Various package updates (#12998)

* Various package updates * bioconductor-rnaseqpower * more blacklisted packages * A few last updates
bioconda · Jan 9, 2019 · 272fa9e · 272fa9e
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commit 272fa9e
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -848,12 +848,15 @@ recipes/bioconductor-primirtss
 
 # new bioconductor blacklist
 recipes/bioconductor-rtandem
+recipes/bioconductor-shinytandem
+recipes/bioconductor-sapfinder
 recipes/bioconductor-proteoqc
 recipes/bioconductor-msgfplus
 recipes/bioconductor-msgfgui
 recipes/bioconductor-hpaanalyze
 recipes/bioconductor-hilbertvisgui
 recipes/bioconductor-ggtree
+recipes/bioconductor-philr
 recipes/bioconductor-singlecelltk
 recipes/bioconductor-explorase
 recipes/bioconductor-envisionquery
@@ -871,6 +874,7 @@ recipes/bioconductor-selex
 recipes/bioconductor-bprmeth
 recipes/bioconductor-flipflop
 recipes/bioconductor-openprimer
+recipes/bioconductor-openprimerui
 recipes/bioconductor-tfarm
 recipes/bioconductor-reqon
 recipes/bioconductor-sictools
@@ -962,6 +966,8 @@ recipes/bioconductor-seqcna
 recipes/bioconductor-ampliqueso
 recipes/bioconductor-slingshot
 recipes/bioconductor-moonlightr
+recipes/bioconductor-fci
+recipes/bioconductor-easyqpcr
 
 # Not enough memory on circleci
 recipes/bioconductor-conumee

diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 {% set name = "decontam" %}
 {% 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 }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
-  md5: f1e2437a912018381ddcbe50b78825b1
+  md5: 9ff6703e6bc65320f3eeffb89ef3a097
 build:
   number: 0
   rpaths:
@@ -34,4 +34,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: Artistic-2.0
   summary: 'Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.'
+extra:
+  parent_recipe:
+    name: bioconductor-decontam
+    path: recipes/bioconductor-decontam
+    version: 1.2.0
 
diff --git a/recipes/bioconductor-elbow/meta.yaml b/recipes/bioconductor-elbow/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.18.0" %}
+{% set version = "1.18.1" %}
 {% set name = "ELBOW" %}
 {% 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: 9bc217d096532f8d8b2e97c6b7fab889
+  md5: 66a2e8881b2fb3ea5cd7d76785a8c123
 build:
   number: 0
   rpaths:
@@ -30,4 +30,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: 'file LICENSE'
   summary: 'Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.'
+extra:
+  parent_recipe:
+    name: bioconductor-elbow
+    path: recipes/bioconductor-elbow
+    version: 1.18.0
 
diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %}
+{% set version = "1.0.1" %}
 {% set name = "EnhancedVolcano" %}
 {% 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: be835575dbb171d59157118fdf6f9471
+  md5: 2981aa06d982fff46fbbf4728e8d957e
 build:
   number: 0
   rpaths:
@@ -34,4 +34,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
   summary: 'Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many transcript names in the plot window as possible, thus avoiding ''clogging'' up the plot with labels that could not otherwise have been read.'
+extra:
+  parent_recipe:
+    name: bioconductor-enhancedvolcano
+    path: recipes/bioconductor-enhancedvolcano
+    version: 1.0.0
 
diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.18.0" %}
+{% set version = "1.18.1" %}
 {% set name = "flowCyBar" %}
 {% 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: 9fb23129a64b85f512c8df306e7c4c5d
+  md5: 6a4ece4b4aa8ca2d846ec89e431a9abc
 build:
   number: 0
   rpaths:
@@ -33,4 +33,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-2
   summary: 'A package to analyze flow cytometric data using gate information to follow population/community dynamics'
+extra:
+  parent_recipe:
+    name: bioconductor-flowcybar
+    path: recipes/bioconductor-flowcybar
+    version: 1.18.0
 
diff --git a/recipes/bioconductor-flowmap/meta.yaml b/recipes/bioconductor-flowmap/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.20.0" %}
+{% set version = "1.20.1" %}
 {% set name = "flowMap" %}
 {% 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: cab65dfb9ca11db06ec0f2ea9dfb75e6
+  md5: b92e0c86d27f34410419826317e8277f
 build:
   number: 0
   rpaths:
@@ -49,5 +49,5 @@ extra:
   parent_recipe:
     name: bioconductor-flowmap
     path: recipes/bioconductor-flowmap
-    version: 1.18.0
+    version: 1.20.0
 
diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.30.0" %}
+{% set version = "1.30.1" %}
 {% set name = "flowPlots" %}
 {% 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: 54e171f83d6699850b8149ebbc75e81e
+  md5: 99408a38d1bddc7dca85ef37e60d4b27
 build:
   number: 0
   rpaths:
@@ -30,4 +30,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: Artistic-2.0
   summary: 'Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.'
+extra:
+  parent_recipe:
+    name: bioconductor-flowplots
+    path: recipes/bioconductor-flowplots
+    version: 1.30.0
 
diff --git a/recipes/bioconductor-flowrepositoryr/meta.yaml b/recipes/bioconductor-flowrepositoryr/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.14.0" %}
+{% set version = "1.14.1" %}
 {% set name = "FlowRepositoryR" %}
 {% 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: 93c8d4c92bc54a491809e12f17a42ebc
+  md5: e634ffe0fd712764deadd08271b7bc2e
 build:
   number: 0
   rpaths:
@@ -43,5 +43,5 @@ extra:
   parent_recipe:
     name: bioconductor-flowrepositoryr
     path: recipes/bioconductor-flowrepositoryr
-    version: 1.12.0
+    version: 1.14.0
 
diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.8.0" %}
+{% set version = "1.8.1" %}
 {% set name = "GAprediction" %}
 {% 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: b8446cfccb0b45f63fc64b4cd4fc67b0
+  md5: 181fe65adf80c170982cfe2c8b21e273
 build:
   number: 0
   rpaths:
@@ -41,5 +41,5 @@ extra:
   parent_recipe:
     name: bioconductor-gaprediction
     path: recipes/bioconductor-gaprediction
-    version: 1.6.0
+    version: 1.8.0
 
diff --git a/recipes/bioconductor-geecc/meta.yaml b/recipes/bioconductor-geecc/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.16.0" %}
+{% set version = "1.16.1" %}
 {% set name = "geecc" %}
 {% 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 }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
-  md5: 2599b369944d75ec0eea0969f6686923
+  md5: 48ad185a3e1ba4bdf4b1bb868221b507
 build:
   number: 0
   rpaths:
@@ -42,4 +42,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: 'GPL (>= 2)'
   summary: 'Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, ....'
+extra:
+  parent_recipe:
+    name: bioconductor-geecc
+    path: recipes/bioconductor-geecc
+    version: 1.16.0
 
diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.10.0" %}
+{% set version = "1.10.1" %}
 {% set name = "globalSeq" %}
 {% 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: ca6270790a85180a55d30c1ac8ee9191
+  md5: b8378c9ceb14159be27fb3fcd47ee8fc
 build:
   number: 0
   rpaths:
@@ -36,5 +36,5 @@ extra:
   parent_recipe:
     name: bioconductor-globalseq
     path: recipes/bioconductor-globalseq
-    version: 1.8.0
+    version: 1.10.0
 
diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.26.0" %}
+{% set version = "1.26.1" %}
 {% set name = "iASeq" %}
 {% 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: e6b9e4315f60d5530a2ed3985e9da304
+  md5: 42f397bcc34329c812ef8d7c46cd774a
 build:
   number: 0
   rpaths:
@@ -36,5 +36,5 @@ extra:
   parent_recipe:
     name: bioconductor-iaseq
     path: recipes/bioconductor-iaseq
-    version: 1.24.0
+    version: 1.26.0
 
diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.10.2" %}
+{% set version = "1.10.3" %}
 {% set name = "iCARE" %}
 {% 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: c450b066a76a00c07fba5ec1475518d2
+  md5: 1c0bd342ec42f95b64b8ffe717abac8b
 build:
   number: 0
   rpaths:
@@ -38,4 +38,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: 'GPL-3 + file LICENSE'
   summary: 'An R package to compute Individualized Coherent Absolute Risk Estimators.'
+extra:
+  parent_recipe:
+    name: bioconductor-icare
+    path: recipes/bioconductor-icare
+    version: 1.10.2
 
diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %}
+{% set version = "1.0.1" %}
 {% set name = "INDEED" %}
 {% 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: 5438bb5d85aa0489e92f2876736954e9
+  md5: d7292e9c864bf73b2f3c4ecad7b459aa
 build:
   number: 0
   rpaths:
@@ -34,4 +34,9 @@ about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: Artistic-2.0
   summary: 'An Implementation of Integrated Differential Expression and Differential Network Analysis of Omic Data. The differential network is obtained based on partial correlation or correlation.'
+extra:
+  parent_recipe:
+    name: bioconductor-indeed
+    path: recipes/bioconductor-indeed
+    version: 1.0.0
 
diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 {% set name = "IsoCorrectoR" %}
 {% 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: 87ddda98d204e951ce8063456c77bb86
+  md5: 3f06be0cf58841751ea3031be9d33fe5
 build:
   number: 0
   rpaths:
@@ -47,5 +47,10 @@ test:
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
-  summary: 'IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR.'
+  summary: 'IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. IsoCorrectoRGUI is currently only available in the devel version of Bioconductor.'
+extra:
+  parent_recipe:
+    name: bioconductor-isocorrector
+    path: recipes/bioconductor-isocorrector
+    version: 1.0.4