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Merge pull request #25096 from peti/r-updates

Browse Source 
R 3.4.0 and package set updates
This commit is contained in:
Peter Simons 2017-04-24 15:41:36 +02:00 committed by GitHub
commit 7369fd0b51
6 changed files with 2677 additions and 2281 deletions
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6
pkgs/applications/science/math/R/default.nix
View File

@ -7,11 +7,11 @@
}:
stdenv.mkDerivation rec {
name = "R-3.3.3";
name = "R-3.4.0";
src = fetchurl {
url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
sha256 = "0v7wpj89b0i3ad3fi1wak5c93hywmbxv8sdnixhq8l17782nidss";
sha256 = "14cb8bwi3akvdb6934kqic2862f2qgav6cq4g0h7gi2p4ka9x3i8";
};
buildInputs = [
@ -62,7 +62,7 @@ stdenv.mkDerivation rec {
installTargets = [ "install" "install-info" "install-pdf" ];
doCheck = true;
preCheck = "bin/Rscript -e 'sessionInfo()'";
preCheck = "export TZ=CET; bin/Rscript -e 'sessionInfo()'";
enableParallelBuilding = true;

5
pkgs/development/r-modules/README.md
View File

@ -12,7 +12,7 @@ use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix fil
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
packages = with self.rPackages; [
devtools
ggplot2
reshape2
@ -65,7 +65,7 @@ set `useRPackages` to `true`, like below:
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
packages = with self.rPackages; [
devtools
ggplot2
reshape2
@ -106,4 +106,3 @@ nix-build test-evaluation.nix --dry-run
```
If this exits fine, the expression is ok. If not, you have to edit `default.nix`

2504
pkgs/development/r-modules/bioc-packages.nix
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File diff suppressed because it is too large Load Diff

2372
pkgs/development/r-modules/cran-packages.nix
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File diff suppressed because it is too large Load Diff

68
pkgs/development/r-modules/default.nix
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@ -409,7 +409,6 @@ let
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
qtutils = [ pkgs.qt4 ];
ecoretriever = [ pkgs.which ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
rPython = [ pkgs.which ];
@ -630,7 +629,6 @@ let
"rioja"
"ripa"
"rite"
"rnbn"
"RNCEP"
"RQDA"
"RSDA"
@ -662,7 +660,6 @@ let
"SYNCSA"
"SyNet"
"tcltk2"
"TDMR"
"TED"
"TestScorer"
"TIMP"
@ -695,24 +692,29 @@ let
# Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [
"acs" # build is broken
"AffyTiling" # build is broken
"agRee" # depends on broken package BRugs-0.8-6
"aLFQ" # depends on broken package bio3d-2.3-1
"anamiR" # depends on broken package RMySQL-0.10.11
"AneuFinder" # depends on broken package Rhtslib-1.6.0
"animation" # build is broken
"anim_plots" # depends on broken package animation-2.4
"annmap" # depends on broken package RMySQL-0.10.9
"apaStyle" # depends on broken package gdtools-0.1.3
"apaTables" # depends on broken package OpenMx-2.7.4
"aptg" # depends on broken package brranching-0.2.0
"ArrayExpressHTS" # build is broken
"arrayQualityMetrics" # build is broken
"auRoc" # depends on broken package OpenMx-2.7.4
"bamsignals" # depends on broken package Rhtslib-1.6.0
"BatchQC" # build is broken
"bayesCL" # build is broken
"bayou" # depends on broken package animation-2.4
"bedr" # build is broken
"BETS" # build is broken
"BiGGR" # depends on broken package rsbml-2.30.0
"bio3d" # build is broken
"bioassayR" # depends on broken package ChemmineR-2.24.2
"bioCancer" # depends on broken package covr-2.2.2
"biomformat" # depends on broken package r-rhdf5-2.16.0
"biotools" # depends on broken package rpanel-1.1-3
"birte" # build is broken
@ -734,6 +736,8 @@ let
"categoryCompare" # depends on broken package RCytoscape-1.21.1
"Causata" # depends on broken package RMySQL-0.10.9
"cdcfluview" # depends on broken package V8-1.2
"CexoR" # depends on broken package Rhtslib-1.6.0
"ChAMP" # depends on broken package goseq-1.26.0
"ChemmineDrugs" # depends on broken package ChemmineR-2.24.2
"ChemmineR" # build is broken
"chinese_misc" # build is broken
@ -762,13 +766,14 @@ let
"csaw" # build is broken
"ctsem" # depends on broken package OpenMx-2.7.4
"cudaBayesreg" # build is broken
"curlconverter" # depends on broken package V8-1.2
"cytofkit" # depends on broken package flowCore-1.38.2
"CytoML" # depends on broken package flowCore-1.40.6
"daff" # depends on broken package V8-1.2
"dagbag" # build is broken
"dagitty" # depends on broken package V8-1.2
"dagLogo" # depends on broken package MotIV-1.28.0
"DAISIE" # depends on broken package animation-2.4
"DataEntry" # build is broken
"dataMaid" # build is broken
"dataone" # build is broken
"datapack" # build is broken
@ -777,7 +782,9 @@ let
"DCM" # build is broken
"DDD" # depends on broken package animation-2.4
"deBInfer" # depends on broken package PBSddesolve-1.12.2
"debrowser" # depends on broken package V8-1.4
"DecisionCurve" # build is broken
"DeepBlueR" # build is broken
"deepSNV" # build is broken
"DEGraph" # depends on broken package RCytoscape-1.21.1
"DEploid" # build is broken
@ -787,7 +794,6 @@ let
"DirichletMultinomial" # build is broken
"diveRsity" # build is broken
"DmelSGI" # depends on broken package r-rhdf5-2.16.0
"DNAprofiles" # build is broken
"docxtools" # build is broken
"DOQTL" # depends on broken package r-rhdf5-2.16.0
"DOT" # depends on broken package V8-1.2
@ -801,11 +807,14 @@ let
"euroMix" # build is broken
"evobiR" # depends on broken package animation-2.4
"exifr" # build is broken
"ExperimentHubData" # build is broken
"exprso" # build is broken
"fastR" # build is broken
"fCCAC" # depends on broken package Rhtslib-1.6.0
"fdq" # depends on broken package gdtools-0.1.3
"Fgmutils" # depends on broken package gdtools-0.1.3
"flan" # build is broken
"flextable" # depends on broken package gdtools-0.1.4
"flowAI" # depends on broken package r-flowCore-1.38.2
"flowBeads" # depends on broken package r-flowCore-1.38.2
"flowBin" # depends on broken package r-flowCore-1.38.2
@ -822,6 +831,7 @@ let
"flowMeans" # depends on broken package r-flowCore-1.38.2
"flowMerge" # depends on broken package r-flowCore-1.38.2
"flowPeaks" # build is broken
"flowPloidy" # depends on broken package flowCore-1.40.6
"flowQB" # depends on broken package r-flowCore-1.38.2
"flowQ" # depends on broken package flowCore-1.38.2
"FlowSOM" # depends on broken package r-flowCore-1.38.2
@ -848,6 +858,8 @@ let
"gazepath" # build is broken
"gdtools" # build is broken
"GENE_E" # depends on broken package r-rhdf5-2.16.0
"GenoGAM" # build is broken
"genomation" # depends on broken package Rhtslib-1.6.0
"geojson" # depends on broken package r-protolite-1.5
"geojsonio" # depends on broken package V8-1.2
"geojsonlint" # depends on broken package V8-1.2
@ -855,19 +867,22 @@ let
"gfer" # depends on broken package V8-1.2
"ggcyto" # depends on broken package r-flowCore-1.38.2
"ggghost" # depends on broken package animation-2.4
"ggimage" # depends on broken package gridGraphics-0.1-5
"ggiraph" # depends on broken package gdtools-0.1.3
"ggiraphExtra" # depends on broken package gdtools-0.1.3
"ggseas" # build is broken
"gmapR" # build is broken
"gmatrix" # depends on broken package cudatoolkit-8.0.61
"gMCP" # build is broken
"gmDatabase" # depends on broken package RMySQL-0.10.9
"gmum_r" # build is broken
"goldi" # build is broken
"googleformr" # build is broken
"goseq" # build is broken
"gpg" # build is broken
"gpuR" # build is broken
"gputools" # depends on broken package cudatoolkit-8.0.61
"GraphPAC" # build is broken
"greengenes13_5MgDb" # build is broken
"gridGraphics" # build is broken
"GSCA" # depends on broken package r-rhdf5-2.16.0
"GUIDE" # depends on broken package rpanel-1.1-3
@ -877,11 +892,14 @@ let
"harrietr" # build is broken
"HDF5Array" # depends on broken package r-rhdf5-2.16.0
"healthyFlowData" # depends on broken package r-flowCore-1.38.2
"hexSticker" # depends on broken package gridGraphics-0.1-5
"HierO" # build is broken
"HilbertVisGUI" # build is broken
"HiPLARM" # build is broken
"hisse" # depends on broken package animation-2.4
"hoardeR" # depends on broken package Rhtslib-1.6.0
"homomorpheR" # depends on broken package sodium-0.4
"HTSeqGenie" # depends on broken package gmapR-1.16.0
"HTSSIP" # depends on broken package r-rhdf5-2.16.0
"idm" # depends on broken package animation-2.4
"ifaTools" # depends on broken package OpenMx-2.7.4
@ -889,7 +907,7 @@ let
"IHWpaper" # depends on broken package r-lpsymphony-1.0.2
"IlluminaHumanMethylation450k_db" # build is broken
"immunoClust" # depends on broken package r-flowCore-1.38.2
"inSilicoMerging" # build is broken
"imputeR" # depends on broken package ridge-2.2
"intansv" # build is broken
"interactiveDisplay" # build is broken
"ionicons" # depends on broken package rsvg-1.0
@ -902,8 +920,10 @@ let
"KoNLP" # build is broken
"largeList" # build is broken
"largeVis" # build is broken
"lavaan_shiny" # depends on broken package OpenMx-2.7.10
"lawn" # depends on broken package V8-1.2
"LCMCR" # build is broken
"LeArEst" # depends on broken package opencpu-1.6.1
"lefse" # build is broken
"lfe" # build is broken
"lgcp" # depends on broken package rpanel-1.1-3
@ -926,6 +946,7 @@ let
"MBESS" # depends on broken package OpenMx-2.7.4
"mBvs" # build is broken
"mcaGUI" # build is broken
"mcPAFit" # build is broken
"mdsr" # depends on broken package RMySQL-0.10.9
"Mediana" # depends on broken package gdtools-0.1.3
"melviewr" # build is broken
@ -936,13 +957,14 @@ let
"metagear" # build is broken
"MetaIntegrator" # depends on broken package RMySQL-0.10.9
"metaSEM" # depends on broken package OpenMx-2.7.4
"methylKit" # depends on broken package Rhtslib-1.6.0
"MigClim" # build is broken
"minimist" # depends on broken package V8-1.2
"miscF" # depends on broken package BRugs-0.8-6
"mixlink" # build is broken
"MLSeq" # build is broken
"MMDiff" # depends on broken package r-DiffBind-2.0.9
"mmnet" # build is broken
"MODIStsp" # build is broken
"MonetDBLite" # build is broken
"mongolite" # build is broken
"monogeneaGM" # depends on broken package animation-2.4
@ -969,7 +991,9 @@ let
"ndjson" # build is broken
"ndtv" # depends on broken package animation-2.4
"NetRep" # depends on broken package r-RhpcBLASctl-0.15-148
"networkBMA" # build is broken
"nlts" # build is broken
"normr" # depends on broken package Rhtslib-1.6.0
"NORRRM" # build is broken
"odbc" # build is broken
"officer" # depends on broken package gdtools-0.1.3
@ -979,10 +1003,12 @@ let
"OpenMx" # build is broken
"optbdmaeAT" # build is broken
"optBiomarker" # depends on broken package rpanel-1.1-3
"optrcdmaeAT" # build is broken
"ora" # depends on broken package ROracle-1.3-1
"OUwie" # depends on broken package animation-2.4
"PAA" # build is broken
"paleotree" # depends on broken package animation-2.4
"PathoStat" # depends on broken package BatchQC-1.2.1
"PathSelectMP" # build is broken
"PatternClass" # build is broken
"PBD" # depends on broken package animation-2.4
@ -999,6 +1025,7 @@ let
"PGA" # build is broken
"PGPC" # depends on broken package ChemmineR-2.24.2
"ph2bye" # depends on broken package animation-2.4
"PharmacoGx" # build is broken
"PhyInformR" # depends on broken package animation-2.4
"phylocurve" # depends on broken package animation-2.4
"phyloseq" # depends on broken package r-rhdf5-2.16.0
@ -1008,6 +1035,7 @@ let
"PING" # depends on broken package PICS-2.16.0
"plateCore" # depends on broken package r-flowCore-1.38.2
"plfMA" # build is broken
"plink" # build is broken
"podkat" # build is broken
"PottsUtils" # depends on broken package BRugs-0.8-6
"powell" # build is broken
@ -1043,11 +1071,12 @@ let
"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
"RAppArmor" # build is broken
"raptr" # depends on broken package PBSmapping-2.69.76
"RBerkeley" # build is broken
"RbioRXN" # depends on broken package ChemmineR-2.24.2
"Rblpapi" # build is broken
"RCAS" # depends on broken package Rhtslib-1.6.0
"Rchemcpp" # depends on broken package ChemmineR-2.24.2
"rchess" # depends on broken package V8-1.2
"RchivalTag" # depends on broken package PBSmapping-2.69.76
"RchyOptimyx" # depends on broken package r-flowCore-1.38.2
"RcmdrPlugin_FuzzyClust" # build is broken
"RcmdrPlugin_PcaRobust" # build is broken
@ -1060,6 +1089,7 @@ let
"rcqp" # build is broken
"rcrypt" # build is broken
"RCytoscape" # build is broken
"rdataretriever" # build is broken
"rDEA" # build is broken
"RDieHarder" # build is broken
"REBayes" # depends on broken package Rmosek-1.2.5.1
@ -1075,8 +1105,10 @@ let
"Rgnuplot" # build is broken
"rgp" # build is broken
"rgpui" # depends on broken package rgp-0.4-1
"rgsepd" # depends on broken package goseq-1.26.0
"rhdf5" # build is broken
"RhpcBLASctl" # build is broken
"Rhtslib" # build is broken
"ridge" # build is broken
"rjade" # depends on broken package V8-1.2
"rJPSGCS" # build is broken
@ -1089,12 +1121,14 @@ let
"rmapshaper" # depends on broken package V8-1.2
"rMAT" # build is broken
"Rmosek" # build is broken
"rmumps" # build is broken
"RMySQL" # build is broken
"rnaturalearth" # depends on broken package sf-0.4-1
"RnavGraph" # build is broken
"rnetcarto" # build is broken
"ROI_plugin_clp" # depends on broken package clpAPI-1.2.7
"ROI_plugin_cplex" # depends on broken package Rcplex-0.3-3
"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-26
"Rolexa" # build is broken
"ROracle" # build is broken
"RPA" # depends on broken package r-rhdf5-2.16.0
"RPANDA" # depends on broken package animation-2.4
@ -1103,6 +1137,7 @@ let
"Rphylopars" # depends on broken package animation-2.4
"Rpoppler" # build is broken
"RQuantLib" # build is broken
"Rsampletrees" # build is broken
"RSAP" # build is broken
"rsbml" # build is broken
"RSCABS" # build is broken
@ -1119,9 +1154,9 @@ let
"RVideoPoker" # depends on broken package rpanel-1.1-3
"rzmq" # build is broken
"s2" # build is broken
"Sabermetrics" # build is broken
"sapFinder" # build is broken
"sbrl" # build is broken
"SC3" # depends on broken package scater-1.2.0
"scater" # depends on broken package r-rhdf5-2.16.0
"scran" # depends on broken package r-rhdf5-2.16.0
"SDD" # depends on broken package rpanel-1.1-3
@ -1129,6 +1164,7 @@ let
"seasonalview" # build is broken
"Sejong" # build is broken
"SemiCompRisks" # build is broken
"semPlot" # depends on broken package OpenMx-2.7.10
"semtree" # depends on broken package OpenMx-2.7.4
"seqbias" # build is broken
"SeqGrapheR" # build is broken
@ -1141,11 +1177,11 @@ let
"SimInf" # build is broken
"simsalapar" # build is broken
"smapr" # depends on broken package r-rhdf5-2.16.0
"SMITE" # depends on broken package goseq-1.26.0
"SnakeCharmR" # build is broken
"sodium" # build is broken
"soilphysics" # depends on broken package rpanel-1.1-3
"sortinghat" # build is broken
"spade" # depends on broken package r-flowCore-1.38.2
"spdynmod" # depends on broken package animation-2.4
"spocc" # depends on broken package V8-1.2
"spongecake" # build is broken
@ -1159,20 +1195,24 @@ let
"subspaceMOA" # depends on broken package animation-2.4
"svglite" # depends on broken package gdtools-0.1.3
"sybilSBML" # build is broken
"SymTS" # build is broken
"synthACS" # depends on broken package acs-2.0
"tcpl" # depends on broken package RMySQL-0.10.9
"TDA" # build is broken
"TED" # depends on broken package animation-2.4
"tesseract" # build is broken
"texPreview" # depends on broken package magick-0.4
"textreadr" # build is broken
"textTinyR" # build is broken
"TFBSTools" # depends on broken package CNEr-1.8.3
"tilegramsR" # depends on broken package sf-0.4-1
"TKF" # depends on broken package animation-2.4
"tmap" # depends on broken package V8-1.2
"tmaptools" # depends on broken package V8-1.2
"tofsims" # build is broken
"toxboot" # depends on broken package RMySQL-0.10.9
"TransView" # build is broken
"treatSens" # build is broken
"treeplyr" # depends on broken package animation-2.4
"TSMySQL" # depends on broken package RMySQL-0.10.9
"uaparserjs" # depends on broken package V8-1.2
@ -1181,12 +1221,14 @@ let
"umx" # depends on broken package OpenMx-2.7.4
"userfriendlyscience" # depends on broken package OpenMx-2.7.4
"V8" # build is broken
"VariantTools" # depends on broken package gmapR-1.16.0
"VBmix" # build is broken
"vcfR" # build is broken
"vdiffr" # depends on broken package gdtools-0.1.3
"vmsbase" # depends on broken package PBSmapping-2.69.76
"wallace" # depends on broken package V8-1.2
"wand" # build is broken
"WebGestaltR" # depends on broken package PythonInR-0.1-3
"webp" # build is broken
"wordbankr" # depends on broken package RMySQL-0.10.9
"x13binary" # build is broken

3
pkgs/development/r-modules/generate-shell.nix
View File

@ -6,7 +6,8 @@ stdenv.mkDerivation {
buildCommand = "exit 1";
buildInputs = [ wget ];
nativeBuildInputs = [
nativeBuildInputs = [
(rWrapper.override {
packages = with rPackages; [
data_table