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R: Update CRAN and bioconductor packages

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wip/yesman
Alex Branham 4 years ago
parent 385b9aee08
commit e206c37550
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GPG Key ID: 1E4227A253E99AC7
3 changed files with 1760 additions and 1745 deletions
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  1. 14
      pkgs/development/r-modules/bioc-packages.nix
  2. 3468
      pkgs/development/r-modules/cran-packages.nix
  3. 23
      pkgs/development/r-modules/default.nix

14
pkgs/development/r-modules/bioc-packages.nix generated
Unescape View File

@ -370,7 +370,7 @@ in with self; {
GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.4.0"; sha256="0xcj10r85hxh5qy43cjb6ypd849b5wphhhv528simxq4glhgrhxp"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; };
GraphAT = derive2 { name="GraphAT"; version="1.54.0"; sha256="1xfd0i0j1fai58c15mc3lrg2jc4iwswyfpyg0ff5hnyhmgr3wnsa"; depends=[graph MCMCpack]; };
GraphAlignment = derive2 { name="GraphAlignment"; version="1.46.0"; sha256="1qql33ikps9x0dkvc31sxvyf8w119ax7519v5bv35s3i5yxh16i6"; depends=[]; };
GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC RMallow TSP]; };
GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC TSP]; };
GreyListChIP = derive2 { name="GreyListChIP"; version="1.14.0"; sha256="1hsjv4r88ldb7pgl5a3im8vdhmbiaj0rrn0clij7jfh5p5r81r1r"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; };
Guitar = derive2 { name="Guitar"; version="1.20.1"; sha256="1d4j54jdnsi8gi6p0kk6zxkk6kzd1r1k77mw142xlvh8b6zrl3nq"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; };
Gviz = derive2 { name="Gviz"; version="1.26.5"; sha256="1dpkcaar7qgzg3vgafvkplprhwmhzpb7ph009kr6ajm36hx4z81c"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
@ -457,7 +457,7 @@ in with self; {
M3C = derive2 { name="M3C"; version="1.4.1"; sha256="0l9063bn0sfcq5qxghaj8f98x0pg91fwsd8l64ga8d7pnlm8i5fm"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; };
M3D = derive2 { name="M3D"; version="1.16.0"; sha256="0a7xs3kqvyxswsa4zcdakij4rvpv1pr4fmplnvxyskhh2zps7xyl"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; };
M3Drop = derive2 { name="M3Drop"; version="1.8.1"; sha256="0bzxv4lnmbz4d7y1c2w7i013rfjscnj1ndb05k9n1i4c9gsknqya"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; };
MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr rbamtools Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; };
MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; };
MADSEQ = derive2 { name="MADSEQ"; version="1.8.0"; sha256="1b7d6niz8lhvd17xjl4hy1yyki049cg6wd3g8wp38bm3zs6dzfd1"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; };
MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.2.3"; sha256="1d2lllsz2jdqma1ifdg7xj9fby85az7bifn0h0hj705m6dyla42z"; depends=[biomaRt bladderbatch clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png sva]; };
MAIT = derive2 { name="MAIT"; version="1.16.1"; sha256="0fg3cah81c4gzm3hw590h4grrja2qgfs8mrpkbifrgsclbybnp95"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; };
@ -479,7 +479,7 @@ in with self; {
MIGSA = derive2 { name="MIGSA"; version="1.6.0"; sha256="19gfb98qmb8wbi343lw92sf7d29xliyzb3wz095pd2npsjr69qkl"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; };
MIMOSA = derive2 { name="MIMOSA"; version="1.20.1"; sha256="0vj7z95pjq62glg1akipydbybxsxc69yjpqrffpc33kqhf46nhfb"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; };
MIRA = derive2 { name="MIRA"; version="1.4.1"; sha256="0wy4iisp6c0kfns34pr5am055b1x7wdnbdh8lgr5ll91wxz48sg9"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.1"; sha256="1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.1"; sha256="1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rpart sfsmisc shiny threejs]; };
MLP = derive2 { name="MLP"; version="1.30.0"; sha256="03h7k5v620x2hw6k3gddaba40fwh6zvpmlnhf6mcml7ldsni95y9"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; };
MLSeq = derive2 { name="MLSeq"; version="2.0.1"; sha256="1jaw2blnl7jsd2px069af7zqk69d04bma8m5vpqb941vx6yhk095"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; };
MMDiff2 = derive2 { name="MMDiff2"; version="1.10.0"; sha256="0ljdr6y3plzpf9j70ghw41x3jpb8p52lqb9987gm1mw7lxw9iraf"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
@ -538,7 +538,7 @@ in with self; {
NADfinder = derive2 { name="NADfinder"; version="1.6.1"; sha256="0kz7dz95kdz5dz05bh7x6czrwdr1imaq1mv6bncxxhv1mffhmb9v"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NBSplice = derive2 { name="NBSplice"; version="1.0.6"; sha256="1nalcpj7n4qghmkrfq65xd4i0aack2yq4l2wwsy4z0sfi7gh6m49"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.30.0"; sha256="16mxxrq6g4szig29cah2a13qp1ybsh8ci37izlq6gpxn0h00maym"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint rbamtools Xmisc]; };
NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint Xmisc]; };
NOISeq = derive2 { name="NOISeq"; version="2.26.1"; sha256="1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"; depends=[Biobase Matrix]; };
NTW = derive2 { name="NTW"; version="1.32.0"; sha256="10ndg6mina5wz3w87wpv4mnbxdyj6rhvc9jqf954wmh6gj04vyin"; depends=[mvtnorm]; };
NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.12.0"; sha256="1927ry931ckjrci6yfk3fh774bizh4yb5f7p7x1ra1yxzfizq7k3"; depends=[Biobase matrixStats Rcpp]; };
@ -798,7 +798,7 @@ in with self; {
TFutils = derive2 { name="TFutils"; version="1.2.0"; sha256="1gppabscwfbqyvwrnl7mppw9wp528plp3bxq7g73hhgackfwnwkc"; depends=[dplyr magrittr miniUI shiny]; };
TIN = derive2 { name="TIN"; version="1.14.0"; sha256="0n5lx8pg066z9adjsfnslxw6fv0w0ibv7nk2yz8qaiq6zivvcc1y"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; };
TMixClust = derive2 { name="TMixClust"; version="1.4.0"; sha256="03i9fgq29xr3h72c2scb4fa6305l7bpwj6hgk0j1v7ark6xz5xqz"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; };
TPP = derive2 { name="TPP"; version="3.10.1"; sha256="00rfxhzamz45phav239xki8jy9bj7f0r03wrl9d09ir5amis271p"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown sme stringr tidyr VennDiagram VGAM]; };
TPP = derive2 { name="TPP"; version="3.10.1"; sha256="00rfxhzamz45phav239xki8jy9bj7f0r03wrl9d09ir5amis271p"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tidyr VennDiagram VGAM]; };
TRONCO = derive2 { name="TRONCO"; version="2.14.2"; sha256="1cqkk6zsfsjpq8iidvmpfvkfak3ryp2bl9p04in0sn8sl9is6nsq"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; };
TSCAN = derive2 { name="TSCAN"; version="1.20.0"; sha256="1yas32djld4dlsmzi65dflmnrff48m7vb6j7wgr44jip416mh7l1"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; };
TSRchitect = derive2 { name="TSRchitect"; version="1.8.9"; sha256="0i5i7m2rfqgnr2n39hfdgbvlhm8aqa6c77i7jvp66lapskww4rgb"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
@ -1558,7 +1558,7 @@ in with self; {
spikeLI = derive2 { name="spikeLI"; version="2.42.0"; sha256="055zbrbh6wf3vvnc9p8px2ffz9wdhdg0h96260r7c72ax3v6wi5g"; depends=[]; };
spkTools = derive2 { name="spkTools"; version="1.38.0"; sha256="0rm2vlzid3wjm1g1kzmjklga1gcf852aznhxb1xr50v8drivkkz9"; depends=[Biobase gtools RColorBrewer]; };
splatter = derive2 { name="splatter"; version="1.6.1"; sha256="1kw9shzqwph44q2fksgp79mrjq23j3806clc4xydw3ys2w4kspj8"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; };
spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; };
spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges seqLogo]; };
splicegear = derive2 { name="splicegear"; version="1.54.0"; sha256="0phpkgjkc4c8lfr8xsciqyz7imsjpc3sxwsh95glxhrsm7i2mnip"; depends=[annotate Biobase XML]; };
splineTimeR = derive2 { name="splineTimeR"; version="1.10.0"; sha256="15dzhijkhpy7d8hwif59bic83fk6fnyjpp4qi7y7vwq139j6yaj2"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; };
splots = derive2 { name="splots"; version="1.48.0"; sha256="0s10ha17p4yf6id0h0r0a2fk992jp4ah7v8ani689zy6pcc0w34d"; depends=[RColorBrewer]; };
@ -1581,7 +1581,7 @@ in with self; {
switchBox = derive2 { name="switchBox"; version="1.18.0"; sha256="1s49vi0vyh0bmrc6marn69hi9ln12j3kyjkkm2z5fpvv3rvxhgw7"; depends=[gplots pROC]; };
switchde = derive2 { name="switchde"; version="1.8.1"; sha256="1ydc9h62iyfz0786c5zhz3189p2f7sf3z6fjlvqwjqxva5j0f12b"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; };
synapter = derive2 { name="synapter"; version="2.6.1"; sha256="19rf8kkqf070ldhnrdi3xl23j2slv4qadw9cx8wvc4p994f2abj9"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; };
synergyfinder = derive2 { name="synergyfinder"; version="1.8.0"; sha256="1idc0lnjw8zx6nih1hrzfq9h40zkbdv0iv9si214wx4ynf0w18iv"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; };
synergyfinder = derive2 { name="synergyfinder"; version="1.8.0"; sha256="1idc0lnjw8zx6nih1hrzfq9h40zkbdv0iv9si214wx4ynf0w18iv"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2]; };
synlet = derive2 { name="synlet"; version="1.12.1"; sha256="13rghqqbkxni121ds0slf6cnj2g5zbm3sbbcli95z7mxy2wn3syg"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
systemPipeR = derive2 { name="systemPipeR"; version="1.16.1"; sha256="0qzydz87rld2nhwzbfgrw5jfgh8maa9y54mjx9c4285m11qj2shq"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; };
tRNA = derive2 { name="tRNA"; version="1.0.0"; sha256="1kzl79q0zim9y7px0dirk41qay96nl2bz8sw76nx56pr1d5jh245"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges S4Vectors scales stringr XVector]; };

3468
pkgs/development/r-modules/cran-packages.nix generated
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23
pkgs/development/r-modules/default.nix
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@ -264,7 +264,6 @@ let
gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ];
haven = [ pkgs.libiconv pkgs.zlib.dev ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
@ -293,7 +292,6 @@ let
phytools = [ pkgs.which ];
PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
PopGenome = [ pkgs.zlib.dev ];
proj4 = [ pkgs.proj ];
protolite = [ pkgs.protobuf ];
qtbase = [ pkgs.qt4 ];
@ -317,7 +315,6 @@ let
Rhdf5lib = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ];
RJaCGH = [ pkgs.zlib.dev ];
rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
@ -367,7 +364,6 @@ let
udunits2 = [ pkgs.udunits pkgs.expat ];
units = [ pkgs.udunits ];
V8 = [ pkgs.v8_3_14 ];
VBLPCM = [ pkgs.gsl_1 ];
WhopGenome = [ pkgs.zlib.dev ];
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
@ -392,7 +388,6 @@ let
# sort -t '=' -k 2
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_nblast = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
RMark = [ pkgs.which ];
@ -413,7 +408,6 @@ let
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
gdtools = [ pkgs.pkgconfig ];
JuniperKernel = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkgconfig ];
magick = [ pkgs.pkgconfig ];
@ -435,8 +429,6 @@ let
rPython = [ pkgs.which ];
gridGraphics = [ pkgs.which ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
mzR = [ pkgs.netcdf ];
cluster = [ pkgs.libiconv ];
KernSmooth = [ pkgs.libiconv ];
@ -524,7 +516,6 @@ let
"fscaret"
"fSRM"
"gcmr"
"GeoGenetix"
"geomorph"
"geoR"
"geoRglm"
@ -571,7 +562,6 @@ let
"mritc"
"multgee"
"multibiplotGUI"
"nodiv"
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
@ -644,7 +634,6 @@ let
"rsgcc"
"RSurvey"
"RunuranGUI"
"sharpshootR"
"simba"
"Simile"
"SimpleTable"
@ -668,7 +657,6 @@ let
"SYNCSA"
"SyNet"
"tcltk2"
"TED"
"TestScorer"
"TIMP"
"titan"
@ -768,17 +756,6 @@ let
'';
});
JuniperKernel = old.JuniperKernel.overrideDerivation (attrs: {
postPatch = lib.optionalString stdenv.isDarwin ''
for file in {R,src}/*.R; do
sed -i 's#system("which \(otool\|install_name_tool\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
done
'';
preConfigure = ''
patchShebangs configure
'';
});
jqr = old.jqr.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure

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