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R: Update CRAN and bioconductor packages

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Alex Branham 2020-04-26 17:16:34 -04:00
parent 8ce6552d64
commit cb1a13ad98
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GPG key ID: 1E4227A253E99AC7
3 changed files with 722 additions and 707 deletions
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8
pkgs/development/r-modules/bioc-packages.nix generated
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@ -197,7 +197,7 @@ in with self; {
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 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 imp4p 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]; };
@ -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]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
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]; };
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=[]; };
@ -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=[gRain kinship2 snpStats]; };
RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[GENLIB 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]; };

1419
pkgs/development/r-modules/cran-packages.nix generated
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2
pkgs/development/r-modules/default.nix
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@ -328,7 +328,6 @@ let
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
rPython = [ pkgs.python ];
RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ];
Rssa = [ pkgs.fftw.dev ];
@ -425,7 +424,6 @@ let
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
rPython = [ pkgs.which ];
gridGraphics = [ pkgs.which ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
mzR = [ pkgs.netcdf ];