Merge remote-tracking branch 'origin/master' into closure-size

2015-11-25 21:31:09 +01:00
parent 8a664fd5bc b34a6c96ee
commit a412927924
659 changed files with 46562 additions and 13611 deletions
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -11,7 +11,10 @@ let
  #
  # some packages, e.g. cncaGUI, require X running while installation,
  # so that we use xvfb-run if requireX is true.
-  mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({
+  mkDerive = {mkHomepage, mkUrls}: args:
+      # XXX: not ideal ("2.2" would match "2.22") but sufficient
+      assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R));
+      lib.makeOverridable ({
        name, version, sha256,
        depends ? [],
        doCheck ? true,
@@ -22,12 +25,12 @@ let
    name = "${name}-${version}";
    src = fetchurl {
      inherit sha256;
-      urls = mkUrls { inherit name version; };
+      urls = mkUrls (args // { inherit name version; });
    };
    inherit doCheck requireX;
    propagatedBuildInputs = depends;
    nativeBuildInputs = depends;
-    meta.homepage = mkHomepage name;
+    meta.homepage = mkHomepage (args // { inherit name; });
    meta.platforms = R.meta.platforms;
    meta.hydraPlatforms = hydraPlatforms;
    meta.broken = broken;
@@ -37,18 +40,15 @@ let
  # from the name, version, sha256, and optional per-package arguments above
  #
  deriveBioc = mkDerive {
-    mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/";
-    mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
+    mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html";
+    mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ];
  };
  deriveCran = mkDerive {
-    mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
-    mkUrls = {name, version}: [
-      "mirror://cran/src/contrib/${name}_${version}.tar.gz"
-      "mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
-    ];
+    mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
+    mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
  };
  deriveIRkernel = mkDerive {
-    mkHomepage = name: "http://irkernel.github.io/";
+    mkHomepage = {name}: "https://irkernel.github.io/";
    mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ];
  };

@@ -235,7 +235,6 @@ let
    cairoDevice = [ pkgs.gtk2 ];
    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
    Cardinal = [ pkgs.which ];
-    CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
    chebpol = [ pkgs.fftw ];
    ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
    cit = [ pkgs.gsl ];
@@ -285,7 +284,6 @@ let
    rapportools = [ pkgs.which ];
    rapport = [ pkgs.which ];
    rbamtools = [ pkgs.zlib ];
-    RCA = [ pkgs.gmp ];
    rcdd = [ pkgs.gmp ];
    RcppCNPy = [ pkgs.zlib ];
    RcppGSL = [ pkgs.gsl ];
@@ -316,7 +314,6 @@ let
    Rpoppler = [ pkgs.poppler ];
    RPostgreSQL = [ pkgs.postgresql ];
    RProtoBuf = [ pkgs.protobuf ];
-    rpud = [ pkgs.linuxPackages.nvidia_x11 ];
    rPython = [ pkgs.python ];
    RSclient = [ pkgs.openssl ];
    Rserve = [ pkgs.openssl ];
@@ -368,7 +365,6 @@ let
    qtpaint = [ pkgs.cmake ];
    qtbase = [ pkgs.cmake pkgs.perl ];
    gmatrix = [ pkgs.cudatoolkit ];
-    WideLM = [ pkgs.cudatoolkit ];
    RCurl = [ pkgs.curl ];
    R2SWF = [ pkgs.pkgconfig ];
    rggobi = [ pkgs.pkgconfig ];
@@ -392,12 +388,10 @@ let
    qtutils = [ pkgs.qt4 ];
    ecoretriever = [ pkgs.which ];
    tcltk2 = [ pkgs.tcl pkgs.tk ];
-    tikzDevice = [ pkgs.which pkgs.texLive ];
+    tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
    rPython = [ pkgs.which ];
-    CARramps = [ pkgs.which pkgs.cudatoolkit ];
    gridGraphics = [ pkgs.which ];
    gputools = [ pkgs.which pkgs.cudatoolkit ];
-    rpud = [ pkgs.which pkgs.cudatoolkit ];
    adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
    PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
    dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
@@ -511,7 +505,6 @@ let
    "JGR"
    "KappaGUI"
    "likeLTD"
-    "loe"
    "logmult"
    "LS2Wstat"
    "MAR1"
@@ -765,28 +758,37 @@ let
    "backShift" # broken build
    "BAGS" # build is broken
    "ballgown" # depends on broken package Rsamtools-1.21.8
+    "bamdit"
    "bamsignals" # build is broken
+    "BANOVA"
    "bapred" # depends on broken package r-lme4-1.1-9
    "bartMachine" # depends on broken package nlopt-2.4.2
    "Basic4Cseq" # depends on broken package Rsamtools-1.21.8
+    "bayescount"
    "bayesDem" # depends on broken package nlopt-2.4.2
    "bayesLife" # depends on broken package nlopt-2.4.2
+    "BayesMed"
+    "bayesmix"
    "BayesPeak" # broken build
    "bayesPop" # depends on broken package nlopt-2.4.2
    "Bayesthresh" # depends on broken package nlopt-2.4.2
    "bayou" # broken build
    "baySeq" # broken build
+    "BaySIC"
    "BBCAnalyzer" # depends on broken package r-Rsamtools-1.21.18
    "BBRecapture" # depends on broken package nlopt-2.4.2
    "BCA" # depends on broken package nlopt-2.4.2
    "BcDiag" # broken build
    "BCRANK" # broken build
+    "bcrypt"
    "beadarray" # broken build
    "beadarrayFilter" # broken build
    "beadarrayMSV" # broken build
    "beadarraySNP" # broken build
    "BEAT" # depends on broken package Rsamtools-1.21.8
+    "BEDMatrix" # broken build
    "bedr" # broken build
+    "BEST"
    "betr" # broken build
    "bgmm" # depends on broken package nlopt-2.4.2
    "bgx" # depends on broken package affyio-1.37.0
@@ -797,6 +799,7 @@ let
    "bigmemoryExtras" # broken build
    "bioassayR" # broken build
    "Biobase" # broken build
+    "biobroom" # depends on broken package r-Biobase-2.30.0
    "BiocCaseStudies" # broken build
    "BiocCheck" # broken build
    "BiocGenerics" # broken build
@@ -826,9 +829,11 @@ let
    "blme" # depends on broken package nlopt-2.4.2
    "bmd" # depends on broken package nlopt-2.4.2
    "bmem" # depends on broken package nlopt-2.4.2
+    "bmeta" # depends on broken package r-R2jags-0.5-7
    "BMhyd" # broken build
    "bnclassify" # broken build
    "bootnet" # depends on broken package nlopt-2.4.2
+    "boral"
    "boss" # depends on broken package nlopt-2.4.2
    "BradleyTerry2" # depends on broken package nlopt-2.4.2
    "BrailleR" # broken build
@@ -840,6 +845,7 @@ let
    "BRugs" # build is broken
    "BSgenome" # depends on broken package Rsamtools-1.21.8
    "bsseq" # broken build
+    "BTSPAS"
    "BubbleTree" # depends on broken package r-biovizBase-1.17.2
    "bumphunter" # depends on broken package Rsamtools-1.21.8
    "CADFtest" # depends on broken package nlopt-2.4.2
@@ -864,6 +870,7 @@ let
    "categoryCompare" # depends on broken package Category-2.35.1
    "Causata" # broken build
    "CCpop" # depends on broken package nlopt-2.4.2
+    "CCTpack"
    "cdcfluview" # broken build
    "cellHTS2" # depends on broken package Category-2.35.1
    "cellHTS" # broken build
@@ -893,8 +900,8 @@ let
    "chroGPS" # broken build
    "chromDraw" # broken build
    "ChromHeatMap" # depends on broken package Rsamtools-1.21.8
-    "Claddis" # broken build
    "classGraph" # broken build
+    "classify"
    "ClassifyR" # broken build
    "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8
    "cleaver" # broken build
@@ -917,6 +924,7 @@ let
    "CNORfeeder" # broken build
    "CNORfuzzy" # depends on broken package nlopt-2.4.2
    "CNORode" # broken build
+    "CNPBayes" # depends on broken package r-BiocGenerics-0.16.1
    "CNTools" # broken build
    "cnvGSA" # broken build
    "CNVPanelizer" # depends on broken cn.mops-1.15.1
@@ -959,6 +967,7 @@ let
    "CRISPRseek" # depends on broken package Rsamtools-1.21.8
    "crlmm" # depends on broken package affyio-1.37.0
    "crmn" # broken build
+    "crmPack" # depends on broken package r-rjags-4-4
    "Crossover" # Build Is Broken
    "CrypticIBDcheck" # depends on broken package nlopt-2.4.2
    "CSAR" # broken build
@@ -975,13 +984,17 @@ let
    "dagbag" # build is broken
    "dagLogo" # depends on broken package Rsamtools-1.21.8
    "DAMisc" # depends on broken package nlopt-2.4.2
+    "DAPAR" # depends on broken package r-imputeLCMD-2.0
    "DASiR" # broken build
    "datafsm" # depends on broken package r-caret-6.0-52
    "DBChIP" # broken build
    "dbConnect" # broken build
    "DBKGrad" # depends on broken package rpanel-1.1-3
    "dcGOR" # broken build
+    "DChIPRep" # depends on broken package r-DESeq2-1.10.0
+    "dcmle"
    "ddCt" # broken build
+    "DDD" # depends on broken package r-phytools-0.5-00
    "ddgraph" # broken build
    "ddst" # broken build
    "DECIPHER" # broken build
@@ -1038,6 +1051,7 @@ let
    "dyebias" # broken build
    "dynlm" # depends on broken package nlopt-2.4.2
    "easyanova" # depends on broken package nlopt-2.4.2
+    "EasyMARK"
    "easyRNASeq" # depends on broken package Rsamtools-1.21.8
    "EBarrays" # broken build
    "EBcoexpress" # broken build
@@ -1103,6 +1117,7 @@ let
    "FIACH" # broken build
    "FindMyFriends" # broken build
    "FISHalyseR" # broken build
+    "fishmethods" # depends on broken package r-lme4-1.1-10
    "flagme" # depends on broken package mzR-2.3.1
    "flipflop" # broken build
    "flowBeads" # broken build
@@ -1114,6 +1129,7 @@ let
    "flowClust" # broken build
    "flowCore" # broken build
    "flowDensity" # depends on broken package nlopt-2.4.2
+    "flowDiv" # depends on broken package r-flowCore-1.35.11
    "flowFit" # broken build
    "flowFP" # broken build
    "flowMatch" # broken build
@@ -1144,6 +1160,7 @@ let
    "fulltext" # broken build
    "FunciSNP" # depends on broken package snpStats-1.19.0
    "FunctionalNetworks" # Build Is Broken
+    "funcy" # depends on broken package r-car-2.1-0
    "fxregime" # depends on broken package nlopt-2.4.2
    "gaga" # broken build
    "gage" # broken build
@@ -1158,7 +1175,10 @@ let
    "gcmr" # depends on broken package nlopt-2.4.2
    "gcrma" # depends on broken package affyio-1.37.0
    "GDAtools" # depends on broken package nlopt-2.4.2
+    "gdtools" # broken build
+    "gemtc"
    "GeneAnswers" # broken build
+    "GeneBreak" # depends on broken package r-CGHbase-1.30.0
    "GENE_E" # depends on broken package rhdf5-2.13.1
    "GeneExpressionSignature" # depends on broken package annaffy-1.41.1
    "genefilter" # broken build
@@ -1196,6 +1216,7 @@ let
    "GEOquery" # broken build
    "GEOsearch" # broken build
    "GEOsubmission" # depends on broken package affyio-1.37.0
+    "GERGM"
    "gespeR" # depends on broken package Category-2.35.1
    "GEWIST" # depends on broken package nlopt-2.4.2
    "GExMap" # broken build
@@ -1212,6 +1233,7 @@ let
    "gmapR" # depends on broken package Rsamtools-1.21.8
    "gmatrix" # depends on broken package cudatoolkit-5.5.22
    "gMCP" # build is broken
+    "gmum_r" # broken build
    "GOexpress" # broken build
    "GOFunction" # build is broken
    "GOGANPA" # depends on broken package WGCNA-1.47
@@ -1221,11 +1243,13 @@ let
    "GOSemSim" # Build Is Broken
    "goseq" # build is broken
    "GOSim" # depends on broken package topGO-2.21.0
+    "Goslate" # depends on broken package r-PythonInR-0.1-2
    "GOstats" # depends on broken package AnnotationForge-1.11.3
    "GOTHiC" # depends on broken package Rsamtools-1.21.8
    "goTools" # build is broken
    "GPC" # broken build
    "gplm" # depends on broken package nlopt-2.4.2
+    "gpuR" # depends on GPU-specific header files
    "gputools" # depends on broken package cudatoolkit-5.5.22
    "gQTLBase" # depends on broken package r-GenomicFiles-1.5.8
    "gQTLstats" # depends on broken package snpStats-1.19.0
@@ -1253,6 +1277,7 @@ let
    "GSRI" # broken build
    "GSVA" # broken build
    "GUIDE" # depends on broken package rpanel-1.1-3
+    "GUIDEseq" # depends on broken package r-BiocGenerics-0.16.1
    "GUIProfiler" # broken build
    "Guitar" # depends on broken package r-GenomicAlignments-1.5.18
    "Gviz" # depends on broken package Rsamtools-1.21.8
@@ -1272,6 +1297,7 @@ let
    "HEM" # broken build
    "heplots" # depends on broken package nlopt-2.4.2
    "hiAnnotator" # depends on broken package Rsamtools-1.21.8
+    "HiCfeat" # depends on broken package r-GenomeInfoDb-1.5.16
    "HiDimMaxStable" # broken build
    "hierGWAS"
    "HierO" # Build Is Broken
@@ -1285,6 +1311,7 @@ let
    "HiTC" # depends on broken package Rsamtools-1.21.8
    "HLMdiag" # depends on broken package nlopt-2.4.2
    "HMMcopy" # broken build
+    "homomorpheR" # broken build
    "hopach" # broken build
    "hpcwld" # broken build
    "hpoPlot" # broken build
@@ -1305,15 +1332,16 @@ let
    "ibh" # build is broken
    "iBMQ" # broken build
    "iccbeta" # depends on broken package nlopt-2.4.2
+    "iCheck" # depends on broken package r-affy-1.48.0
    "IdeoViz" # depends on broken package Rsamtools-1.21.8
    "idiogram" # broken build
    "IdMappingAnalysis" # broken build
    "IdMappingRetrieval" # broken build
    "idm" # broken build
    "ifaTools" # depends on broken package r-OpenMx-2.2.6
-    "iFes" # depends on broken package cudatoolkit-5.5.22
    "imageHTS" # depends on broken package Category-2.35.1
    "imager" # broken build
+    "Imetagene" # depends on broken package r-metagene-2.2.0
    "immer" # depends on broken package r-sirt-1.8-9
    "immunoClust" # build is broken
    "imputeLCMD" # broken build
@@ -1342,11 +1370,14 @@ let
    "IsoGene" # depends on broken package affyio-1.37.0
    "IsoGeneGUI" # depends on broken package affyio-1.37.0
    "ITALICS" # depends on broken package oligo-1.33.0
+    "ITEMAN" # depends on broken package r-car-2.1-0
    "iteRates" # broken build
    "iterativeBMA" # broken build
    "iterpc" # broken build
+    "IUPS"
    "IVAS" # depends on broken package nlopt-2.4.2
    "ivpack" # depends on broken package nlopt-2.4.2
+    "jagsUI"
    "JAGUAR" # depends on broken package nlopt-2.4.2
    "jetset"
    "jmosaics" # broken build
@@ -1364,6 +1395,8 @@ let
    "ktspair" # broken build
    "kza" # broken build
    "kzft" # broken build
+    "LANDD" # depends on broken package r-GOSemSim-1.27.4
+    "LaplaceDeconv" # depends on broken package r-orthopolynom-1.0-5
    "lapmix" # broken build
    "lawn" # depends on broken package V8-0.6
    "ldamatch" # broken build
@@ -1375,9 +1408,12 @@ let
    "lessR" # depends on broken package nlopt-2.4.2
    "lfe" # build is broken
    "lgcp" # depends on broken package rpanel-1.1-3
+    "Libra" # broken build
    "limmaGUI" # depends on broken package affyio-1.37.0
    "LinRegInteractive" # depends on broken package rpanel-1.1-3
    "LiquidAssociation" # build is broken
+    "lira"
+    "littler" # broken build
    "lmdme" # build is broken
    "lme4" # depends on broken package nlopt-2.4.2
    "LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
@@ -1385,6 +1421,7 @@ let
    "LMGene" # depends on broken package affyio-1.37.0
    "lmSupport" # depends on broken package nlopt-2.4.2
    "LogisticDx" # depends on broken package nlopt-2.4.2
+    "LOGIT" # depends on broken package r-caret-6.0-58
    "logitT" # depends on broken package affyio-1.37.0
    "LOLA" # broken build
    "longpower" # depends on broken package nlopt-2.4.2
@@ -1397,6 +1434,7 @@ let
    "M3D" # depends on broken package Rsamtools-1.21.8
    "maanova" # broken build
    "macat" # broken build
+    "maGUI" # depends on broken package r-affy-1.47.1
    "maigesPack" # broken build
    "MAIT" # depends on broken package nlopt-2.4.2
    "makecdfenv" # depends on broken package affyio-1.37.0
@@ -1420,6 +1458,7 @@ let
    "mcaGUI" # depends on broken package Rsamtools-1.21.8
    "MCRestimate" # build is broken
    "mdgsa" # build is broken
+    "MEAL" # depends on broken package r-Biobase-2.30.0
    "meboot" # depends on broken package nlopt-2.4.2
    "medflex" # depends on broken package r-car-2.1-0
    "mediation" # depends on broken package r-lme4-1.1-8
@@ -1441,10 +1480,13 @@ let
    "MetaDE" # broken build
    "metagear" # build is broken
    "metagene" # depends on broken package Rsamtools-1.21.8
+    "metagenomeFeatures" # depends on broken package r-Biobase-2.30.0
    "metagenomeSeq" # broken build
    "MetaLandSim" # broken build
+    "metamisc"
    "metaMix" # build is broken
    "metaMS" # depends on broken package mzR-2.3.1
+    "MetaPath" # depends on broken package r-Biobase-2.29.1
    "metaplus" # depends on broken package nlopt-2.4.2
    "metaSEM" # depends on broken package OpenMx-2.2.4
    "metaSeq" # broken build
@@ -1478,6 +1520,7 @@ let
    "MinimumDistance" # depends on broken package affyio-1.37.0
    "MiPP" # broken build
    "MiRaGE" # broken build
+    "miRcomp" # depends on broken package r-Biobase-2.30.0
    "mirIntegrator" # build is broken
    "miRLAB" # broken build
    "miRNAtap" # broken build
@@ -1491,6 +1534,7 @@ let
    "mixlm" # depends on broken package nlopt-2.4.2
    "MixMAP" # depends on broken package nlopt-2.4.2
    "MLInterfaces" # broken build
+    "mlma" # depends on broken package r-lme4-1.1-10
    "mlmRev" # depends on broken package nlopt-2.4.2
    "MLP" # depends on broken package affyio-1.37.0
    "MLSeq" # depends on broken package nlopt-2.4.2
@@ -1502,10 +1546,13 @@ let
    "mmnet" # broken build
    "MmPalateMiRNA" # depends on broken package affyio-1.37.0
    "mogsa" # broken build
+    "molaR" # depends on broken package r-geomorph-2.1.7-1
    "mongolite" # build is broken
    "monocle" # build is broken
    "monogeneaGM" # broken build
+    "MonoPhy" # depends on broken package r-phytools-0.5-00
    "MoPS" # broken build
+    "morse"
    "mosaic" # depends on broken package nlopt-2.4.2
    "mosaics" # broken build
    "motifbreakR" # depends on broken package r-BSgenome-1.37.5
@@ -1548,7 +1595,9 @@ let
    "mzID" # broken build
    "mzR" # build is broken
    "NanoStringDiff" # broken build
+    "NanoStringNorm" # depends on broken package r-vsn-3.38.0
    "NanoStringQCPro" # build is broken
+    "NAPPA" # depends on broken package r-vsn-3.38.0
    "NarrowPeaks" # broken build
    "nCal" # depends on broken package nlopt-2.4.2
    "ncdfFlow" # build is broken
@@ -1561,10 +1610,10 @@ let
    "netresponse" # broken build
    "NetSAM" # broken build
    "nettools" # depends on broken package WGCNA-1.47
-    "netweavers" # broken build
    "NGScopy"
    "nhanesA" # broken build
    "NHPoisson" # depends on broken package nlopt-2.4.2
+    "NIPTeR" # depends on broken package r-Rsamtools-1.21.18
    "nloptr" # depends on broken package nlopt-2.4.2
    "nlsem" # broken build
    "nlts" # broken build
@@ -1590,6 +1639,7 @@ let
    "opencpu" # broken build
    "openCyto" # depends on broken package ncdfFlow-2.15.2
    "OpenMx" # build is broken
+    "openssl"
    "OperaMate" # depends on broken package Category-2.35.1
    "oposSOM" # broken build
    "optBiomarker" # depends on broken package rpanel-1.1-3
@@ -1642,6 +1692,7 @@ let
    "pcalg" # broken build
    "pcaMethods" # broken build
    "PCGSE" # broken build
+    "pcnetmeta"
    "pcot2" # broken build
    "PCpheno" # depends on broken package Category-2.35.1
    "PCS" # broken build
@@ -1655,7 +1706,6 @@ let
    "pepStat" # broken build
    "pequod" # depends on broken package nlopt-2.4.2
    "PerfMeas" # broken build
-    "permGPU" # build is broken
    "PGA" # depends on broken package Rsamtools-1.21.8
    "PGSEA" # depends on broken package annaffy-1.41.1
    "PharmacoGx"
@@ -1666,10 +1716,10 @@ let
    "phreeqc" # broken build
    "phylocurve" # depends on broken package nlopt-2.4.2
    "phyloseq" # broken build
-    "phyloTop" # depends on broken package nlopt-2.4.2
    "phytools" # broken build
    "piano" # broken build
    "PICS" # depends on broken package Rsamtools-1.21.8
+    "piecewiseSEM" # depends on broken package r-lme4-1.1-10
    "PING" # depends on broken package Rsamtools-1.21.8
    "pkgDepTools" # broken build
    "plateCore" # depends on broken package ncdfFlow-2.15.2
@@ -1689,7 +1739,6 @@ let
    "polyester" # broken build
    "Polyfit" # broken build
    "polynom" # broken build
-    "polytomous" # depends on broken package nlopt-2.4.2
    "pomp" # depends on broken package nlopt-2.4.2
    "ppiPre" # depends on broken package GOSemSim-1.27.3
    "ppiStats" # depends on broken package Category-2.35.1
@@ -1698,6 +1747,8 @@ let
    "PREDA" # broken build
    "predictionet" # broken build
    "predictmeans" # depends on broken package nlopt-2.4.2
+    "preprocomb" # depends on broken package r-caret-6.0-58
+    "prevalence"
    "pRF" # broken build
    "prLogistic" # depends on broken package nlopt-2.4.2
    "proBAMr" # depends on broken package Rsamtools-1.21.8
@@ -1707,6 +1758,7 @@ let
    "PROMISE" # broken build
    "PROPER" # broken build
    "propOverlap" # broken build
+    "Prostar" # depends on broken package r-imputeLCMD-2.0
    "prot2D" # broken build
    "ProteomicsAnnotationHubData" # depends on broken package r-AnnotationHub-2.1.40
    "proteoQC" # depends on broken package affyio-1.37.0
@@ -1718,8 +1770,10 @@ let
    "PSICQUIC" # broken build
    "ptw" # depends on broken nloptr-1.0.4
    "puma" # depends on broken package affyio-1.37.0
+    "PurBayes"
    "purge" # depends on broken package r-lme4-1.1-9
    "pvac" # depends on broken package affyio-1.37.0
+    "PVAClone"
    "pvca" # depends on broken package nlopt-2.4.2
    "Pviz" # depends on broken package Rsamtools-1.21.8
    "PWMEnrich" # broken build
@@ -1744,12 +1798,12 @@ let
    "QuasiSeq" # broken build
    "QuasR" # depends on broken package Rsamtools-1.21.8
    "qusage" # broken build
+    "R2jags"
    "R2STATS" # depends on broken package nlopt-2.4.2
    "R3CPET" # depends on broken package Rsamtools-1.21.8
    "r3Cseq" # depends on broken package Rsamtools-1.21.8
    "R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8
    "RADami" # broken build
-    "radiant" # depends on broken package nlopt-2.4.2
    "rain" # broken build
    "raincpc" # build is broken
    "rainfreq" # build is broken
@@ -1775,6 +1829,7 @@ let
    "rcellminer" # broken build
    "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
    "RchyOptimyx" # broken build
    "Rcmdr" # depends on broken package nlopt-2.4.2
    "RcmdrMisc" # depends on broken package nlopt-2.4.2
@@ -1787,6 +1842,7 @@ let
    "RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
    "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
    "RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_Export" # depends on broken package r-Rcmdr-2.2-3
    "RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
    "RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
    "RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
@@ -1820,6 +1876,7 @@ let
    "RcppOctave" # build is broken
    "RcppRedis" # build is broken
    "rcrypt" # broken build
+    "RCy3" # depends on broken package r-graph-1.48.0
    "RCyjs" # broken build
    "RCytoscape" # Build Is Broken
    "RDAVIDWebService" # depends on broken package Category-2.35.1
@@ -1860,11 +1917,13 @@ let
    "rgsepd" # depends on broken package goseq-1.21.1
    "rhdf5" # build is broken
    "rHVDM" # depends on broken package affyio-1.37.0
+    "RiboProfiling" # depends on broken package r-BiocGenerics-0.16.1
    "riboSeqR" # broken build
    "Ringo" # depends on broken package affyio-1.37.0
    "RIPSeeker" # depends on broken package Rsamtools-1.21.8
    "Risa" # depends on broken package affyio-1.37.0
    "rjade" # depends on broken package V8-0.6
+    "rjags"
    "rJPSGCS" # build is broken
    "rLindo" # build is broken
    "RLRsim" # depends on broken package r-lme4-1.1-9
@@ -1884,6 +1943,7 @@ let
    "RnaSeqSampleSize" # Build Is Broken
    "RnavGraph" # build is broken
    "RnBeads" # depends on broken package Rsamtools-1.21.8
+    "rnetcarto" # broken build
    "Rnits" # depends on broken package affyio-1.37.0
    "rNOMADS" # broken build
    "roar" # depends on broken package Rsamtools-1.21.8
@@ -1910,6 +1970,7 @@ let
    "rqubic" # broken build
    "rr" # depends on broken package nlopt-2.4.2
    "rRDP" # broken build
+    "RRreg" # depends on broken package r-lme4-1.1-10
    "Rsamtools" # Build Is Broken
    "RSAP" # build is broken
    "rsbml" # build is broken
@@ -1917,6 +1978,7 @@ let
    "RSDA" # depends on broken package nlopt-2.4.2
    "RSeed" # broken build
    "rSFFreader" # depends on broken package Rsamtools-1.21.8
+    "Rsomoclu"
    "RStoolbox" # depends on broken package r-caret-6.0-52
    "Rsubread" # Build Is Broken
    "RSVSim" # depends on broken package Rsamtools-1.21.8
@@ -1951,6 +2013,7 @@ let
    "sapFinder" # depends on broken package rTANDEM-1.9.0
    "saps" # broken build
    "SCAN_UPC" # depends on broken package affyio-1.37.0
+    "scholar" # depends on broken package r-rvest-0.3.1
    "ScISI" # depends on broken package apComplex-2.35.0
    "scmamp" # broken build
    "scsR" # broken build
@@ -1984,9 +2047,13 @@ let
    "SeqVarTools" # depends on broken package Rsamtools-1.21.8
    "SGSeq" # depends on broken package Rsamtools-1.21.8
    "SharpeR" # broken build
+    "sharx"
    "shinyMethyl" # depends on broken package Rsamtools-1.21.8
    "shinyTANDEM" # depends on broken package rTANDEM-1.9.0
    "ShortRead" # depends on broken package Rsamtools-1.21.8
+    "Shrinkage" # depends on broken package r-multtest-2.25.2
+    "SIBER"
+    "SICtools" # depends on broken package r-Biostrings-2.38.2
    "SID" # broken build
    "sigaR" # broken build
    "SigCheck" # broken build
@@ -1998,12 +2065,15 @@ let
    "SimBindProfiles" # depends on broken package affyio-1.37.0
    "SIM" # broken build
    "similaRpeak" # depends on broken package Rsamtools-1.21.8
+    "simmr"
    "simpleaffy" # depends on broken package affyio-1.37.0
    "simPop" # depends on broken package r-VIM-4.4.1
    "SimRAD" # depends on broken package Rsamtools-1.21.8
+    "simr" # depends on broken package r-lme4-1.1-10
    "SimReg" # broken build
    "simulatorZ" # broken build
    "sirt" # depends on broken package nlopt-2.4.2
+    "SISPA" # depends on broken package r-GSVA-1.18.0
    "SJava" # broken build
    "sjPlot" # depends on broken package nlopt-2.4.2
    "skewr" # depends on broken package affyio-1.37.0
@@ -2014,11 +2084,13 @@ let
    "snm" # depends on broken package nlopt-2.4.2
    "SNPchip" # depends on broken package affyio-1.37.0
    "snpEnrichment" # depends on broken package snpStats-1.19.0
+    "SNPhood" # depends on broken package r-BiocGenerics-0.16.1
    "snplist" # broken build
    "snpStats" # build is broken
    "snpStatsWriter" # depends on broken package snpStats-1.19.0
    "SNPtools" # depends on broken package Rsamtools-1.21.8
    "SOD" # depends on broken package cudatoolkit-5.5.22
+    "sodium" # broken build
    "soGGi" # depends on broken package Rsamtools-1.21.8
    "soilphysics" # depends on broken package rpanel-1.1-3
    "SomatiCA" # broken build
@@ -2028,8 +2100,10 @@ let
    "SpacePAC" # broken build
    "spacom" # depends on broken package nlopt-2.4.2
    "spade" # broken build
+    "SparseLearner" # depends on broken package r-qgraph-1.3.1
    "spdynmod" # broken build
    "specificity" # depends on broken package nlopt-2.4.2
+    "specmine" # depends on broken package r-caret-6.0-58
    "SpeCond" # broken build
    "SPEM" # broken build
    "SPIA" # broken build
@@ -2051,6 +2125,7 @@ let
    "staRank" # depends on broken package Category-2.35.1
    "Starr" # depends on broken package affyio-1.37.0
    "STATegRa" # depends on broken package affyio-1.37.0
+    "StatMethRank"
    "Statomica" # broken build
    "stcm" # depends on broken package nlopt-2.4.2
    "stepp" # depends on broken package nlopt-2.4.2
@@ -2061,6 +2136,7 @@ let
    "stringgaussnet" # build is broken
    "structSSI" # broken build
    "strum" # broken build
+    "subSeq" # depends on broken package r-Biobase-2.30.0
    "SummarizedExperiment" # broken build
    "superbiclust" # broken build
    "Surrogate" # depends on broken package nlopt-2.4.2
@@ -2070,9 +2146,9 @@ let
    "sybilSBML" # build is broken
    "synapter" # depends on broken package affyio-1.37.0
    "systemfit" # depends on broken package nlopt-2.4.2
-    "systemPipeRdata" # broken build
    "systemPipeR" # depends on broken package AnnotationForge-1.11.3
    "TargetSearch" # depends on broken package mzR-2.3.1
+    "TarSeqQC" # depends on broken package r-BiocGenerics-0.16.1
    "TCC" # broken build
    "TCGA2STAT" # broken build
    "TCGAbiolinks" # depends on broken package r-affy-1.47.1
@@ -2090,8 +2166,10 @@ let
    "TIN" # depends on broken package WGCNA-1.47
    "TitanCNA" # depends on broken package Rsamtools-1.21.8
    "TKF" # broken build
+    "TLBC" # depends on broken package r-caret-6.0-58
    "tmle" # broken build
    "tnam" # depends on broken package r-lme4-1.1-9
+    "tolBasis" # depends on broken package r-polynom-1.3-8
    "ToPASeq" # depends on broken package Rsamtools-1.21.8
    "topGO" # build is broken
    "topologyGSA" # depends on broken package Rsamtools-1.21.8
@@ -2148,8 +2226,8 @@ let
    "wfe" # depends on broken package nlopt-2.4.2
    "WGCNA" # build is broken
    "wgsea" # depends on broken package snpStats-1.19.0
-    "WideLM" # depends on broken package cudatoolkit-5.5.22
    "wikipediatrend" # broken build
+    "wordbankr" # depends on broken package r-RMySQL-0.10.7
    "XBSeq" # broken build
    "xcms" # depends on broken package mzR-2.3.1
    "XDE" # broken build
@@ -2158,8 +2236,11 @@ let
    "xps" # build is broken
    "XVector" # broken build
    "yaqcaffy" # depends on broken package affyio-1.37.0
+    "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
    "zetadiv" # depends on broken package nlopt-2.4.2
+    "zoib"
  ];

  otherOverrides = old: new: {
@@ -2188,10 +2269,6 @@ let
      preConfigure = "patchShebangs configure";
    });

-    iFes = old.iFes.overrideDerivation (attrs: {
-      CUDA_HOME = "${pkgs.cudatoolkit}";
-    });
-
    RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
      patchPhase = "patchShebangs configure";
    });
@@ -2271,14 +2348,6 @@ let
      CUDA_HOME = "${pkgs.cudatoolkit}";
    });

-    # It seems that we cannot override meta attributes with overrideDerivation.
-    CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
-      patches = [ ./patches/CARramps.patch ];
-      configureFlags = [
-        "--with-cuda-home=${pkgs.cudatoolkit}"
-      ];
-    });
-
    gmatrix = old.gmatrix.overrideDerivation (attrs: {
      patches = [ ./patches/gmatrix.patch ];
      CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
@@ -2286,19 +2355,6 @@ let
      CUDA_INC_PATH = "${pkgs.cudatoolkit}/include";
    });

-    # It seems that we cannot override meta attributes with overrideDerivation.
-    rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
-      patches = [ ./patches/rpud.patch ];
-      CUDA_HOME = "${pkgs.cudatoolkit}";
-    });
-
-    WideLM = old.WideLM.overrideDerivation (attrs: {
-      patches = [ ./patches/WideLM.patch ];
-      configureFlags = [
-        "--with-cuda-home=${pkgs.cudatoolkit}"
-      ];
-    });
-
    EMCluster = old.EMCluster.overrideDerivation (attrs: {
      patches = [ ./patches/EMCluster.patch ];
    });
--- a/pkgs/development/r-modules/generate-r-packages.R
+++ b/pkgs/development/r-modules/generate-r-packages.R
@@ -7,14 +7,16 @@ mirrorType <- commandArgs(trailingOnly=TRUE)[1]
 stopifnot(mirrorType %in% c("bioc","cran", "irkernel"))

 packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
-readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines(packagesFile), -1)))
+readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
+rVersion <- paste(R.Version()$major, strsplit(R.Version()$minor, ".", fixed=TRUE)[[1]][1], sep=".")
+snapshotDate <- Sys.Date()

-mirrorUrls <- list( bioc="http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/src/contrib/"
-                  , cran="http://cran.r-project.org/src/contrib/"
-                  , irkernel="http://irkernel.github.io/src/contrib/"
+mirrorUrls <- list( bioc=paste0("https://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/bioc/src/contrib/")
+                  , cran=paste0("https://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
+                  , irkernel="https://irkernel.github.io/src/contrib/"
                  )
 mirrorUrl <- mirrorUrls[mirrorType][[1]]
-knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates"))))
+knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
 pkgs <- knownPackages[mirrorType][[1]]
 setkey(pkgs, Package)
 knownPackages <- c(unique(do.call("rbind", knownPackages)$Package))
@@ -38,12 +40,12 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
    depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
    depends <- depends[depends %in% knownPackages]
    depends <- paste(sort(unique(depends)), collapse=" ")
-    paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
+    paste0("  ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }

 clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))

-pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates")))
+pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
 pkgs <- pkgs[order(Package)]
 pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))

@@ -54,8 +56,14 @@ cat("# Execute the following command to update the file.\n")
 cat("#\n")
 cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packagesFile))
 cat("\n\n")
-cat("{ self, derive }: with self; {\n")
-cat(paste(nix, collapse="\n"), "\n")
+cat("{ self, derive }:\n")
+cat("let derive2 = derive ")
+if (mirrorType == "bioc") { cat("{ rVersion = \"", rVersion, "\"; }", sep="")
+} else if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
+} else if (mirrorType == "irkernel") { cat("{}") }
+cat(";\n")
+cat("in with self; {\n")
+cat(paste(nix, collapse="\n"), "\n", sep="")
 cat("}\n")

 stopCluster(cl)
--- a/pkgs/development/r-modules/generate-shell.nix
+++ b/pkgs/development/r-modules/generate-shell.nix
@@ -0,0 +1,16 @@
+with import <nixpkgs> {};
+
+stdenv.mkDerivation {
+  name = "generate-r-packages-shell";
+
+  buildCommand = "exit 1";
+
+  nativeBuildInputs = [ 
+    (rWrapper.override {
+      packages = with rPackages; [
+        data_table
+        parallel
+      ];
+    })
+  ];
+}
--- a/pkgs/development/r-modules/irkernel-packages.nix
+++ b/pkgs/development/r-modules/irkernel-packages.nix
@@ -3,9 +3,11 @@
 #
 # Rscript generate-r-packages.R irkernel >new && mv new irkernel-packages.nix

-{ self, derive }: with self; {
-IRdisplay = derive { name="IRdisplay"; version="0.3"; sha256="0aa7v3x6s9jd5kzwfh4659gm3dqkmadbk40a0jdpm856mf9r5w6s"; depends=[base64enc repr]; };
-IRkernel = derive { name="IRkernel"; version="0.5"; sha256="0v9f01j1ysadq2f8d4mpbimrspj7051cncl0rd1n97rb8wlb9rrf"; depends=[digest evaluate IRdisplay jsonlite repr rzmq uuid]; };
-repr = derive { name="repr"; version="0.4"; sha256="1mhvslkxr5nkxiijapzm29jpmjnhhjs1v9s84xvhqpxlcav8dsn6"; depends=[]; };
-rzmq = derive { name="rzmq"; version="0.7.7"; sha256="0cds9wsbfb7lhgfjjfisv1i3905ny7x3i2wbb1rcih03ba4a1ij3"; depends=[]; };
+{ self, derive }:
+let derive2 = derive {};
+in with self; {
+  IRdisplay = derive2 { name="IRdisplay"; version="0.3"; sha256="0aa7v3x6s9jd5kzwfh4659gm3dqkmadbk40a0jdpm856mf9r5w6s"; depends=[base64enc repr]; };
+  IRkernel = derive2 { name="IRkernel"; version="0.5"; sha256="0v9f01j1ysadq2f8d4mpbimrspj7051cncl0rd1n97rb8wlb9rrf"; depends=[digest evaluate IRdisplay jsonlite repr rzmq uuid]; };
+  repr = derive2 { name="repr"; version="0.4"; sha256="1mhvslkxr5nkxiijapzm29jpmjnhhjs1v9s84xvhqpxlcav8dsn6"; depends=[]; };
+  rzmq = derive2 { name="rzmq"; version="0.7.7"; sha256="0cds9wsbfb7lhgfjjfisv1i3905ny7x3i2wbb1rcih03ba4a1ij3"; depends=[]; };
 }