add missing R pkgs

easybuilders · Jul 14, 2015 · 2557dc5 · 2557dc5
1 parent 4fbe021
commit 2557dc5
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Showing 2 changed files with 21 additions and 5 deletions.
diff --git a/...ild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/...ild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb
@@ -51,6 +51,9 @@ exts_list = [
     ('Biostrings', '2.36.1', bioconductor_options),
     ('GenomicRanges', '1.20.5', bioconductor_options),
     ('Rsamtools', '1.20.4', bioconductor_options),
+    ('lambda.r', '1.1.7', ext_options),
+    ('futile.options', '1.0.0', ext_options),
+    ('futile.logger', '1.4.1', ext_options),
     ('BiocParallel', '1.2.9', bioconductor_options),
     ('GenomicAlignments', '1.4.1', bioconductor_options),
     ('ShortRead', '1.26.0', bioconductor_options),
@@ -70,12 +73,17 @@ exts_list = [
     ('oligoClasses', '1.30.0', bioconductor_options),
     ('edgeR', '3.10.2', bioconductor_options),
     ('PFAM.db', '3.1.2', bioconductor_options),
+    ('perm', '1.0-0.0', ext_options),
     ('baySeq', '2.2.0', bioconductor_options),
     ('qvalue', '2.0.0', bioconductor_options),
     ('impute', '1.42.0', bioconductor_options),
+    ('samr', '2.0', ext_options),
     ('DEGseq', '1.22.0', bioconductor_options),
     ('hgu133plus2.db', '3.1.3', bioconductor_options),
     ('illuminaio', '0.10.0', bioconductor_options),
+    ('rtracklayer', '1.28.6', bioconductor_options),
+    ('biomaRt', '2.24.0', bioconductor_options),
+    ('GenomicFeatures', '1.20.1', bioconductor_options),
     ('bumphunter', '1.8.0', bioconductor_options),
     ('multtest', '2.24.0', bioconductor_options),
     ('siggenes', '1.42.0', bioconductor_options),
@@ -84,14 +92,11 @@ exts_list = [
     ('NOISeq', '2.12.0', bioconductor_options),
     ('Rgraphviz', '2.12.0', bioconductor_options),
     ('RNASeqPower', '1.8.0', bioconductor_options),
-    ('biomaRt', '2.24.0', bioconductor_options),
     ('annotate', '1.46.1', bioconductor_options),
     ('GSEABase', '1.30.2', bioconductor_options),
     ('genefilter', '1.50.0', bioconductor_options),
     ('Category', '2.34.2', bioconductor_options),
     ('GOstats', '2.34.0', bioconductor_options),
-    ('rtracklayer', '1.28.6', bioconductor_options),
-    ('GenomicFeatures', '1.20.1', bioconductor_options),
     ('BSgenome', '1.36.2', bioconductor_options),
     ('VariantAnnotation', '1.14.6', bioconductor_options),
     ('biovizBase', '1.16.0', bioconductor_options),
@@ -111,7 +116,9 @@ exts_list = [
     ('KEGGREST', '1.8.0', bioconductor_options),
     ('KEGGgraph', '1.26.0', bioconductor_options),
     ('KEGGprofile', '1.10.0', bioconductor_options),
+    ('GEOquery', '2.34.0', bioconductor_options),
     ('minfi', '1.14.0', bioconductor_options),
+    ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options),
     ('methylumi', '2.14.0', bioconductor_options),
     ('lumi', '2.20.2', bioconductor_options),
     ('widgetTools', '1.46.0', bioconductor_options),
@@ -121,7 +128,6 @@ exts_list = [
     ('SPIA', '2.20.0', bioconductor_options),
     ('Gviz', '1.12.1', bioconductor_options),
     ('cummeRbund', '2.10.0', bioconductor_options),
-    ('samr', '2.0', ext_options),  # requires impute
 ]
 
 modextrapaths = {'R_LIBS': ''}

diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb
@@ -295,6 +295,11 @@ exts_list = [
     ('DiscriMiner', '0.1-29', ext_options),
     ('ellipse', '0.3-8', ext_options),
     ('leaps', '2.9', ext_options),
+    ('nloptr', '1.0.4', ext_options),
+    ('lme4', '1.1-8', ext_options),
+    ('pbkrtest', '0.4-2', ext_options),
+    ('car', '2.0-25', ext_options),
+    ('flashClust', '1.01-2', ext_options),
     ('FactoMineR', '1.29', ext_options),
     ('modeltools', '0.2-21', ext_options),
     ('flexclust', '1.3-4', ext_options),
@@ -327,6 +332,12 @@ exts_list = [
     ('expsmooth', '2.3', ext_options),
     ('fpp', '0.5', ext_options),
     ('XML', '3.98-1.1', ext_options),
+    ('memoise', '0.2.1', ext_options),
+    ('crayon', '1.3.1', ext_options),
+    ('testthat', '0.10.0', ext_options),
+    ('rmarkdown', '0.7', ext_options),
+    ('curl', '0.9.1', ext_options),
+    ('RCurl', '1.95-4.7', ext_options),
     ('httr', '0.6.1', ext_options),
     ('maptools', '0.8-36', ext_options),
     ('deldir', '0.1-9', ext_options),
@@ -336,7 +347,6 @@ exts_list = [
     ('spatstat', '1.41-1', ext_options),
     ('gdalUtils', '0.3.1', ext_options),
     ('pracma', '1.8.3', ext_options),
-    ('RCurl', '1.95-4.7', ext_options),
     ('bio3d', '2.2-2', ext_options),
 ]