Bioconductor 3.10 release is (more or less) finished

.github/workflows/Bulk.yml

@@ -9,9 +9,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-      max-parallel: 10
+      max-parallel: 5
       matrix:
-        runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+        runner: [0, 1, 2, 3, 4]
     steps:
     - uses: actions/checkout@v1
     - name: Setup Bioconda-utils
@@ -26,16 +26,16 @@ jobs:
         CI: "true"
       run: |
         bioconda-utils build recipes config.yml \
-          --worker-offset ${{ matrix.runner }} --n-workers 10 \
+          --worker-offset ${{ matrix.runner }} --n-workers 5 \
           --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
   build-osx:
     name: Bulk OSX Builds
     runs-on: macOS-latest
     strategy:
       fail-fast: false
-      max-parallel: 5
+      max-parallel: 2
       matrix:
-        runner: [0, 1, 2, 3, 4]
+        runner: [0, 1]
     steps:
     - uses: actions/checkout@v1
     - name: Setup Bioconda-utils
@@ -63,5 +63,5 @@ jobs:
         CI: "true"
       run: |
         bioconda-utils build recipes config.yml \
-          --worker-offset ${{ matrix.runner }} --n-workers 5 \
+          --worker-offset ${{ matrix.runner }} --n-workers 2 \
           --anaconda-upload

build-fail-blacklist

@@ -107,9 +107,6 @@ recipes/quast
 recipes/tadarida-c
 recipes/w4mclstrpeakpics
 
-# This seems to be the same as recipes/bioconductor-chromvar
-recipes/stream_chromvar
-
 # Requests python3, but is written for python2
 recipes/ctat-mutations
 
@@ -614,53 +611,28 @@ recipes/r-soap-nmr
 recipes/r-xmlrpc
 recipes/r-zerone
 
-# Deprecated/build fail in Bioconductor 3.8
-recipes/bioconductor-atlasrdf
-recipes/bioconductor-jmosaics
-recipes/bioconductor-meshsim
-recipes/bioconductor-mmdiff
-recipes/bioconductor-mmnet
-recipes/bioconductor-rcytoscape
-recipes/bioconductor-browservizdemo
-recipes/bioconductor-pannbuilder
-recipes/bioconductor-splicer
-recipes/bioconductor-pbcmc
-recipes/bioconductor-mqtl.nmr
-recipes/bioconductor-nudge
-recipes/bioconductor-phenodist
-recipes/bioconductor-mvgst
-recipes/bioconductor-ramigo
-
-# Old bioconductor version that's no longer available
-recipes/bioconductor-edger/3.12.1
-recipes/bioconductor-masigpro/1.49.4
-
-# Old package, should we still build it?
-recipes/bioconductor-dnacopy/1.48.0
-recipes/bioconductor-ggbio/1.22.0
-recipes/bioconductor-limma/3.28.2
-recipes/bioconductor-limma/3.28.10
-recipes/bioconductor-org.ce.eg.db/3.2.3
-recipes/bioconductor-org.ce.eg.db/3.4.1
-recipes/bioconductor-org.dm.eg.db/3.3.0
-recipes/bioconductor-org.mm.eg.db/3.3.0
-recipes/bioconductor-qdnaseq.mm10/1.4.0
-recipes/bioconductor-rgraphviz/2.13.0
-recipes/bioconductor-ropls/1.2.14
-recipes/r-speaq/1.2.1
-recipes/bioconductor-cummerbund/2.8.2
-recipes/bioconductor-cummerbund/2.12.1
-recipes/bioconductor-diffbind/2.0.9
-recipes/bioconductor-diffbind/2.2.12
-recipes/bioconductor-xcms/1.52.0
-recipes/bioconductor-s4vectors/0.8.11
-
 # Marked as build fails in bioconductor release 3.9
 recipes/bioconductor-birte
 recipes/bioconductor-dsimer
 recipes/bioconductor-flipflop
-recipes/bioconductor-flowq
-recipes/bioconductor-appreci8r
+
+# Marked as build fails in bioconductor release 3.10
+recipes/bioconductor-rchemcpp
+recipes/bioconductor-gpumagic
+recipes/bioconductor-rhvdm
+recipes/bioconductor-platecore
+recipes/bioconductor-charm
+recipes/bioconductor-charmdata
+recipes/bioconductor-pathnet
+recipes/bioconductor-exomepeak
+recipes/bioconductor-sepa
+recipes/bioconductor-cnpbayes
+recipes/bioconductor-condcomp
+recipes/bioconductor-brainimager
+recipes/bioconductor-mbqn
+recipes/bioconductor-brainflowprobes
+recipes/bioconductor-biocset
+recipes/bioconductor-mlm4omics
 
 # stringify can't find libmysqlclient.18
 recipes/ucsc-overlapselect
@@ -670,81 +642,43 @@ recipes/ucsc-pslcdnafilter
 # Source seems to have moved
 recipes/discovar
 
-# Requires GTK+
-recipes/bioconductor-hilbertvisgui
-
 # missing dependency r-dagitty
 recipes/r-pcalg
-recipes/bioconductor-mirlab
 recipes/bioconductor-epinem
 recipes/bioconductor-mnem
+recipes/bioconductor-mirlab
 
 # Source no longer exists at the URL
 recipes/recon
 
-# Fails compilation everywhere, including the bioconductor build system
-recipes/bioconductor-mlm4omics
-
-# compilation errors on Linux and OSX
-recipes/bioconductor-bgmix
-recipes/bioconductor-grenits
-recipes/bioconductor-mulcom
-recipes/bioconductor-prot2d
-recipes/bioconductor-genphen
-recipes/bioconductor-bgx
-recipes/bioconductor-netboost
-
-# Needs a root5 rebuild
-recipes/bioconductor-xps
-
-# Needs to be patched to work with something other that gfortran
-recipes/bioconductor-iclusterplus
-
-# Needs to have the source patched to look in ${PREFIX} for zlib
+# compilation errors
 recipes/bioconductor-sictools
-
-# object ‘ebayes’ is not exported by 'namespace:limma'
-recipes/bioconductor-charm
-recipes/bioconductor-charmdata
-
-# Checks for the java version incorrectly, need to patch the source
+recipes/bioconductor-iclusterplus
+recipes/bioconductor-bgmix
 recipes/bioconductor-msgfplus
 recipes/bioconductor-msgfgui
-
-# openbabel error
+recipes/bioconductor-rcwl
+recipes/bioconductor-rcwlpipelines
 recipes/bioconductor-chemmineob
-
-# Has issues finding sbml
+recipes/bioconductor-netboost
+recipes/bioconductor-discorhythm
+recipes/bioconductor-interactivedisplay
 recipes/bioconductor-rsbml
 recipes/bioconductor-biggr
+recipes/bioconductor-omicspca
+recipes/bioconductor-scalign
+recipes/bioconductor-hilbertvisgui
+recipes/bioconductor-bgx
+recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5
+recipes/bioconductor-mafdb.gnomad.r3.0.grch38
+recipes/bioconductor-mafdb.gnomad.r2.1.grch38
 
-# Installing package into $PREFIX/lib/R/library/00LOCK-work/00new (as "lib" is unspecified)
-recipes/bioconductor-interactivedisplay
+# Needs a root5 rebuild
+recipes/bioconductor-xps
 
 # never completes
 recipes/bioconductor-cancer
 
-# No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
-recipes/bioconductor-platecore
-
-# Error in library("FlowSorted.CordBlood.450k") : there is no package called 'FlowSorted.CordBlood.450k'
-recipes/bioconductor-flowsorted.blood.450k
-recipes/bioconductor-flowsorted.cordblood.450k
-recipes/bioconductor-flowsorted.cordbloodnorway.450k
-
-# cwltool is not found
-recipes/bioconductor-rcwl
-recipes/bioconductor-rcwlpipelines
-
-# unable to load shared object '$PREFIX/lib/R/library/sf/libs/sf.so': libtiledb.so.1.6.0: cannot open shared object file
-recipes/bioconductor-anamir
-
-# Compilation errors on OSX
-recipes/bioconductor-rchemcpp
-recipes/bioconductor-gmapr
-recipes/bioconductor-flowtype
-recipes/bioconductor-rchyoptimyx
-
 # Packages that should be moved to conda-forge
 recipes/argutils
 recipes/aria2
@@ -1403,3 +1337,64 @@ recipes/wtforms-components
 recipes/xmlbuilder
 recipes/yaggo
 recipes/zeroc-ice
+
+# Blacklisted root nodes to help with parallel processing
+# 1879
+recipes/bioconductor-biocgenerics
+# 1728
+recipes/bioconductor-biobase
+# 1342
+recipes/bioconductor-annotationdbi
+# 1000
+recipes/bioconductor-genomeinfodbdata
+# 862
+recipes/bioconductor-genomicranges
+# 807
+recipes/bioconductor-biostrings
+# 737
+recipes/bioconductor-iranges
+# 683
+recipes/bioconductor-genomeinfodb
+# 652
+recipes/bioconductor-s4vectors
+# 625
+recipes/bioconductor-biocparallel
+# 551
+recipes/bioconductor-delayedarray
+# 516
+recipes/bioconductor-zlibbioc
+# 500
+recipes/bioconductor-biocfilecache
+# 375
+recipes/bioconductor-genomicalignments
+# 366
+recipes/bioconductor-affyio
+# 323
+recipes/bioconductor-annotate
+recipes/bioconductor-bsgenome
+# 311
+recipes/bioconductor-rsamtools
+# 286
+recipes/bioconductor-summarizedexperiment
+# 267
+recipes/bioconductor-biomart
+# 265
+recipes/bioconductor-rtracklayer
+# 220
+recipes/bioconductor-preprocesscore
+# 196
+recipes/bioconductor-affxparser
+# 182
+recipes/bioconductor-oligoclasses
+# 157
+recipes/bioconductor-limma
+# 153
+recipes/bioconductor-graph
+recipes/bioconductor-biocversion
+recipes/bioconductor-xvector
+recipes/bioconductor-rhtslib
+recipes/bioconductor-affy
+recipes/bioconductor-oligo
+recipes/bioconductor-genefilter
+recipes/bioconductor-annotationfilter
+recipes/bioconductor-genomicfeatures

recipes/bioconductor-a4/meta.yaml

@@ -1,6 +1,6 @@
-{% set version = "1.32.0" %}
+{% set version = "1.34.0" %}
 {% set name = "a4" %}
-{% set bioc = "3.9" %}
+{% set bioc = "3.10" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -10,28 +10,28 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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: 00e7562c4412f2a31b54919b66137388
+  md5: 7210d289aaa5b6fee8863d57f9c69767
 build:
-  number: 1
+  number: 0
   rpaths:
     - lib/R/lib/
     - lib/
   noarch: generic
 # Suggests: MLP, nlcv, ALL, Cairo
 requirements:
   host:
-    - 'bioconductor-a4base >=1.32.0,<1.33.0'
-    - 'bioconductor-a4classif >=1.32.0,<1.33.0'
-    - 'bioconductor-a4core >=1.32.0,<1.33.0'
-    - 'bioconductor-a4preproc >=1.32.0,<1.33.0'
-    - 'bioconductor-a4reporting >=1.32.0,<1.33.0'
+    - 'bioconductor-a4base >=1.34.0,<1.35.0'
+    - 'bioconductor-a4classif >=1.34.0,<1.35.0'
+    - 'bioconductor-a4core >=1.34.0,<1.35.0'
+    - 'bioconductor-a4preproc >=1.34.0,<1.35.0'
+    - 'bioconductor-a4reporting >=1.34.0,<1.35.0'
     - r-base
   run:
-    - 'bioconductor-a4base >=1.32.0,<1.33.0'
-    - 'bioconductor-a4classif >=1.32.0,<1.33.0'
-    - 'bioconductor-a4core >=1.32.0,<1.33.0'
-    - 'bioconductor-a4preproc >=1.32.0,<1.33.0'
-    - 'bioconductor-a4reporting >=1.32.0,<1.33.0'
+    - 'bioconductor-a4base >=1.34.0,<1.35.0'
+    - 'bioconductor-a4classif >=1.34.0,<1.35.0'
+    - 'bioconductor-a4core >=1.34.0,<1.35.0'
+    - 'bioconductor-a4preproc >=1.34.0,<1.35.0'
+    - 'bioconductor-a4reporting >=1.34.0,<1.35.0'
     - r-base
 test:
   commands:
@@ -40,4 +40,6 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
   summary: 'Automated Affymetrix Array Analysis Umbrella Package'
+  description: 'Automated Affymetrix Array Analysis Umbrella Package'
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'