastq * [ci skip] remove build failure record for recipe recipes/bioconductor-h5vc * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] remove build failure record for recipe recipes/bioconductor-scatac.explorer * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * [ci skip] remove build failure record for recipe recipes/bioconductor-diffhic * [ci skip] add build failure record for recipe recipes/bioconductor-bandle * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * annotate various build failures * [ci skip] add build failure record for recipe recipes/bioconductor-nestlink * [ci skip] add build failure record for recipe recipes/bioconductor-muscdata * [ci skip] add build failure record for recipe recipes/bioconductor-merfishdata * bump some data packages * bioconductor-prolocdata: update meta.yaml * annotate various build failures * delete some build failures * bioconductor-mastr: update recipe for new msigdb * bioconductor-msquality: update recipe to reflect new msdata pkg * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] remove build failure record for recipe recipes/bioconductor-msquality * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * [ci skip] remove build failure record for recipe recipes/bioconductor-nestlink * [ci skip] remove build failure record for recipe recipes/bioconductor-muscdata * [ci skip] remove build failure record for recipe recipes/bioconductor-merfishdata * [ci skip] remove build failure record for recipe recipes/bioconductor-blacksheepr * [ci skip] add build failure record for recipe recipes/bioconductor-splicewiz * [ci skip] remove build failure record for recipe recipes/bioconductor-mastr * [ci skip] add build failure record for recipe recipes/bioconductor-visse * [ci skip] add build failure record for recipe recipes/bioconductor-spatiallibd * bioconductor-splicewiz: zlib and liblzma-devel as host deps * bioconductor-visse: update msigdb version * bioconductor-spatiallibd: update version; also bump data-packages * annotate build failures for dependents of osx-64 bioconductor-alabaster.base * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * [ci skip] add build failure record for recipe recipes/bioconductor-alabaster.base * [ci skip] remove build failure record for recipe recipes/bioconductor-splicewiz * [ci skip] remove build failure record for recipe recipes/bioconductor-splicewiz * [ci skip] remove build failure record for recipe recipes/bioconductor-visse * [ci skip] remove build failure record for recipe recipes/bioconductor-spatiallibd * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/cancerit-allelecount * [ci skip] add build failure record for recipe recipes/bioconductor-rbowtie2 * [ci skip] add build failure record for recipe recipes/bioconductor-bambu * [ci skip] add build failure record for recipe recipes/bioconductor-gmapr * bioconductor-glad: revert overwrite of build.sh * add reason to build failures * rebuild recipes that depend on bioconductor-glad * rebuild bioconductor-ideal * update bioconductor-version * bioconductor-rnainteractmapk: add reason to build failure * reenable bulk for osx-arm64 * annotate build failures for linux-aarch64 * bioconductor-bandle: fix prolocdata version (again) * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-italics * [ci skip] add build failure record for recipe recipes/bioconductor-variancepartition * [ci skip] add build failure record for recipe recipes/bioconductor-bandle * [ci skip] add build failure record for recipe recipes/bioconductor-zenith * [ci skip] add build failure record for recipe recipes/bioconductor-adacgh2 * [ci skip] add build failure record for recipe recipes/bioconductor-adacgh2 * bioconductor-variancepartition: fix limma version * [ci skip] add build failure record for recipe recipes/bioconductor-bandle * bioconductor-bandle: now broken for a new reason * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-variancepartition * bioconductor-limma: built latest version * [ci run] trigger bulk run * rebuild bioconductor-zenith * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-zenith * [ci skip] remove build failure record for recipe recipes/bioconductor-variancepartition * rebuild bioconductor-zenith * [ci run] trigger bulk run * [ci skip] remove build failure record for recipe recipes/bioconductor-zenith * bioconductor-motifmatchr: actually already built * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/khmer * [ci skip] remove build failure record for recipe recipes/sdm * [ci skip] remove build failure record for recipe recipes/metabuli * [ci skip] remove build failure record for recipe recipes/metabuli * [ci skip] remove build failure record for recipe recipes/sdm * [ci skip] remove build failure record for recipe recipes/teloscope * [ci skip] add build failure record for recipe recipes/gsearch * [ci skip] add build failure record for recipe recipes/khmer * [ci skip] remove build failure record for recipe recipes/splitcode * [ci skip] remove build failure record for recipe recipes/splitcode * [ci skip] remove build failure record for recipe recipes/sdm * revbayes: fix yaml syntax error * khmer: skip * [ci skip] add build failure record for recipe recipes/snapatac2 * [ci skip] remove build failure record for recipe recipes/biscuit * annotate build failures * [ci skip] add build failure record for recipe recipes/proteinortho * proteinortho: annotate build failure * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/gfaffix * bioconductor-lpsymphony: add fortran compiler --------- Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com> Co-authored-by: Ryan Dale <ryan.dale@nih.gov> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>

BiocondaBot and others added 30 commits January 2, 2025 12:21

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BiocondaBot and others added 20 commits January 7, 2025 16:37

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aliciaaevans requested review from daler and bgruening January 7, 2025 22:42

bgruening approved these changes Jan 8, 2025

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Merge branch 'master' into bulk

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aliciaaevans merged commit c7b640b into master Jan 8, 2025
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corneliusroemer added a commit that referenced this pull request Jan 30, 2025

Bump build numbers that were forgotten in bulk PR #53091

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corneliusroemer commented Jan 30, 2025

		@@ -1,47 +1,52 @@
		{% set version = "1.50.0" %}
		{% set version = "1.54.0" %}

Bulk #53091

Bulk #53091

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