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* a round of fixes and build-skips

* add some build failures

* correct version for bioconductor-data-packages

* add build failure for STdeconvolve

* [ci run] trigger bulk run

* run_exports on bioconductor-data-packages

* [ci run] trigger bulk run

* build failure for omnipathr

* [ci run] trigger bulk run

* Build important packages first

* [ci run] trigger bulk run

* revert to full build

* [ci run] trigger bulk run

* build failure files

* skip iclusterplus

* skip bioconductor-lpsymphony

* bump bioconda-repodata-patches build number

* [ci run]

* build failures

* next round of high priority packages

* [ci run] trigger bulk run

* [ci run] add dependency

* [ci run] finish priority packages

* re-enable full bulk

* [ci run] trigger bulk run

* build failures

* [ci run] trigger bulk run

* next round of high priority packages

* [ci run] trigger bulk run

* build more high priority packages

* [ci run] test local channel fix

* [ci run] increase workers

* Try building bioconductor-geoquery (#44726)

* Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml

* Update meta.yaml

* try fixing parsing error

* [ci run] try rebuilding bioconductor-coregx (#44727)
* try rebuilding bioconductor-coregx
* Update meta.yaml

* add opencl loading libraries - will this work

* [ci run] remove a few build failure files

* [ci run] Bioconductor graph (#44733)

* remove build failure file
* trigger build
* Update meta.yaml
* add patch back
[ci run]

* build failures

* [ci run] high priority packages

* bulk wiki page

* [ci run] add missing packges

* build failure for bioconductor-sictools

* [ci run] missed one

* [ci run] full run

* Update build.sh

* [ci run] fix dexseq

* [ci run] next round of high priority packages

* [ci run] missing packages

* [ci run] high priority package

* [ci run] build all bioconductor-bsgenome

* [ci run] remove failures associated with bioconductor-bsgenome dependency

* full build

* use bioconda-common version

* build failures: test dev version of utils

* escape characters correctly

* build failure for bioconductor-pics

* use branch

* build failure for bioconductor-inspect

* try to fix build failure git range

* build failure for bioconductor-distinct

* use head branch

* trigger build failure wf

* [ci run] trigger bulk run

* build failures fetch depth

* build failure for biconductor-benchdamic

* build failures

* build failures with log

* don't run build failures if last commit has ci skip

* [ci skip] test build failure wiki

* test build failure wiki job

* [ci run] reenable record-build-failures

* re-add token for build failure updates

* build failures add category column

* trigger wiki update

* fix libsbml version for bioconductor-rsbml

* build failure updates

* fix bioconductor-glad

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-wppi

* [ci skip] add build failure record for recipe recipes/bioconductor-gars

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-metascope

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader

* [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r

* [ci skip] add build failure record for recipe recipes/bioconductor-gesper

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-seqcna

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-inpas

* [ci skip] add build failure record for recipe recipes/bioconductor-factr

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble

* [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile

* [ci skip] add build failure record for recipe recipes/bioconductor-extrachips

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc

* [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats

* [ci skip] add build failure record for recipe recipes/bioconductor-chipqc

* [ci skip] add build failure record for recipe recipes/bioconductor-outsplice

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk

* [ci skip] add build failure record for recipe recipes/bioconductor-ritan

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-vulcan

* [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk

* [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-deconvr

* [ci skip] add build failure record for recipe recipes/bioconductor-ideal

* [ci skip] add build failure record for recipe recipes/bioconductor-esatac

* [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr

* [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate

* [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps

* [ci skip] add build failure record for recipe recipes/bioconductor-lemur

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-regionreport

* [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-cageminer

* [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-scpipe

* Rbowtie2 (#44856)

[ci run] fix rbowtie2 builds

* [ci run] remove build file

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* failure for bioconda-multirnaflow

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* bioconductor-lpsymphony fix from master

* remove build failures for finished dependencies

* restore skip osx-64

* fix bioconductor-rawrr

* high priority packages

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] remove build failure record for recipe recipes/bioconductor-proloc

* fix bioconductor-chemmineob

* [ci run] remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* remove easy build failures

* [ci run] next round of dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-pigengene

* [ci skip] add build failure record for recipe recipes/bioconductor-repitools

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* build failure updates

* [ci run] next batch of fixes

* [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run]remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-gatom

* [ci run] set failures to skip

* [ci run] reduce resources that are wasted

* [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1

* fix accidental reverts

* add GSL to bioconductor-pics

* add back fix from master for omnipathr

* remove build failure

* [ci run] skip root nodes to spread out builds

* [ci run] include more root nodes in blacklist

* update build failures

* [ci run] add more blacklist items and do osx build

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* [ci skip] add build failure record for recipe recipes/bioconductor-mumosa

* [ci skip] add build failure record for recipe recipes/bioconductor-chromscape

* [ci skip] add build failure record for recipe recipes/bioconductor-scmerge

* [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare

* fix build errors

* [ci run] more skipped builds

* [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay

* [ci run] reduce workers

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler

* [ci run] manually distribute packages

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-condiments

* [ci skip] add build failure record for recipe recipes/bioconductor-scclassify

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-gcapc

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-traviz

* remove build failures

* remove colon that breaks yaml parsing

* remove temporary bioconductor bulk skips

* [ci run] remaining packages

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-promise

* [ci skip] add build failure record for recipe recipes/bioconductor-otubase

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* retry http error

* [ci run] full bulk build

* [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer

* [ci skip] remove build failure record for recipe recipes/bioconductor-meb

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci run] categorize failures

* add bioconductor-cdi

* remove old failure files

* update bioconductor-reusedata to 3.18

* remove failures for dependencies that have been built

* [ci run] build certain packages

* bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986)

* update bioconductor-ccfindr with gsl

* update bioconductor-rjmcmcnucleosomes with gsl

* [ci run] build updated recipes

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-reusedata

* remove temporary changes from workflows

* build got bumped in merge

* remove temp files

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
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@aliciaaevans @daler
@bgruening @BiocondaBot
5 people authored Dec 29, 2023
1 parent 0cda261 commit 3bb4fba
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14 changes: 10 additions & 4 deletions .github/workflows/Bulk.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,10 @@ jobs:
runner: [0, 1, 2, 3, 4, 5]
steps:
- uses: actions/checkout@v3

with:
# checkout as BiocondaBot in order to have the permission to push fail logs
token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}}

- name: set git user
run: |
git config user.name BiocondaBot
Expand Down Expand Up @@ -68,7 +71,7 @@ jobs:
bioconda-utils build recipes config.yml \
--worker-offset ${{ matrix.runner }} --n-workers 6 \
--docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
--record-build-failures --skiplist-leafs
--lint --record-build-failures --skiplist-leafs
conda clean -y --all
build-osx:
Expand All @@ -82,7 +85,10 @@ jobs:
runner: [0, 1, 2, 3]
steps:
- uses: actions/checkout@v3

with:
# checkout as BiocondaBot in order to have the permission to push fail logs
token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}}

- name: set git user
run: |
git config user.name BiocondaBot
Expand Down Expand Up @@ -139,5 +145,5 @@ jobs:
echo '============'
bioconda-utils build recipes config.yml \
--worker-offset ${{ matrix.runner }} --n-workers 4 \
--anaconda-upload --record-build-failures --skiplist-leafs
--lint --anaconda-upload --record-build-failures --skiplist-leafs
conda clean -y --all
2 changes: 1 addition & 1 deletion .github/workflows/build-failures.yml
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Expand Up @@ -64,4 +64,4 @@ jobs:
OWNER: bioconda
REPO_NAME: bioconda-recipes
MD_FOLDER: build-failures


4 changes: 4 additions & 0 deletions build-fail-blacklist
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
# ----- 2023-12-02 problematic on bulk -----
r-ramclustr
# ------------------------------------------

# Currently kills bulk, and dependants
recipes/bioconductor-missmethyl
recipes/bioconductor-conumee
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27 changes: 14 additions & 13 deletions recipes/bioconductor-a4/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,28 +11,29 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
md5: 5d945210d12e19d845e8949ef53b9d43
md5: 54c9c4300db0c04edd9b531bb0f121a0
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4", max_pin="x.x") }}'
noarch: generic
# Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats
requirements:
host:
- 'bioconductor-a4base >=1.48.0,<1.49.0'
- 'bioconductor-a4classif >=1.48.0,<1.49.0'
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-a4reporting >=1.48.0,<1.49.0'
- 'bioconductor-a4base >=1.50.0,<1.51.0'
- 'bioconductor-a4classif >=1.50.0,<1.51.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-a4reporting >=1.50.0,<1.51.0'
- r-base
run:
- 'bioconductor-a4base >=1.48.0,<1.49.0'
- 'bioconductor-a4classif >=1.48.0,<1.49.0'
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-a4reporting >=1.48.0,<1.49.0'
- 'bioconductor-a4base >=1.50.0,<1.51.0'
- 'bioconductor-a4classif >=1.50.0,<1.51.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-a4reporting >=1.50.0,<1.51.0'
- r-base
test:
commands:
Expand Down
35 changes: 18 additions & 17 deletions recipes/bioconductor-a4base/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4Base" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,35 +11,36 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: b4727840ebfa0c2fdb548b54320e4e39
md5: 927ee5147653a1ee4df6380f52ad055a
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4base", max_pin="x.x") }}'
noarch: generic
# Suggests: Cairo, ALL, hgu95av2.db, nlcv
requirements:
host:
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-annaffy >=1.72.0,<1.73.0'
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-genefilter >=1.82.0,<1.83.0'
- 'bioconductor-limma >=3.56.0,<3.57.0'
- 'bioconductor-multtest >=2.56.0,<2.57.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-annaffy >=1.74.0,<1.75.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-genefilter >=1.84.0,<1.85.0'
- 'bioconductor-limma >=3.58.0,<3.59.0'
- 'bioconductor-multtest >=2.58.0,<2.59.0'
- r-base
- r-glmnet
- r-gplots
- r-mpm
run:
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-annaffy >=1.72.0,<1.73.0'
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-genefilter >=1.82.0,<1.83.0'
- 'bioconductor-limma >=3.56.0,<3.57.0'
- 'bioconductor-multtest >=2.56.0,<2.57.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-annaffy >=1.74.0,<1.75.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-genefilter >=1.84.0,<1.85.0'
- 'bioconductor-limma >=3.58.0,<3.59.0'
- 'bioconductor-multtest >=2.58.0,<2.59.0'
- r-base
- r-glmnet
- r-gplots
Expand Down
19 changes: 10 additions & 9 deletions recipes/bioconductor-a4classif/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4Classif" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,28 +11,29 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: 44dc4f5d280303effaedb954307fb336
md5: 2af82160c9909dd6fdec620de5710cfa
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4classif", max_pin="x.x") }}'
noarch: generic
# Suggests: ALL, hgu95av2.db, knitr, rmarkdown
requirements:
host:
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- r-base
- r-glmnet
- r-pamr
- r-rocr
- r-varselrf
run:
- 'bioconductor-a4core >=1.48.0,<1.49.0'
- 'bioconductor-a4preproc >=1.48.0,<1.49.0'
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-a4core >=1.50.0,<1.51.0'
- 'bioconductor-a4preproc >=1.50.0,<1.51.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- r-base
- r-glmnet
- r-pamr
Expand Down
11 changes: 6 additions & 5 deletions recipes/bioconductor-a4core/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4Core" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,21 +11,22 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: 5f0cb8b9e0ac23f1cd176b17c4ef84aa
md5: fdca418afe3a74d9114d8d28afca2037
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4core", max_pin="x.x") }}'
noarch: generic
# Suggests: knitr, rmarkdown
requirements:
host:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- r-base
- r-glmnet
run:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- r-base
- r-glmnet
test:
Expand Down
15 changes: 8 additions & 7 deletions recipes/bioconductor-a4preproc/meta.yaml
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4Preproc" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,22 +11,23 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: 268368ed5be41d5484b7b5967e2fa716
md5: 5d9eea3d9957fc99156115052398f0cb
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4preproc", max_pin="x.x") }}'
noarch: generic
# Suggests: ALL, hgu95av2.db, knitr, rmarkdown
requirements:
host:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-biocgenerics >=0.48.0,<0.49.0'
- r-base
run:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-biocgenerics >=0.48.0,<0.49.0'
- r-base
test:
commands:
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9 changes: 5 additions & 4 deletions recipes/bioconductor-a4reporting/meta.yaml
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.48.0" %}
{% set version = "1.50.0" %}
{% set name = "a4Reporting" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,12 +11,13 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: aace068e89a5238b844b694e81ef185b
md5: 3ba7f3c5606c2f898d84314ba63208fa
build:
number: 0
number: 1
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-a4reporting", max_pin="x.x") }}'
noarch: generic
# Suggests: knitr, rmarkdown
requirements:
Expand Down
15 changes: 8 additions & 7 deletions recipes/bioconductor-abarray/meta.yaml
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.68.0" %}
{% set version = "1.70.0" %}
{% set name = "ABarray" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,22 +11,23 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: c2ae9c221317ee561584dec59cd0ed37
md5: 59e686f9daf6990fbe6e1594b8676197
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-abarray", max_pin="x.x") }}'
noarch: generic
# Suggests: limma, LPE
requirements:
host:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-multtest >=2.56.0,<2.57.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-multtest >=2.58.0,<2.59.0'
- r-base
run:
- 'bioconductor-biobase >=2.60.0,<2.61.0'
- 'bioconductor-multtest >=2.56.0,<2.57.0'
- 'bioconductor-biobase >=2.62.0,<2.63.0'
- 'bioconductor-multtest >=2.58.0,<2.59.0'
- r-base
test:
commands:
Expand Down
15 changes: 8 additions & 7 deletions recipes/bioconductor-abseqr/meta.yaml
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "1.18.0" %}
{% set version = "1.20.0" %}
{% set name = "abseqR" %}
{% set bioc = "3.17" %}
{% set bioc = "3.18" %}

package:
name: 'bioconductor-{{ name|lower }}'
Expand All @@ -11,19 +11,20 @@ source:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: aef896b0c639d90e59a64148f07587c5
md5: f35214f635511b611297a3730386b205
build:
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports: '{{ pin_subpackage("bioconductor-abseqr", max_pin="x.x") }}'
noarch: generic
# Suggests: testthat
# SystemRequirements: pandoc (>= 1.19.2.1)
requirements:
host:
- 'bioconductor-biocparallel >=1.34.0,<1.35.0'
- 'bioconductor-biocstyle >=2.28.0,<2.29.0'
- 'bioconductor-biocparallel >=1.36.0,<1.37.0'
- 'bioconductor-biocstyle >=2.30.0,<2.31.0'
- r-base
- r-circlize
- r-flexdashboard
Expand All @@ -43,8 +44,8 @@ requirements:
- r-venndiagram
- 'pandoc >=1.19.2.1'
run:
- 'bioconductor-biocparallel >=1.34.0,<1.35.0'
- 'bioconductor-biocstyle >=2.28.0,<2.29.0'
- 'bioconductor-biocparallel >=1.36.0,<1.37.0'
- 'bioconductor-biocstyle >=2.30.0,<2.31.0'
- r-base
- r-circlize
- r-flexdashboard
Expand Down
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