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Merge branch 'staging' into closure-size

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This commit is contained in:
Vladimír Čunát
2016-01-19 09:55:31 +01:00
parent f8472457a4 53b389327e
commit 716aac2519
1293 changed files with 75245 additions and 28520 deletions
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pkgs/development/r-modules/cran-packages.nix
+761 -555
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File diff suppressed because it is too large Load Diff
pkgs/development/r-modules/default.nix
+52 -1
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@@ -5,7 +5,10 @@
let
inherit (pkgs) fetchurl stdenv lib;
buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
buildRPackage = pkgs.callPackage ./generic-builder.nix {
inherit R;
inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation;
};
# Generates package templates given per-repository settings
#
@@ -735,6 +738,7 @@ let
"aop" # broken build
"apaTables" # depends on broken package r-car-2.1-0
"apComplex" # build is broken
"apex" # depends on broken package Biostrings-2.38.2
"apmsWAPP" # broken build
"apt" # depends on broken package nlopt-2.4.2
"ArfimaMLM" # depends on broken package nlopt-2.4.2
@@ -752,6 +756,7 @@ let
"AssetPricing" # broken build
"AtelieR" # broken build
"attract" # depends on broken package AnnotationForge-1.11.3
"auRoc" # depends on broken package rjags-4-4
"AutoModel" # depends on broken package r-car-2.1-0
"babel" # broken build
"BACA" # depends on broken package Category-2.35.1
@@ -781,6 +786,7 @@ let
"BcDiag" # broken build
"BCRANK" # broken build
"bcrypt"
"bdynsys" # depends on broken package car-2.1
"beadarray" # broken build
"beadarrayFilter" # broken build
"beadarrayMSV" # broken build
@@ -838,7 +844,9 @@ let
"BradleyTerry2" # depends on broken package nlopt-2.4.2
"BrailleR" # broken build
"BRAIN" # broken build
"brainGraph" # build is broken
"BrainStars" # broken build
"brms" # build is broken
"BrowserViz" # broken build
"BrowserVizDemo" # broken build
"brr" # broken build
@@ -929,14 +937,17 @@ let
"cnvGSA" # broken build
"CNVPanelizer" # depends on broken cn.mops-1.15.1
"CNVrd2" # depends on broken package Rsamtools-1.21.8
"coalescentMCMC" # depends on broken package Biostrings-2.38.2
"cobindR" # depends on broken package Rsamtools-1.21.8
"CoCiteStats" # Build Is Broken
"codelink" # broken build
"CODEX" # depends on broken package Rsamtools-1.21.8
"coefplot" # build is broken
"cogena" # broken build
"COHCAP" # build is broken
"colorscience"
"coMET" # depends on broken package Rsamtools-1.21.8
"CommT" # depends on broken package Biostrings-2.38.2
"compcodeR" # broken build
"compendiumdb" # broken build
"compEpiTools" # depends on broken package topGO-2.21.0
@@ -947,6 +958,7 @@ let
"convert" # broken build
"convevol" # broken build
"copa" # broken build
"CopulaDTA" # depends on broken package r-rstan-2.8.2
"CopyNumber450k" # depends on broken package Rsamtools-1.21.8
"copynumber" # broken build
"CopywriteR" # depends on broken package Rsamtools-1.21.8
@@ -962,6 +974,7 @@ let
"cpgen" # depends on broken package r-pedigreemm-0.3-3
"cplexAPI" # build is broken
"cpvSNP" # depends on broken package Rsamtools-1.21.8
"cquad" # depends on broken package car-2.1-1
"creditr" # broken build
"CRImage" # broken build
"CRISPRseek" # depends on broken package Rsamtools-1.21.8
@@ -1013,6 +1026,7 @@ let
"derfinder" # depends on broken package Rsamtools-1.21.8
"derfinderHelper" # broken build
"derfinderPlot" # depends on broken package Rsamtools-1.21.8
"DescribeDisplay" # build is broken
"DESeq2" # broken build
"DESeq" # broken build
"DESP" # broken build
@@ -1030,6 +1044,7 @@ let
"discSurv" # depends on broken package nlopt-2.4.2
"DistatisR" # depends on broken package nlopt-2.4.2
"diveRsity" # depends on broken package nlopt-2.4.2
"DJL" # depends on broken package r-car-2.1-0
"DMRcaller" # broken build
"DMRcate" # depends on broken package Rsamtools-1.21.8
"DMRforPairs" # depends on broken package Rsamtools-1.21.8
@@ -1056,6 +1071,7 @@ let
"EBarrays" # broken build
"EBcoexpress" # broken build
"EBImage" # broken build
"ecd" # depends on broken package r-polynom-1.3-8
"ecolitk" # broken build
"EDASeq" # depends on broken package Rsamtools-1.21.8
"EDDA" # broken build
@@ -1090,6 +1106,7 @@ let
"erpR" # depends on broken package rpanel-1.1-3
"ESKNN" # depends on broken package r-caret-6.0-52
"eulerian" # broken build
"euroMix" # build is broken
"evobiR" # broken build
"evolqg" # broken build
"ExiMiR" # depends on broken package affyio-1.37.0
@@ -1099,6 +1116,7 @@ let
"ExpressionView" # depends on broken package Category-2.35.1
"extRemes" # depends on broken package nlopt-2.4.2
"ez" # depends on broken package nlopt-2.4.2
"ezec" # depends on broken package drc-2.5
"fabia" # broken build
"facopy" # depends on broken package nlopt-2.4.2
"factDesign" # broken build
@@ -1156,6 +1174,7 @@ let
"frma" # depends on broken package affyio-1.37.0
"frmaTools" # depends on broken package affyio-1.37.0
"frmqa" # broken build
"FSA" # depends on broken package car-2.1-1
"fscaret" # depends on broken package nlopt-2.4.2
"fulltext" # broken build
"FunciSNP" # depends on broken package snpStats-1.19.0
@@ -1223,6 +1242,8 @@ let
"gfcanalysis" # broken build
"GGBase" # depends on broken package snpStats-1.19.0
"ggbio" # depends on broken package Rsamtools-1.21.8
"ggsubplot" # build is broken
"ggtern" # build is broken
"GGtools" # depends on broken package snpStats-1.19.0
"ggtree" # broken build
"gimme" # depends on broken package nlopt-2.4.2
@@ -1266,6 +1287,7 @@ let
"gRc" # broken build
"GreyListChIP" # depends on broken package Rsamtools-1.21.8
"gridDebug" # broken build
"gridGraphics" # build is broken
"gridGraphviz" # broken build
"gRim" # broken build
"groHMM" # depends on broken package Rsamtools-1.21.8
@@ -1333,6 +1355,7 @@ let
"iBMQ" # broken build
"iccbeta" # depends on broken package nlopt-2.4.2
"iCheck" # depends on broken package r-affy-1.48.0
"iClick" # depends on broken package rugarch-1.3-6
"IdeoViz" # depends on broken package Rsamtools-1.21.8
"idiogram" # broken build
"IdMappingAnalysis" # broken build
@@ -1444,6 +1467,7 @@ let
"maPredictDSC" # depends on broken package nlopt-2.4.2
"mar1s" # broken build
"marked" # depends on broken package nlopt-2.4.2
"markophylo" # depends on broken package r-Biostrings-2.38.2
"maSigPro" # broken build
"maskBAD" # depends on broken package affyio-1.37.0
"massiR" # broken build
@@ -1455,6 +1479,7 @@ let
"mbest" # depends on broken package nlopt-2.4.2
"MBmca" # depends on broken nloptr-1.0.4
"mBPCR" # depends on broken package affyio-1.37.0
"mBvs" # build is broken
"mcaGUI" # depends on broken package Rsamtools-1.21.8
"MCRestimate" # build is broken
"mdgsa" # build is broken
@@ -1482,6 +1507,7 @@ let
"metagene" # depends on broken package Rsamtools-1.21.8
"metagenomeFeatures" # depends on broken package r-Biobase-2.30.0
"metagenomeSeq" # broken build
"metaheur" # depends on broken package r-preprocomb-0.2.0
"MetaLandSim" # broken build
"metamisc"
"metaMix" # build is broken
@@ -1531,6 +1557,7 @@ let
"mitoODE" # build is broken
"mixAK" # depends on broken package nlopt-2.4.2
"MixedPoisson" # broken build
"MIXFIM" # build is broken
"mixlm" # depends on broken package nlopt-2.4.2
"MixMAP" # depends on broken package nlopt-2.4.2
"MLInterfaces" # broken build
@@ -1607,6 +1634,7 @@ let
"netbenchmark" # build is broken
"netClass" # broken build
"nethet" # broken build
"NetPreProc" # depends on broken package graph-1.48.0
"netresponse" # broken build
"NetSAM" # broken build
"nettools" # depends on broken package WGCNA-1.47
@@ -1631,6 +1659,7 @@ let
"oligoClasses" # depends on broken package affyio-1.37.0
"oligo" # depends on broken package affyio-1.37.0
"OmicCircos" # broken build
"omics" # depends on broken package lme4-1.1-10
"OmicsMarkeR" # depends on broken package nlopt-2.4.2
"OncoSimulR" # broken build
"oneChannelGUI" # depends on broken package affyio-1.37.0
@@ -1707,7 +1736,9 @@ let
"pequod" # depends on broken package nlopt-2.4.2
"PerfMeas" # broken build
"PGA" # depends on broken package Rsamtools-1.21.8
"pglm" # depends on broken package car-2.1-1
"PGSEA" # depends on broken package annaffy-1.41.1
"phangorn" # depends on broken package Biostrings-2.38.2
"PharmacoGx"
"phenoDist" # depends on broken package Category-2.35.1
"phenoTest" # depends on broken package Category-2.35.1
@@ -1716,6 +1747,7 @@ let
"phreeqc" # broken build
"phylocurve" # depends on broken package nlopt-2.4.2
"phyloseq" # broken build
"PhySortR" # depends on broken package phytools-0.5-10
"phytools" # broken build
"piano" # broken build
"PICS" # depends on broken package Rsamtools-1.21.8
@@ -1727,6 +1759,7 @@ let
"plfMA" # broken build
"plgem" # broken build
"plier" # depends on broken package affyio-1.37.0
"plm" # depends on broken package car-2.1-1
"PLPE" # broken build
"plrs" # broken build
"plsRbeta" # depends on broken package nlopt-2.4.2
@@ -1740,6 +1773,8 @@ let
"Polyfit" # broken build
"polynom" # broken build
"pomp" # depends on broken package nlopt-2.4.2
"poppr" # depends on broken package Biostrings-2.38.2
"popprxl" # depends on broken package Biostrings-2.38.2
"ppiPre" # depends on broken package GOSemSim-1.27.3
"ppiStats" # depends on broken package Category-2.35.1
"prada" # broken build
@@ -1810,6 +1845,7 @@ let
"RAM" # broken build
"RamiGO" # depends on broken package RCytoscape-1.19.0
"randPack" # broken build
"RANKS" # depends on broken package graph-1.48.0
"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
"RAPIDR" # depends on broken package Rsamtools-1.21.8
"RareVariantVis" # depends on broken VariantAnnotation-1.15.19
@@ -1830,6 +1866,7 @@ let
"rCGH" # depends on broken package r-affy-1.47.1
"Rchemcpp" # depends on broken package ChemmineR-2.21.7
"rchess" # depends on broken package r-V8-0.9
"Rchoice" # depends on broken package car-2.1
"RchyOptimyx" # broken build
"Rcmdr" # depends on broken package nlopt-2.4.2
"RcmdrMisc" # depends on broken package nlopt-2.4.2
@@ -1898,6 +1935,7 @@ let
"regioneR" # depends on broken package Rsamtools-1.21.8
"regionReport" # depends on broken package Rsamtools-1.21.8
"regRSM" # broken build
"REndo" # depends on broken package AER-1.2-4
"repijson" # depends on broken package V8-0.6
"Repitools" # depends on broken package affyio-1.37.0
"ReportingTools" # depends on broken package Category-2.35.1
@@ -1935,6 +1973,7 @@ let
"rminer" # depends on broken package nlopt-2.4.2
"RmiR" # Build Is Broken
"Rmosek" # build is broken
"rmumps" # build is broken
"RMySQL" # broken build
"RNAinteract" # depends on broken package Category-2.35.1
"RNAither" # depends on broken package nlopt-2.4.2
@@ -1979,6 +2018,7 @@ let
"RSeed" # broken build
"rSFFreader" # depends on broken package Rsamtools-1.21.8
"Rsomoclu"
"rstan" # build is broken
"RStoolbox" # depends on broken package r-caret-6.0-52
"Rsubread" # Build Is Broken
"RSVSim" # depends on broken package Rsamtools-1.21.8
@@ -2040,6 +2080,7 @@ let
"SeqFeatR" # broken build
"SeqGrapheR" # Build Is Broken
"SeqGSEA" # broken build
"seqHMM" # depends on broken package nloptr-1.0.4
"seqPattern" # broken build
"seqplots" # depends on broken package Rsamtools-1.21.8
"seqTools" # build is broken
@@ -2112,6 +2153,7 @@ let
"spliceR" # depends on broken package Rsamtools-1.21.8
"spliceSites" # broken build
"SplicingGraphs" # depends on broken package Rsamtools-1.21.8
"splm" # depends on broken package car-2.1-1
"spocc" # depends on broken package V8-0.6
"spoccutils" # depends on broken spocc-0.3.0
"spsann" # depends on broken package r-pedometrics-0.6-2
@@ -2142,9 +2184,12 @@ let
"Surrogate" # depends on broken package nlopt-2.4.2
"Sushi" # broken build
"sva" # broken build
"svglite" # depends on broken package gdtools-0.0.6
"SVM2CRM" # depends on broken package Rsamtools-1.21.8
"sybilSBML" # build is broken
"synapter" # depends on broken package affyio-1.37.0
"synchronicity" # build is broken
"synthpop" # build is broken
"systemfit" # depends on broken package nlopt-2.4.2
"systemPipeR" # depends on broken package AnnotationForge-1.11.3
"TargetSearch" # depends on broken package mzR-2.3.1
@@ -2157,12 +2202,14 @@ let
"TDMR" # depends on broken package nlopt-2.4.2
"TED" # broken build
"TEQC" # depends on broken package Rsamtools-1.21.8
"TextoMineR" # depends on broken package FactoMineR-1.31.4
"TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
"tigerstats" # depends on broken package nlopt-2.4.2
"tigre" # broken build
"tilingArray" # depends on broken package affyio-1.37.0
"timecourse" # broken build
"timeSeq" # broken build
"timetree" # depends on broken package Biostrings-2.38.2
"TIN" # depends on broken package WGCNA-1.47
"TitanCNA" # depends on broken package Rsamtools-1.21.8
"TKF" # broken build
@@ -2180,6 +2227,7 @@ let
"tRanslatome" # depends on broken package GOSemSim-1.27.3
"TransView" # depends on broken package Rsamtools-1.21.8
"traseR"
"treescape" # depends on broken package Biostrings-2.38.2
"triform" # broken build
"trigger" # broken build
"TriMatch" # depends on broken package nlopt-2.4.2
@@ -2206,6 +2254,7 @@ let
"V8" # build is broken
"VanillaICE" # depends on broken package affyio-1.37.0
"varComp" # depends on broken package r-lme4-1.1-9
"varian" # build is broken
"variancePartition" # depends on broken package lme4-1.1-8
"VariantAnnotation" # depends on broken package Rsamtools-1.21.8
"VariantFiltering" # depends on broken package Rsamtools-1.21.8
@@ -2223,6 +2272,7 @@ let
"wavClusteR" # depends on broken package Rsamtools-1.21.8
"waveTiling" # depends on broken package affyio-1.37.0
"webbioc" # depends on broken package affyio-1.37.0
"webp" # build is broken
"wfe" # depends on broken package nlopt-2.4.2
"WGCNA" # build is broken
"wgsea" # depends on broken package snpStats-1.19.0
@@ -2236,6 +2286,7 @@ let
"xps" # build is broken
"XVector" # broken build
"yaqcaffy" # depends on broken package affyio-1.37.0
"yCrypticRNAs" # depends on broken package biomaRt-2.26.1
"ZeligChoice" # depends on broken package r-AER-1.2-4
"Zelig" # depends on broken package r-AER-1.2-4
"ZeligMultilevel" # depends on broken package nlopt-2.4.2
pkgs/development/r-modules/generic-builder.nix
+6 -2
View File
@@ -1,10 +1,14 @@
{ stdenv, R, xvfb_run, utillinux }:
{ stdenv, R, libcxx, xvfb_run, utillinux, Cocoa, Foundation }:
{ name, buildInputs ? [], ... } @ attrs:
stdenv.mkDerivation ({
buildInputs = buildInputs ++ [R] ++
stdenv.lib.optionals attrs.requireX [utillinux xvfb_run];
stdenv.lib.optionals attrs.requireX [utillinux xvfb_run] ++
stdenv.lib.optionals stdenv.isDarwin [Cocoa Foundation];
NIX_CFLAGS_COMPILE =
stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";
configurePhase = ''
runHook preConfigure