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

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This commit is contained in:
Luca Bruno
2015-11-25 21:37:30 +01:00
parent 8a664fd5bc b34a6c96ee
commit a412927924
659 changed files with 46562 additions and 13611 deletions
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pkgs/development/r-modules/bioc-packages.nix
+1107 -1085
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pkgs/development/r-modules/cran-packages.nix
+7509 -7230
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pkgs/development/r-modules/default.nix
+109 -53
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@@ -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 ];
});
pkgs/development/r-modules/generate-r-packages.R
+17 -9
View File
@@ -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)
pkgs/development/r-modules/generate-shell.nix
+16
View File
@@ -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
];
})
];
}
pkgs/development/r-modules/irkernel-packages.nix
+7 -5
View File
@@ -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=[]; };
}