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R: Update CRAN and bioconductor packages

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Alex Branham 2020-04-08 10:01:19 -04:00
parent 9ea40782c0
commit f5afc20d06
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3 changed files with 2870 additions and 2718 deletions
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pkgs/development/r-modules/bioc-packages.nix generated
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@ -123,7 +123,7 @@ in with self; {
CGHcall = derive2 { name="CGHcall"; version="2.44.0"; sha256="1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"; depends=[Biobase CGHbase DNAcopy impute snowfall]; };
CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.36.0"; sha256="1j92x5dyxp6hjj87g1hgw5q8fd4k2q5rb97ir47xkalkcskg0ddh"; depends=[Biobase CGHbase CGHcall]; };
CGHregions = derive2 { name="CGHregions"; version="1.40.0"; sha256="04j87bd2ygda6np72vs1bx857y5mbaga19ky6pgyxv9lahi62xyw"; depends=[Biobase CGHbase]; };
CHARGE = derive2 { name="CHARGE"; version="1.2.0"; sha256="0230pvgsf775lq4n9cpxb95bqq438f4z0wx9mmbj4yir8bljy0mk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats modes plyr SummarizedExperiment]; };
CHARGE = derive2 { name="CHARGE"; version="1.2.0"; sha256="0230pvgsf775lq4n9cpxb95bqq438f4z0wx9mmbj4yir8bljy0mk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats plyr SummarizedExperiment]; };
CHRONOS = derive2 { name="CHRONOS"; version="1.10.1"; sha256="03j4qcak7bpgw80gzxb2mj6k134jqp5frzd5ls6b5290lkknj720"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl XML]; };
CINdex = derive2 { name="CINdex"; version="1.10.0"; sha256="0c4p3v9a0njf28gdhvdbnydlhjgpnwzakhnvkvngs3mhbwpy9ih5"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; };
CMA = derive2 { name="CMA"; version="1.40.0"; sha256="1v77yiqmvd90pxbs64xfpglwy006w88b4zrb5rk90r0vasnvdl5n"; depends=[Biobase]; };
@ -192,12 +192,12 @@ in with self; {
CopywriteR = derive2 { name="CopywriteR"; version="2.14.1"; sha256="1hbiw0m9hmx4na9v502pxf8y5wvxzr68r4d3fqr2755gxx86qck6"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
CorMut = derive2 { name="CorMut"; version="1.24.0"; sha256="1p4xj8f5hf1z31943s51inc0mc28bphzy5qs4ay2nccwshbypq0l"; depends=[igraph seqinr]; };
Cormotif = derive2 { name="Cormotif"; version="1.28.0"; sha256="0lb691mvr9zim7z5yplncmlzyr799jym1wvrgfm1diqjz2daixai"; depends=[affy limma]; };
CountClust = derive2 { name="CountClust"; version="1.10.1"; sha256="1b129r97wv3gm25pk3ccg5bmp2476jyhz1pphapqlrb1im3fixq6"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; };
CountClust = derive2 { name="CountClust"; version="1.10.1"; sha256="1b129r97wv3gm25pk3ccg5bmp2476jyhz1pphapqlrb1im3fixq6"; depends=[cowplot flexmix ggplot2 gtools limma picante plyr reshape2 slam SQUAREM]; };
CoverageView = derive2 { name="CoverageView"; version="1.20.1"; sha256="164lla4v6ll0kqzapm3kmwz39k5shl0cwwashpbwiixrrxhcy8d2"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
CrispRVariants = derive2 { name="CrispRVariants"; version="1.10.1"; sha256="0n1mw3ybbdaybbcms12cj4vy21wahq5srny0qnbxjlzyl1zjbpr0"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
CytoDx = derive2 { name="CytoDx"; version="1.2.1"; sha256="05apvaf4dmkdfsp2aary14i7znjyzk0k6rqcbsk6m98fkp3d9r8b"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
CytoML = derive2 { name="CytoML"; version="1.8.1"; sha256="18isg4kjdn975q8vpziisnyxj1jxm4lkq7hi9jy4imf7bffc234i"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; };
DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
DART = derive2 { name="DART"; version="1.30.0"; sha256="0dxwy95p43c0shx30y95sj1pl64kqkh2bsnj680q196zgyg937s6"; depends=[igraph]; };
DBChIP = derive2 { name="DBChIP"; version="1.26.0"; sha256="1wk8nvfcfhsymhbi6id0kd1jzcykh6hhikl2040g0v6gi252gv2v"; depends=[DESeq edgeR]; };
DChIPRep = derive2 { name="DChIPRep"; version="1.12.0"; sha256="1avcjr7r54grh3yn5pjbzji3syc8vvah9as7asv3cwmyqzaya4r0"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; };
@ -225,7 +225,7 @@ in with self; {
DNABarcodes = derive2 { name="DNABarcodes"; version="1.12.0"; sha256="0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"; depends=[BH Matrix Rcpp]; };
DNAcopy = derive2 { name="DNAcopy"; version="1.56.0"; sha256="04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"; depends=[]; };
DNAshapeR = derive2 { name="DNAshapeR"; version="1.10.0"; sha256="1rplgi36jn33npihhmk0vdsiali814y5v1wz5fdna3k9b47id6b6"; depends=[Biostrings fields GenomicRanges Rcpp]; };
DOQTL = derive2 { name="DOQTL"; version="1.18.0"; sha256="0ligqm4l2x5dz794djapri770j27rhibhdzc48y980768gjpkm8k"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel regress rhdf5 Rsamtools RUnit VariantAnnotation XML]; };
DOQTL = derive2 { name="DOQTL"; version="1.18.0"; sha256="0ligqm4l2x5dz794djapri770j27rhibhdzc48y980768gjpkm8k"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel rhdf5 Rsamtools RUnit VariantAnnotation XML]; };
DOSE = derive2 { name="DOSE"; version="3.8.2"; sha256="1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; };
DRIMSeq = derive2 { name="DRIMSeq"; version="1.10.1"; sha256="021xzx7ndvjdahi715qvq2xxnnhdsn9h8g6imps5ls3qmk5024d2"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; };
DSS = derive2 { name="DSS"; version="2.30.1"; sha256="0m18793vqaqamx3rj3pwrirc7ygmmg4774il8d59qmwinlppyxqw"; depends=[Biobase bsseq DelayedArray]; };
@ -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 TSP]; };
GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC RMallow 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]; };
@ -491,8 +491,8 @@ in with self; {
MSnID = derive2 { name="MSnID"; version="1.16.1"; sha256="077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; };
MSnbase = derive2 { name="MSnbase"; version="2.8.3"; sha256="1kl1d7byphnfpmbl5fzbgs68dxskhpsdyx7ka51bpfn0nv3pp492"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; };
MSstats = derive2 { name="MSstats"; version="3.14.1"; sha256="1bgvdq1mfq6rxjf5ag2slrhy4056906wghsirrymf53nw3qz5g6s"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; };
MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; };
MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.1.2"; sha256="0aaw3qillcfrjczdmd7s21v551hclnq8fn2zvn91wyr4i82q43rr"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; };
MTseeker = derive2 { name="MTseeker"; version="1.0.6"; sha256="0fsb7k6pkl15q8csygpsjrz4jvy20mfd5rfmhl7q7ffj4d7sprxh"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; };
MVCClass = derive2 { name="MVCClass"; version="1.56.0"; sha256="1hw36gd1z19dir6fl7j3dzqzi5p1668zbwpcz7l21hbyycv27l0j"; depends=[]; };
@ -602,7 +602,7 @@ in with self; {
PepsNMR = derive2 { name="PepsNMR"; version="1.0.2"; sha256="0x7n8faxrczqwn1kkcp22vwag905pswvr2q198kqbh4fjkxgkmrx"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; };
PharmacoGx = derive2 { name="PharmacoGx"; version="1.12.0"; sha256="1ddh6bmrddbdmqdpmyy5mlkqvhrk39c19lzybrirfclq6cydfh5g"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; };
PhenStat = derive2 { name="PhenStat"; version="2.18.1"; sha256="1fq01k4cb4gyzh9knbidcqds2qm1wvlz114s6nldzhl3h0x5h6x5"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; };
Pi = derive2 { name="Pi"; version="1.10.0"; sha256="03wzmcz57kdflicjb2wmnxg0fvfmbgizvql5164cf24fsi2lvbgi"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; };
Pi = derive2 { name="Pi"; version="1.10.0"; sha256="03wzmcz57kdflicjb2wmnxg0fvfmbgizvql5164cf24fsi2lvbgi"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex]; };
Pigengene = derive2 { name="Pigengene"; version="1.8.1"; sha256="13pmw7nf8fvn9bnnh7fwqgrlg589796nqv83snanqwqsp4fcklid"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; };
Polyfit = derive2 { name="Polyfit"; version="1.16.1"; sha256="0nlclhj5ni09blwf5prpcp2iiflqk17ca3gqjl5shvl9y9v8nbqb"; depends=[DESeq]; };
PowerExplorer = derive2 { name="PowerExplorer"; version="1.2.2"; sha256="14dzv3p79x95w6185r2srnmw1i8n6x2b1fd2chbx42b3xa65xliy"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; };
@ -670,7 +670,7 @@ in with self; {
RUVSeq = derive2 { name="RUVSeq"; version="1.16.1"; sha256="0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"; depends=[Biobase EDASeq edgeR MASS]; };
RUVcorr = derive2 { name="RUVcorr"; version="1.14.0"; sha256="05lg37rmf9skqcpnd08v6wnh7sfs449hwwq6nw2hkgy9faip14lz"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; };
RUVnormalize = derive2 { name="RUVnormalize"; version="1.16.0"; sha256="1habqdv35v9ypvfmfaxjqpka67bs6hzf4ph9b0gqd67mbfnb49dv"; depends=[Biobase RUVnormalizeData]; };
RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[GENLIB gRain kinship2 snpStats]; };
RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[gRain kinship2 snpStats]; };
RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.6.0"; sha256="1w02nnxpmx05gn6d9kjnahdn9kynbg1szm96c03gh4961zknn3r3"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.2.0"; sha256="022vckcc46bkhfhi2fzgawhf54hi6y2p5ia4v3x3lj221d7hcaax"; depends=[dnet igraph Matrix]; };
RankProd = derive2 { name="RankProd"; version="3.8.0"; sha256="0jmpwpmj3y13ylk7riyicywpring14dhq4862jgalsjjwa22zzd0"; depends=[gmp Rmpfr]; };
@ -932,7 +932,7 @@ in with self; {
celaref = derive2 { name="celaref"; version="1.0.1"; sha256="0sb1mg2ql09jf7hc5kszh3h9cajma0pdwzf8f58pridwhafw5z0p"; depends=[BiocGenerics dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; };
cellGrowth = derive2 { name="cellGrowth"; version="1.26.1"; sha256="0zmn45i6shr2d6q2dg2p2raz38cy6k8363maq4r4648fx2bmvkb2"; depends=[lattice locfit]; };
cellHTS2 = derive2 { name="cellHTS2"; version="2.46.1"; sha256="1fj1gshgphbbqhywwzvm3xrw8zfp19dc8fi6kbzv20ikf3am9fml"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; };
cellTree = derive2 { name="cellTree"; version="1.12.1"; sha256="1qr68f39bqykvjbjp5bw71g41wfp369yc88dqz9wppkzi16vl6z0"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; };
cellTree = derive2 { name="cellTree"; version="1.12.1"; sha256="1qr68f39bqykvjbjp5bw71g41wfp369yc88dqz9wppkzi16vl6z0"; depends=[gplots igraph slam topGO topicmodels xtable]; };
cellbaseR = derive2 { name="cellbaseR"; version="1.6.1"; sha256="0052wvb6jijs1v8yv1z049n6cy4qcjbrv20gqbsgl14xj0mif26x"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; };
cellity = derive2 { name="cellity"; version="1.10.1"; sha256="1ifm50ff9q6lwxyi52qzksimnwvd8yddrp7jkidzlykamh5dg05p"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; };
cellscape = derive2 { name="cellscape"; version="1.6.0"; sha256="062x43n5jq8hwlrlgd1ffgbpnifac79j9dzd35f6phb6vc1g63dl"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; };
@ -969,7 +969,7 @@ in with self; {
coGPS = derive2 { name="coGPS"; version="1.26.0"; sha256="0jsbgx6xdasqii9wcfn4ilf2dfc790lzzby1bhpzlq94nwlr896h"; depends=[]; };
coMET = derive2 { name="coMET"; version="1.14.0"; sha256="09r81ag9ix4jh3zvwyzym9g7rc7vkyhagcv934r8i4fzzvpiqsz4"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; };
coRdon = derive2 { name="coRdon"; version="1.0.3"; sha256="1v4zvzff4r54wjgp48l5vazvfy8w0gvvqxxhajm35p6d2bbpfsvd"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; };
cobindR = derive2 { name="cobindR"; version="1.20.0"; sha256="1bkwjj825srwm3rn3j88p1q35x03f129ca1hk919nnf92psh47nc"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; };
cobindR = derive2 { name="cobindR"; version="1.20.0"; sha256="1bkwjj825srwm3rn3j88p1q35x03f129ca1hk919nnf92psh47nc"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust seqinr yaml]; };
codelink = derive2 { name="codelink"; version="1.50.0"; sha256="1nfnb9iz8j31ia9979mjvs9gzdbh9zwfy14qxvjrp3dv8d1gf2rx"; depends=[annotate Biobase BiocGenerics limma]; };
coexnet = derive2 { name="coexnet"; version="1.4.0"; sha256="0751781vsr46xs3dpq2n29li1zipzad9qv6xnfdm34v62yaggy94"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; };
cogena = derive2 { name="cogena"; version="1.16.0"; sha256="12r86h6fzr6wqvf70jjxf02zm72ks577m6qcv60wiss609c0b0dn"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; };
@ -1336,7 +1336,7 @@ in with self; {
nem = derive2 { name="nem"; version="2.56.0"; sha256="02j5rm0h9bjghgba244k0acshbnhrr38ghvx6cmf8za8fw19k3v2"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; };
netReg = derive2 { name="netReg"; version="1.6.0"; sha256="01qxq7zlbmvh0mazw069fm6bjw0ks90baj8y5i0jc7m101dsm2qi"; depends=[Rcpp RcppArmadillo]; };
netSmooth = derive2 { name="netSmooth"; version="1.2.0"; sha256="1cz3rca9ig9jl8ddcadbij129v5rpb86ncfrdmfj4m9qy0krlyac"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; };
netbenchmark = derive2 { name="netbenchmark"; version="1.14.0"; sha256="1gc8dnma4pr1j9wq422x8xh89mvb15kyvjvv86fhhshvdisihngw"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet PCIT pracma Rcpp]; };
netbenchmark = derive2 { name="netbenchmark"; version="1.14.0"; sha256="1gc8dnma4pr1j9wq422x8xh89mvb15kyvjvv86fhhshvdisihngw"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet pracma Rcpp]; };
netbiov = derive2 { name="netbiov"; version="1.16.0"; sha256="0zg4wkf4z6yi84sdp4h8dg8cq5sm6m04abg15hm68y27vw42prs2"; depends=[igraph]; };
nethet = derive2 { name="nethet"; version="1.14.0"; sha256="1xp08ad4lsmrjgvqydr85k4y0b57hcaxicndh4hz4plqswzl7qpf"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; };
netprioR = derive2 { name="netprioR"; version="1.8.1"; sha256="1phdaklcwhv1rv94dvz4mcwi5f1b3gya7bwv7489hsx7pa149sac"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; };
@ -1501,7 +1501,7 @@ in with self; {
savR = derive2 { name="savR"; version="1.20.0"; sha256="13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
scDD = derive2 { name="scDD"; version="1.6.1"; sha256="0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; };
scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.2.1"; sha256="04bk4kzs42mi022qr8whngkqxapngnvpxifd0m60r57skz3v6yqa"; depends=[dplyr ggplot2 magrittr rlang tibble]; };
scPipe = derive2 { name="scPipe"; version="1.4.1"; sha256="1kl1ik1wd3cq7h2njzdnzs9r26qnim4r63c86pfbfymz23n4aqns"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue hashmap magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase rtracklayer S4Vectors scales SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; };
scPipe = derive2 { name="scPipe"; version="1.4.1"; sha256="1kl1ik1wd3cq7h2njzdnzs9r26qnim4r63c86pfbfymz23n4aqns"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase rtracklayer S4Vectors scales SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; };
scater = derive2 { name="scater"; version="1.10.1"; sha256="0rijhy7g5qmcn927y1wyd63la1fhyar9fv1hccsqd23jd98yc55a"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 Matrix plyr Rcpp reshape2 Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment viridis]; };
scde = derive2 { name="scde"; version="2.10.1"; sha256="1n1r08wqx1bds7lwz2bbksw5l084cmcbgs03jr8s2l92z43kqmm6"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; };
scfind = derive2 { name="scfind"; version="1.4.1"; sha256="07lzjqxvdjjzli8ibqvlndgf9n1x477q1pniv91ynrh6jc8dz8cb"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; };
@ -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]; };
synergyfinder = derive2 { name="synergyfinder"; version="1.8.0"; sha256="1idc0lnjw8zx6nih1hrzfq9h40zkbdv0iv9si214wx4ynf0w18iv"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; };
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]; };

5544
pkgs/development/r-modules/cran-packages.nix generated
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File diff suppressed because it is too large Load diff

16
pkgs/development/r-modules/default.nix
View file

@ -256,7 +256,6 @@ let
fftw = [ pkgs.fftw.dev ];
fftwtools = [ pkgs.fftw.dev ];
Formula = [ pkgs.gmp ];
geoCount = [ pkgs.gsl_1 ];
gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkgconfig ];
GLAD = [ pkgs.gsl_1 ];
@ -323,11 +322,9 @@ let
Rmpi = [ pkgs.openmpi ];
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBCext = [ pkgs.libiodbc ];
RODBC = [ pkgs.libiodbc ];
rpanel = [ pkgs.bwidget ];
rpg = [ pkgs.postgresql ];
rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
@ -335,7 +332,6 @@ let
RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ];
Rssa = [ pkgs.fftw.dev ];
rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtiff = [ pkgs.libtiff.dev ];
runjags = [ pkgs.jags ];
RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
@ -364,7 +360,6 @@ let
udunits2 = [ pkgs.udunits pkgs.expat ];
units = [ pkgs.udunits ];
V8 = [ pkgs.v8 ];
WhopGenome = [ pkgs.zlib.dev ];
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
@ -411,7 +406,6 @@ let
cairoDevice = [ pkgs.pkgconfig ];
chebpol = [ pkgs.pkgconfig ];
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
gdtools = [ pkgs.pkgconfig ];
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkgconfig ];
@ -463,14 +457,11 @@ let
"AnnotLists"
"AnthropMMD"
"aplpack"
"aqfig"
"arf3DS4"
"asbio"
"AtelieR"
"BAT"
"bayesDem"
"BCA"
"BEQI2"
"betapart"
"BiodiversityR"
"bio_infer"
@ -523,7 +514,6 @@ let
"gcmr"
"geomorph"
"geoR"
"geoRglm"
"georob"
"GGEBiplotGUI"
"gnm"
@ -561,7 +551,6 @@ let
"miniGUI"
"MissingDataGUI"
"mixsep"
"mlDNA"
"MplusAutomation"
"mpmcorrelogram"
"mritc"
@ -628,7 +617,6 @@ let
"recluster"
"relimp"
"RenextGUI"
"reportRx"
"reshapeGUI"
"rgl"
"RHRV"
@ -636,7 +624,6 @@ let
"RNCEP"
"RQDA"
"RSDA"
"rsgcc"
"RSurvey"
"RunuranGUI"
"simba"
@ -644,7 +631,6 @@ let
"SimpleTable"
"SOLOMON"
"soundecology"
"spacodiR"
"spatsurv"
"sqldf"
"SRRS"
@ -676,10 +662,8 @@ let
"vegan"
"vegan3d"
"vegclust"
"VIMGUI"
"WMCapacity"
"x12GUI"
"xergm"
];
packagesToSkipCheck = [