Wrapped R's package system similarly to perlPackages

pkgs/applications/science/math/R/default.nix

@@ -55,6 +55,8 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  setupHook = ./setup-hook.sh;
+
   meta = {
     homepage = "http://www.r-project.org/";
     description = "a free software environment for statistical computing and graphics";

pkgs/applications/science/math/R/setup-hook.sh

@@ -0,0 +1,5 @@
+addRLibPath () {
+    addToSearchPath R_LIBS_SITE $1/library
+}
+
+envHooks=(${envHooks[@]} addRLibPath)

pkgs/build-support/fetchurl/mirrors.nix

@@ -271,4 +271,100 @@ rec {
     ftp://ftp.xemacs.org/sites/metalab.unc.edu/
   ];
 
+  # CRAN mirrors (from http://cran.r-project.org/mirrors.html)
+  cran = [
+    http://cran.r-project.org/
+    http://cran.rstudio.com/
+    http://mirror.fcaglp.unlp.edu.ar/CRAN/
+    http://r.mirror.mendoza-conicet.gob.ar/
+    http://cran.csiro.au/
+    http://cran.ms.unimelb.edu.au/
+    http://cran.at.r-project.org/
+    http://www.freestatistics.org/cran/
+    http://cran-r.c3sl.ufpr.br/
+    http://cran.fiocruz.br/
+    http://www.vps.fmvz.usp.br/CRAN/
+    http://brieger.esalq.usp.br/CRAN/
+    http://cran.stat.sfu.ca/
+    http://mirror.its.dal.ca/cran/
+    http://probability.ca/cran/
+    http://cran.skazkaforyou.com/
+    http://cran.parentingamerica.com/
+    http://dirichlet.mat.puc.cl/
+    http://ftp.ctex.org/mirrors/CRAN/
+    http://mirror.bjtu.edu.cn/cran
+    http://cran.dataguru.cn/
+    http://mirrors.ustc.edu.cn/CRAN/
+    http://mirrors.xmu.edu.cn/CRAN/
+    http://www.laqee.unal.edu.co/CRAN/
+    http://www.icesi.edu.co/CRAN/
+    http://mirrors.dotsrc.org/cran/
+    http://cran.espol.edu.ec/
+    http://cran.univ-lyon1.fr/
+    http://mirror.ibcp.fr/pub/CRAN/
+    http://ftp.igh.cnrs.fr/pub/CRAN/
+    http://cran.irsn.fr/
+    http://cran.univ-paris1.fr/
+    http://mirrors.softliste.de/cran/
+    http://cran.r-mirror.de/
+    http://ftp5.gwdg.de/pub/misc/cran/
+    http://cran.cc.uoc.gr/
+    http://cran.rapporter.net/
+    http://ftp.iitm.ac.in/cran/
+    http://cran.repo.bppt.go.id/
+    http://cran.um.ac.ir/
+    http://ftp.heanet.ie/mirrors/cran.r-project.org/
+    http://cran.mirror.garr.it/mirrors/CRAN/
+    http://cran.stat.unipd.it/
+    http://dssm.unipa.it/CRAN/
+    http://essrc.hyogo-u.ac.jp/cran/
+    http://cran.md.tsukuba.ac.jp/
+    http://cran.ism.ac.jp/
+    http://cran.nexr.com/
+    http://biostat.cau.ac.kr/CRAN/
+    http://cran.itam.mx/
+    http://www.est.colpos.mx/R-mirror/
+    http://cran.xl-mirror.nl/
+    http://cran-mirror.cs.uu.nl/
+    http://cran.stat.auckland.ac.nz/
+    http://cran.uib.no/
+    http://cran.stat.upd.edu.ph/
+    http://r.meteo.uni.wroc.pl/
+    http://cran.dcc.fc.up.pt/
+    http://cran.gis-lab.info/
+    http://cran.stat.nus.edu.sg/
+    http://cran.fyxm.net/
+    http://r.adu.org.za/
+    http://cran.mirror.ac.za/
+    http://cran.es.r-project.org/
+    http://ftp.sunet.se/pub/lang/CRAN/
+    http://stat.ethz.ch/CRAN/
+    http://cran.cs.pu.edu.tw/
+    http://cran.csie.ntu.edu.tw/
+    http://mirrors.psu.ac.th/pub/cran/
+    http://cran.pau.edu.tr/
+    http://www.stats.bris.ac.uk/R/
+    http://cran.ma.imperial.ac.uk/
+    http://star-www.st-andrews.ac.uk/cran/
+    http://cran.cnr.berkeley.edu/
+    http://cran.stat.ucla.edu/
+    http://streaming.stat.iastate.edu/CRAN/
+    http://ftp.ussg.iu.edu/CRAN/
+    http://rweb.quant.ku.edu/cran/
+    http://watson.nci.nih.gov/cran_mirror/
+    http://cran.mtu.edu/
+    http://cran.wustl.edu/
+    http://cran.case.edu/
+    http://ftp.osuosl.org/pub/cran/
+    http://lib.stat.cmu.edu/R/CRAN/
+    http://cran.mirrors.hoobly.com/
+    http://mirrors.nics.utk.edu/cran/
+    http://cran.revolutionanalytics.com/
+    http://cran.fhcrc.org/
+    http://cran.cs.wwu.edu/
+    http://camoruco.ing.uc.edu.ve/cran/
+    http://cran.vinastat.com/
+    http://lib.stat.cmu.edu/
+  ];
+
 }

pkgs/development/r-modules/generic/builder.sh

@@ -0,0 +1,23 @@
+source $stdenv/setup
+
+export R_LIBS_SITE="$R_LIBS_SITE${R_LIBS_SITE:+:}$out/library"
+
+
+if test -n "$rPreHook"; then
+    eval "$rPreHook"
+fi
+
+installPhase() {
+	runHook preInstall
+	mkdir -p $out/library
+	R CMD INSTALL -l $out/library $src
+	runHook postInstall
+}
+
+postFixup() {
+    if test -e $out/nix-support/propagated-native-build-inputs; then
+        ln -s $out/nix-support/propagated-native-build-inputs $out/nix-support/propagated-user-env-packages
+    fi
+}
+
+genericBuild

pkgs/development/r-modules/generic/default.nix

@@ -0,0 +1,17 @@
+R:
+
+{ buildInputs ? [], ... } @ attrs:
+
+R.stdenv.mkDerivation (
+  {
+  }
+  //
+  attrs
+  //
+  {
+    name = "r-" + attrs.name;
+    builder = ./builder.sh;
+    buildInputs = buildInputs ++ [ R ];
+    phases = [ "installPhase" "fixupPhase" ];
+  }
+)

pkgs/top-level/all-packages.nix

@@ -5975,6 +5975,14 @@ let
 
   ZopeInterface = pythonPackages.zope_interface;
 
+  ### DEVELOPMENT / R MODULES
+
+  buildRPackage = import ../development/r-modules/generic R;
+
+  rPackages = recurseIntoAttrs (import ./r-packages.nix {
+    inherit pkgs;
+    __overrides = (config.rPackageOverrides or (p: {})) pkgs;
+  });
 
   ### SERVERS
 

pkgs/top-level/r-packages.nix

@@ -0,0 +1,246 @@
+/* This file defines the composition for CRAN (R) packages. */
+
+{pkgs, __overrides}:
+
+rec {
+
+  inherit (pkgs) buildRPackage fetchurl stdenv R;
+
+  inherit (stdenv.lib) maintainers;
+
+  inherit __overrides;
+
+  abind = buildRPackage rec {
+    name = "abind-1.4-0";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/abind_1.4-0.tar.gz";
+      sha256 = "1b9634bf6ad68022338d71a23a689f1af4afd9d6c12c0b982b88fc21363ff568";
+    };
+  };
+
+  chron = buildRPackage rec {
+    name = "chron-2.3-44";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/chron_2.3-44.tar.gz";
+      sha256 = "ba7d46223e615b4d09145a364a4c37ccff718384486ca154a6e025cf3ed91148";
+    };
+  };
+
+  colorspace = buildRPackage rec {
+    name = "colorspace-1.2-2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/colorspace_1.2-2.tar.gz";
+      sha256 = "7f6ca98e5d005bc7d6e37b03577d65995809150d1d293ce68b6720e7a6b2054d";
+    };
+  };
+
+  DBI = buildRPackage rec {
+    name = "DBI-0.2-7";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/DBI_0.2-7.tar.gz";
+      sha256 = "e90a988740f99060d5c4aacb1f2b148b0eb81c5b468bafeadf3aaeccf563b5e3";
+    };
+  };
+
+  dichromat = buildRPackage rec {
+    name = "dichromat-2.0-0";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/dichromat_2.0-0.tar.gz";
+      sha256 = "31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1";
+    };
+  };
+
+  digest = buildRPackage rec {
+    name = "digest-0.6.3";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/digest_0.6.3.tar.gz";
+      sha256 = "5be8f1386c0c273fcc915df7b557393c5f3de43c44fd16614db9cc5ba6d1d57c";
+    };
+  };
+
+  ggplot2 = buildRPackage rec {
+    name = "ggplot2-0.9.3.1";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/ggplot2_0.9.3.1.tar.gz";
+      sha256 = "b4c97404fd44571f9980712af963949ed204b5d4e639d97df9ba9a17423a6601";
+    };
+    propagatedBuildInputs = [ digest plyr gtable reshape2 scales proto ];
+  };
+
+  gtable = buildRPackage rec {
+    name = "gtable-0.1.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/gtable_0.1.2.tar.gz";
+      sha256 = "b08ba8e62e0ce05e7a4c07ba3ffa67719161db62438b04f14343f8928d74304d";
+    };
+  };
+
+  gtools = buildRPackage rec {
+    name = "gtools-3.0.0";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/gtools_3.0.0.tar.gz";
+      sha256 = "e35f08ac9df875b57dcf23028baa226372d7482d7814a011f9b1fdd0697ee73c";
+    };
+  };
+
+  gsubfn = buildRPackage rec {
+    name = "gsubfn-0.6-5";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/gsubfn_0.6-5.tar.gz";
+      sha256 = "9a7b51ae6aabd1c99e8633d3dc75232d8c4a175df750c7d1c359bd0f5fc197be";
+    };
+    propagatedBuildInputs = [ proto ];
+  };
+
+  labeling = buildRPackage rec {
+    name = "labeling-0.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/labeling_0.2.tar.gz";
+      sha256 = "8aaa7f8b91923088da4e47ae42620fadcff7f2bc566064c63d138e2145e38aa4";
+    };
+  };
+
+  lars = buildRPackage rec {
+    name = "lars-1.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/lars_1.2.tar.gz";
+      sha256 = "64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e";
+    };
+  };
+
+  LiblineaR = buildRPackage rec {
+    name = "LiblineaR-1.80-7";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/LiblineaR_1.80-7.tar.gz";
+      sha256 = "9ba0280c5165bf0bbd46cb5ec7c66fdece38fc3f73fce2ec800763923ae8e4bd";
+    };
+  };
+
+  linprog = buildRPackage rec {
+    name = "linprog-0.9-2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/linprog_0.9-2.tar.gz";
+      sha256 = "8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce";
+    };
+    propagatedBuildInputs = [ lpSolve ];
+  };
+
+  lpSolve = buildRPackage rec {
+    name = "lpSolve-5.6.7";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/lpSolve_5.6.7.tar.gz";
+      sha256 = "16def9237f38c4d7a59651173fd87df3cd3c563f640c6952e13bdd2a084737ef";
+    };
+  };
+
+  munsell = buildRPackage rec {
+    name = "munsell-0.4.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/munsell_0.4.2.tar.gz";
+      sha256 = "84e787f58f626c52a1e3fc1201f724835dfa8023358bfed742e7001441f425ae";
+    };
+    propagatedBuildInputs = [ colorspace ];
+  };
+
+  pamr = buildRPackage rec {
+    name = "pamr-1.54.1";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/pamr_1.54.1.tar.gz";
+      sha256 = "139dbc39b4eccd6a55b6a3c42a1c8be61dcce0613535a634c3e42731fc315516";
+    };
+  };
+
+  penalized = buildRPackage rec {
+    name = "penalized-0.9-42";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/penalized_0.9-42.tar.gz";
+      sha256 = "98e8e39b02ecbabaa7050211e34941c73e1e687f39250cf3cbacb7c5dcbb1e98";
+    };
+  };
+
+  plyr = buildRPackage rec {
+    name = "plyr-1.8";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/plyr_1.8.tar.gz";
+      sha256 = "0bd6861af241e6c5ce777ef3f1b0eb72b31cc026669a68f6250b8ecfadf71a66";
+    };
+  };
+
+  proto = buildRPackage rec {
+    name = "proto-0.3-10";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/proto_0.3-10.tar.gz";
+      sha256 = "d0d941bfbf247879b3510c8ef3e35853b1fbe83ff3ce952e93d3f8244afcbb0e";
+    };
+  };
+
+  randomForest = buildRPackage rec {
+    name = "randomForest-4.6-7";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/randomForest_4.6-7.tar.gz";
+      sha256 = "8206e88b242c07efc10f148d17dfcc265a31361e1bcf44bfe17aed95c357be0b";
+    };
+    propagatedBuildInputs = [ plyr stringr ];
+  };
+
+  reshape2 = buildRPackage rec {
+    name = "reshape2-1.2.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/reshape2_1.2.2.tar.gz";
+      sha256 = "9131025b8f684e1629ab3e2748d4cf2b907b7c89cfbff667c925bc0fb5dfc103";
+    };
+    propagatedBuildInputs = [ plyr stringr ];
+  };
+
+  RColorBrewer = buildRPackage rec {
+    name = "RColorBrewer-1.0-5";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/RColorBrewer_1.0-5.tar.gz";
+      sha256 = "5ac1c44c1a53f9521134e7ed7c148c72e49271cbd229c5263d2d7fd91c8b8e78";
+    };
+  };
+
+  RSQLite = buildRPackage rec {
+    name = "RSQlite-0.11.4";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/RSQLite_0.11.4.tar.gz";
+      sha256 = "bba0cbf2a1a3120d667a731da1ca5b9bd4db23b813e1abf6f51fb01540c2000c";
+    };
+    propagatedBuildInputs = [ DBI ];
+  };
+
+  RSQLiteExtfuns = buildRPackage rec {
+    name = "RSQlite.extfuns-0.0.1";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/RSQLite.extfuns_0.0.1.tar.gz";
+      sha256 = "ca5c7947c041e17ba83bed3f5866f7eeb9b7f361e5c050c9b58eec5670f03d0e";
+    };
+    propagatedBuildInputs = [ RSQLite ];
+  };
+
+  scales = buildRPackage rec {
+    name = "scales-0.2.3";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/scales_0.2.3.tar.gz";
+      sha256 = "46aef8eb261abc39f87b71184e5484bc8c2c94e01d3714ce4b2fd60727bc40d9";
+    };
+    propagatedBuildInputs = [ RColorBrewer stringr dichromat munsell plyr labeling ];
+  };
+
+  stringr = buildRPackage rec {
+    name = "stringr-0.6.2";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/stringr_0.6.2.tar.gz";
+      sha256 = "c3fc9c71d060ad592d2cfc51c36ab2f8e5f8cf9a25dfe42c637447dd416b6737";
+    };
+  };
+
+  sqldf = buildRPackage rec {
+    name = "sqldf-0.4-6.4";
+    src = fetchurl {
+      url = "mirror://cran/src/contrib/sqldf_0.4-6.4.tar.gz";
+      sha256 = "6c51e4e48b93310f765c661a1756fe068629da775248d38a98c38f5b6f7511c4";
+    };
+    propagatedBuildInputs = [ DBI gsubfn proto chron RSQLite RSQLiteExtfuns ];
+  };
+}