bioconda · dpryan79 · Mar 13, 2019 · Oct 2, 2018 · Oct 9, 2018 · Oct 10, 2018
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -1,3 +1,78 @@
+# compilation or other errors in bulk
+recipes/xxmotif
+recipes/phylip
+recipes/perl-sub-identify/0.12
+recipes/perl-scalar-list-utils/1.45
+recipes/perl-perlio-gzip
+recipes/perl-math-random
+recipes/perl-extutils-constant/0.24
+recipes/perl-compress-raw-zlib
+recipes/perl-time-hires
+recipes/seq-seq-pan
+recipes/moods
+recipes/pylibseq
+recipes/metasnv
+recipes/gqt
+recipes/diamond_add_taxonomy
+recipes/cgat-core
+recipes/gmtk
+recipes/motus
+recipes/shapemapper
+recipes/biom-format
+recipes/bioconductor-tofsims
+recipes/bioconductor-sspa
+recipes/bioconductor-tweedeseq
+recipes/bioconductor-dexus
+recipes/bioconductor-cnordt
+recipes/bioconductor-mimosa
+recipes/bioconductor-scater
+recipes/bioconductor-edda
+recipes/bioconductor-slalom
+recipes/bioconductor-sictools
+recipes/bioconductor-bsgenome.amellifera.beebase.assembly4
+recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6
+recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2
+recipes/bioconductor-bsgenome.drerio.ucsc.danrer7
+recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked
+recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked
+recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked
+recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5
+recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked
+recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5
+recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3
+recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38
+recipes/circulator
+recipes/crossmap
+recipes/lumpy-sv
+recipes/nanoplot
+recipes/igdiscover
+recipes/rnftools
+recipes/seroba
+recipes/tiptoft
+recipes/homer
+recipes/emboss
+recipes/embassy-phylip
+recipes/triform2
+recipes/haploclique/1.3.1
+recipes/genomedata
+recipes/segtools
+recipes/transrate-tools
+recipes/andi
+recipes/lcfit
+recipes/r-sads
+recipes/musicc
+recipes/r-ebimetagenomics
+recipes/treekin/0.4.2
+
+# This seems to be the same as recipes/bioconductor-chromvar
+recipes/stream_chromvar
+
+# Missing tarball
+recipes/isoseq3
+
+# Requests python3, but is written for python2
+recipes/ctat-mutations
+
 # Unclear that the following old versions are still needed
 recipes/hmmer/2.3.2
 recipes/bamtools/2.3.0
@@ -22,6 +97,27 @@ recipes/perl-extutils-makemaker/7.24
 recipes/tabix/0.2.5
 recipes/tabix/0.2.6
 recipes/r-seurat/1.4.0.16
+recipes/cyvcf2/0.7.2
+recipes/rsem/1.2.21
+recipes/w4mclassfilter/0.98.0
+recipes/w4mclassfilter/0.98.1
+recipes/w4mclassfilter/0.98.2
+recipes/w4mclassfilter/0.98.3
+recipes/w4mclassfilter/0.98.6
+recipes/w4mclassfilter/0.98.7
+recipes/w4mclassfilter/0.98.8
+recipes/stringtie/1.0.3
+recipes/stringtie/1.0.4
+recipes/stringtie/1.2.2
+recipes/stringtie/1.2.4
+recipes/stringtie/1.3.0
+recipes/stringtie/1.3.3
+
+# stl_algobase.h:548:18: error: cannot bind non-const lvalue reference of type 'HitSink::batch&' to an rvalue of type 'std::remove_reference<HitSink::batch&>::type {aka HitSink::batch}'
+recipes/bowtie
+
+# Depend on dependency package versions that are no longer maintained
+recipes/pysam/0.9.1
 
 # Depend on dependency package versions that are no longer maintained
 recipes/pysam/0.9.1
@@ -847,6 +943,7 @@ recipes/bioconductor-cancer
 # GL/rgl errors
 recipes/r-fateid
 recipes/r-raceid3
+recipes/r-qpcr
 recipes/bioconductor-slingshot
 recipes/bioconductor-fci
 recipes/bioconductor-rdrtoolbox

diff --git a/recipes/alignstats/meta.yaml b/recipes/alignstats/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   skip: False
 
 requirements:

diff --git a/recipes/andi/meta.yaml b/recipes/andi/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 3
+  number: 4
 
 source:
   url: https://github.com/EvolBioInf/andi/releases/download/v{{ version }}/andi-{{ version }}.tar.gz

diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml
@@ -10,7 +10,7 @@ source:
 
 build:
   skip: true  # [osx]
-  number: 0
+  number: 1
 
 requirements:
   host:

diff --git a/recipes/ataqv/conda_build_config.yaml b/recipes/ataqv/conda_build_config.yaml
diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml
@@ -16,7 +16,7 @@ source:
     - patches/compileSpliceCands.Makefile.patch
 
 build:
-  number: 4
+  number: 5
 
 requirements:
   build:

diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml
@@ -7,7 +7,7 @@ source:
   md5: 58d72588866f16f658ce4f40a3809af9
 
 build:
-  number: 3
+  number: 4
 
 requirements:
   build:

diff --git a/recipes/bcbio-rnaseq/conda_build_config.yaml b/recipes/bcbio-rnaseq/conda_build_config.yaml
diff --git a/recipes/bcftools-snvphyl-plugin/meta.yaml b/recipes/bcftools-snvphyl-plugin/meta.yaml
@@ -9,7 +9,7 @@ about:
     genomes and constructing a phylogenetic tree. This package is the bcftools C plugin
 
 build:
-  number: 0
+  number: 1
   skip: true  # [osx]
 
 package:

diff --git a/recipes/bfc/meta.yaml b/recipes/bfc/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "r181"
 
 build:
-  number: 3
+  number: 4
 
 source:
   url: https://github.com/lh3/bfc/archive/a73dad248dc56d9d4d22eacbbbc51ac276045168.tar.gz

diff --git a/recipes/bio_assembly_refinement/meta.yaml b/recipes/bio_assembly_refinement/meta.yaml
@@ -9,18 +9,18 @@ source:
   sha256: affbc3a82c38388fb3aadc22260e3662fbd7efe0bc2dc6f56dc6ab35e20db2bf
 
 build:
-  skip: True # [py27]
-  number: 1
+  noarch: python
+  number: 2
 
 requirements:
   host:
-    - python
+    - python >=3
     - setuptools
     - pyfastaq >=3.10.0
     - pymummer
 
   run:
-    - python
+    - python >=3
     - pyfastaq >=3.10.0
     - pymummer
 

diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml
@@ -13,7 +13,7 @@ source:
   '{{ hash_type }}': '{{ hash_value }}'
 
 build:
-  number: 0
+  number: 1
   noarch: python
 
 requirements:

diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set version = "0.15.10" %}
-{% set sha256 = "71490dd0547fc18f9a6eafa8fdb29cfd2f41ab19e8d076827679ebb714214095" %}
+{% set sha256 = "681e62aac380693ff24af4d0a7655f6b18f7fc191be011cfba9809b04c85aa2f" %}
 
 package:
   name: bioconda-utils
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: python -m pip install --no-deps --ignore-installed .
   entry_points:
     - bioconda-utils = bioconda_utils.cli:main
@@ -53,6 +53,8 @@ requirements:
     - aiofiles 0.4.*
     - regex 2018.08.29
     - conda-forge-pinning 2019.03.04
+    - aioftp 0.12.*
+    - boltons 18.*
 
 test:
   imports:

diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: de9e8be03e84433a1fc776c563ec4426
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: c4edc5ad12670675bc7fc5b993f29a36
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: e5913da38fe4487202306cacd885840d
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: c28be6c85e4bf0e0fdfd1bf17df43814
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.14.0" %}
+{% set version = "1.14.1" %}
 {% set name = "ALDEx2" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ 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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: c9538d59388ff431ba6ad0eb409b6247
+  md5: de6ce7be75ca2f1b8082a9c91108a046
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 6a2b9b7e9957cf227690060862bd280c
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 9ce2e10cfe00ec4451670e1fd18d2e37
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: c19b72aa3fa5aaefa84b3abf3cd5c303
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 1366b9a8107e13d674be15d742537f2a
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: f98a7b55b903ecd0334b7d3afed5ce95
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.1" %}
+{% set version = "1.0.10" %}
 {% set name = "artMS" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ 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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: d58e7fb03b9626740a8d8ac919c8c03e
+  md5: ad314ff7f1e8ef4203a483ee6aac53c8
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-assessorfdata/meta.yaml b/recipes/bioconductor-assessorfdata/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 53b9314533795f7344f755bccd72a1ec
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.4.0" %}
+{% set version = "1.4.1" %}
 {% set name = "AUCell" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ 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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 3342bbd472f405a1ef5ebeba04a5431b
+  md5: 170badbf1b074c59b28b7fb467f06897
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 6ef49c32242bce2db8d44a695ed756a8
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-bayespeak/meta.yaml b/recipes/bioconductor-bayespeak/meta.yaml
@@ -12,7 +12,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: e92c2c9940b0329142b613fe625eba15
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/