1088 lines
30 KiB
Nix
1088 lines
30 KiB
Nix
/* This file defines the composition for CRAN (R) packages. */
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{ R, pkgs, overrides }:
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let
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inherit (pkgs) fetchurl stdenv lib;
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buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
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# Package template
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#
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# some packages, e.g. cncaGUI, require X running while installation,
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# so that we use xvfb-run if requireX is true.
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derive = lib.makeOverridable ({
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name, version, sha256,
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depends ? [],
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doCheck ? true,
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requireX ? false,
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broken ? false,
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hydraPlatforms ? R.meta.hydraPlatforms
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}: buildRPackage {
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name = "${name}-${version}";
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src = fetchurl {
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urls = [
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"mirror://cran/src/contrib/${name}_${version}.tar.gz"
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"mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
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];
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inherit sha256;
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};
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inherit doCheck requireX;
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propagatedBuildInputs = depends;
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nativeBuildInputs = depends;
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meta.homepage = "http://cran.r-project.org/web/packages/${name}/";
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meta.platforms = R.meta.platforms;
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meta.hydraPlatforms = hydraPlatforms;
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meta.broken = broken;
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});
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# Overrides package definitions with nativeBuildInputs.
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# For example,
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#
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# overrideNativeBuildInputs {
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# foo = [ pkgs.bar ]
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# } old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideDerivation (attrs: {
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# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
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# });
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# }
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overrideNativeBuildInputs = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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nativeBuildInputs = attrs.nativeBuildInputs ++ value;
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})
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) overrides;
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# Overrides package definitions with buildInputs.
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# For example,
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#
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# overrideBuildInputs {
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# foo = [ pkgs.bar ]
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# } old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideDerivation (attrs: {
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# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
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# });
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# }
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overrideBuildInputs = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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buildInputs = attrs.buildInputs ++ value;
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})
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) overrides;
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# Overrides package definitions with new R dependencies.
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# For example,
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#
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# overrideRDepends {
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# foo = [ self.bar ]
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# } old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideDerivation (attrs: {
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# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
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# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
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# });
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# }
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overrideRDepends = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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nativeBuildInputs = attrs.nativeBuildInputs ++ value;
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propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
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})
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) overrides;
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# Overrides package definition requiring X running to install.
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# For example,
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#
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# overrideRequireX [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# requireX = true;
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# };
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# }
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overrideRequireX = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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requireX = true;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition to skip check.
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# For example,
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#
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# overrideSkipCheck [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# doCheck = false;
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# };
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# }
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overrideSkipCheck = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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doCheck = false;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition to mark it broken.
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# For example,
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#
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# overrideBroken [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# broken = true;
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# };
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# }
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overrideBroken = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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broken = true;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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defaultOverrides = old: new:
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let old0 = old; in
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let
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old1 = old0 // (overrideRequireX packagesRequireingX old0);
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old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
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old3 = old2 // (overrideRDepends packagesWithRDepends old2);
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old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
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old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
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old6 = old5 // (overrideBroken brokenPackages old5);
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old = old6;
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in old // (otherOverrides old new);
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# Recursive override pattern.
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# `_self` is a collection of packages;
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# `self` is `_self` with overridden packages;
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# packages in `_self` may depends on overridden packages.
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self = (defaultOverrides _self self) // overrides;
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_self = import ./cran-packages.nix { inherit self derive; };
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# tweaks for the individual packages and "in self" follow
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packagesWithRDepends = {
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FactoMineR = [ self.car ];
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};
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packagesWithNativeBuildInputs = {
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abn = [ pkgs.gsl ];
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adimpro = [ pkgs.imagemagick ];
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audio = [ pkgs.portaudio ];
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BayesSAE = [ pkgs.gsl ];
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BayesVarSel = [ pkgs.gsl ];
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BayesXsrc = [ pkgs.readline pkgs.ncurses ];
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bigGP = [ pkgs.openmpi ];
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bnpmr = [ pkgs.gsl ];
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BNSP = [ pkgs.gsl ];
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cairoDevice = [ pkgs.gtk2 ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
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CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
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chebpol = [ pkgs.fftw ];
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cit = [ pkgs.gsl ];
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curl = [ pkgs.curl pkgs.openldap ];
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devEMF = [ pkgs.xlibs.libXft ];
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diversitree = [ pkgs.gsl pkgs.fftw ];
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EMCluster = [ pkgs.liblapack ];
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fftw = [ pkgs.fftw ];
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fftwtools = [ pkgs.fftw ];
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Formula = [ pkgs.gmp ];
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geoCount = [ pkgs.gsl ];
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git2r = [ pkgs.zlib ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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gmp = [ pkgs.gmp ];
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graphscan = [ pkgs.gsl ];
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gsl = [ pkgs.gsl ];
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HiCseg = [ pkgs.gsl ];
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igraph = [ pkgs.gmp ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg ];
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KFKSDS = [ pkgs.gsl ];
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kza = [ pkgs.fftw ];
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libamtrack = [ pkgs.gsl ];
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mixcat = [ pkgs.gsl ];
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mvabund = [ pkgs.gsl ];
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mwaved = [ pkgs.fftw ];
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ncdf4 = [ pkgs.netcdf ];
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ncdf = [ pkgs.netcdf ];
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nloptr = [ pkgs.nlopt ];
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openssl = [ pkgs.openssl ];
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outbreaker = [ pkgs.gsl ];
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pbdMPI = [ pkgs.openmpi ];
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pbdNCDF4 = [ pkgs.netcdf ];
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pbdPROF = [ pkgs.openmpi ];
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PKI = [ pkgs.openssl ];
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png = [ pkgs.libpng ];
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PopGenome = [ pkgs.zlib ];
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proj4 = [ pkgs.proj ];
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qtbase = [ pkgs.qt4 ];
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qtpaint = [ pkgs.qt4 ];
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R2GUESS = [ pkgs.gsl ];
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R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
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RAppArmor = [ pkgs.libapparmor ];
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rbamtools = [ pkgs.zlib ];
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RCA = [ pkgs.gmp ];
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rcdd = [ pkgs.gmp ];
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RcppCNPy = [ pkgs.zlib ];
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RcppGSL = [ pkgs.gsl ];
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RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
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RcppZiggurat = [ pkgs.gsl ];
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rgdal = [ pkgs.proj pkgs.gdal ];
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rgeos = [ pkgs.geos ];
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rgl = [ pkgs.mesa pkgs.x11 ];
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Rglpk = [ pkgs.glpk ];
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rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
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RGtk2 = [ pkgs.gtk2 ];
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Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
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ridge = [ pkgs.gsl ];
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RJaCGH = [ pkgs.zlib ];
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rjags = [ pkgs.jags ];
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rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
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Rlibeemd = [ pkgs.gsl ];
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rmatio = [ pkgs.zlib ];
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Rmpfr = [ pkgs.gmp pkgs.mpfr ];
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Rmpi = [ pkgs.openmpi ];
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RMySQL = [ pkgs.zlib pkgs.mysql ];
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RNetCDF = [ pkgs.netcdf pkgs.udunits ];
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RODBCext = [ pkgs.libiodbc ];
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RODBC = [ pkgs.libiodbc ];
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rpg = [ pkgs.postgresql ];
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rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
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Rpoppler = [ pkgs.poppler ];
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RPostgreSQL = [ pkgs.postgresql ];
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RProtoBuf = [ pkgs.protobuf ];
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rpud = [ pkgs.linuxPackages.nvidia_x11 ];
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rPython = [ pkgs.python ];
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RSclient = [ pkgs.openssl ];
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Rserve = [ pkgs.openssl ];
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Rssa = [ pkgs.fftw ];
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rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
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rtiff = [ pkgs.libtiff ];
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runjags = [ pkgs.jags ];
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RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
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rzmq = [ pkgs.zeromq3 ];
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SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
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sdcTable = [ pkgs.gmp pkgs.glpk ];
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seewave = [ pkgs.fftw pkgs.libsndfile ];
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SemiCompRisks = [ pkgs.gsl ];
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seqinr = [ pkgs.zlib ];
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seqminer = [ pkgs.zlib pkgs.bzip2 ];
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showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
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simplexreg = [ pkgs.gsl ];
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SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
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spate = [ pkgs.fftw ];
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sprint = [ pkgs.openmpi ];
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ssanv = [ pkgs.proj ];
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stsm = [ pkgs.gsl ];
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survSNP = [ pkgs.gsl ];
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sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
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TAQMNGR = [ pkgs.zlib ];
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tiff = [ pkgs.libtiff ];
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TKF = [ pkgs.gsl ];
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tkrplot = [ pkgs.xlibs.libX11 ];
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topicmodels = [ pkgs.gsl ];
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udunits2 = [ pkgs.udunits pkgs.expat ];
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V8 = [ pkgs.v8 ];
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VBLPCM = [ pkgs.gsl ];
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VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
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WhopGenome = [ pkgs.zlib ];
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XBRL = [ pkgs.zlib pkgs.libxml2 ];
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XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
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};
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packagesWithBuildInputs = {
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# sort -t '=' -k 2
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svKomodo = [ pkgs.which ];
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nat = [ pkgs.which ];
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nat_nblast = [ pkgs.which ];
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nat_templatebrains = [ pkgs.which ];
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RMark = [ pkgs.which ];
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RPushbullet = [ pkgs.which ];
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qtpaint = [ pkgs.cmake ];
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qtbase = [ pkgs.cmake pkgs.perl ];
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gmatrix = [ pkgs.cudatoolkit ];
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WideLM = [ pkgs.cudatoolkit ];
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RCurl = [ pkgs.curl ];
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R2SWF = [ pkgs.pkgconfig ];
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rggobi = [ pkgs.pkgconfig ];
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RGtk2 = [ pkgs.pkgconfig ];
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RProtoBuf = [ pkgs.pkgconfig ];
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Rpoppler = [ pkgs.pkgconfig ];
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VBmix = [ pkgs.pkgconfig ];
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XML = [ pkgs.pkgconfig ];
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cairoDevice = [ pkgs.pkgconfig ];
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chebpol = [ pkgs.pkgconfig ];
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fftw = [ pkgs.pkgconfig ];
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geoCount = [ pkgs.pkgconfig ];
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kza = [ pkgs.pkgconfig ];
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mwaved = [ pkgs.pkgconfig ];
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showtext = [ pkgs.pkgconfig ];
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spate = [ pkgs.pkgconfig ];
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stringi = [ pkgs.pkgconfig ];
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sysfonts = [ pkgs.pkgconfig ];
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Cairo = [ pkgs.pkgconfig ];
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Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
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qtutils = [ pkgs.qt4 ];
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ecoretriever = [ pkgs.which ];
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tcltk2 = [ pkgs.tcl pkgs.tk ];
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tikzDevice = [ pkgs.which pkgs.texLive ];
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rPython = [ pkgs.which ];
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CARramps = [ pkgs.which pkgs.cudatoolkit ];
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gridGraphics = [ pkgs.which ];
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gputools = [ pkgs.which pkgs.cudatoolkit ];
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rpud = [ pkgs.which pkgs.cudatoolkit ];
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adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
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PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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};
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packagesRequireingX = [
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"AnalyzeFMRI"
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"AnnotLists"
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"AnthropMMD"
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"AtelieR"
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"BAT"
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"BCA"
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"BEQI2"
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"BHMSMAfMRI"
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"BioGeoBEARS"
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"BiodiversityR"
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"CCTpack"
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"CommunityCorrelogram"
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"ConvergenceConcepts"
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"DALY"
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"DSpat"
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"Deducer"
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"DeducerExtras"
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"DeducerPlugInExample"
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"DeducerPlugInScaling"
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"DeducerSpatial"
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"DeducerSurvival"
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"HomoPolymer"
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"MetSizeR"
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"DeducerText"
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"Demerelate"
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"DescTools"
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"DivMelt"
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"ENiRG"
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"EcoVirtual"
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"EnQuireR"
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"FAiR"
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"FD"
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"FFD"
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"FeedbackTS"
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"FreeSortR"
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"GGEBiplotGUI"
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"GPCSIV"
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"GUniFrac"
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"Geneland"
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"GeoGenetix"
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"GeoXp"
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"GrammR"
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"GrapheR"
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"GroupSeq"
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|
"HH"
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"HiveR"
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"IsotopeR"
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"JGR"
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"KappaGUI"
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"LS2Wstat"
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"MAR1"
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"MTurkR"
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"MareyMap"
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|
"MergeGUI"
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"Meth27QC"
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"MicroStrategyR"
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"MissingDataGUI"
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"MplusAutomation"
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"OligoSpecificitySystem"
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|
"OpenRepGrid"
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"PBSadmb"
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"PBSmodelling"
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"PCPS"
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"PopGenReport"
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"PredictABEL"
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|
"PrevMap"
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"ProbForecastGOP"
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"QCAGUI"
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"R2STATS"
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|
"RHRV"
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"RNCEP"
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|
"RQDA"
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"RSDA"
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"RSurvey"
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"RandomFields"
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|
"Rcmdr"
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"RcmdrPlugin_BCA"
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"RcmdrPlugin_DoE"
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"RcmdrPlugin_EACSPIR"
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"RcmdrPlugin_EBM"
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"RcmdrPlugin_EZR"
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"RcmdrPlugin_EcoVirtual"
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"RcmdrPlugin_FactoMineR"
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"RcmdrPlugin_HH"
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"RcmdrPlugin_IPSUR"
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"RcmdrPlugin_KMggplot2"
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"RcmdrPlugin_MA"
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"RcmdrPlugin_MPAStats"
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"RcmdrPlugin_ROC"
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"RcmdrPlugin_SCDA"
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"RcmdrPlugin_SLC"
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"RcmdrPlugin_SM"
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"RcmdrPlugin_StatisticalURV"
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"RcmdrPlugin_TeachingDemos"
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"RcmdrPlugin_UCA"
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"RcmdrPlugin_coin"
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"RcmdrPlugin_depthTools"
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"RcmdrPlugin_doex"
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"RcmdrPlugin_epack"
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"RcmdrPlugin_lfstat"
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"RcmdrPlugin_mosaic"
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"RcmdrPlugin_orloca"
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"RcmdrPlugin_plotByGroup"
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"RcmdrPlugin_pointG"
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"RcmdrPlugin_qual"
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"RcmdrPlugin_sampling"
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"RcmdrPlugin_sos"
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"RcmdrPlugin_steepness"
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"RcmdrPlugin_survival"
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"RcmdrPlugin_temis"
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"RenextGUI"
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"RunuranGUI"
|
|
"SOLOMON"
|
|
"SPACECAP"
|
|
"SRRS"
|
|
"SSDforR"
|
|
"STEPCAM"
|
|
"SYNCSA"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"StatDA"
|
|
"SyNet"
|
|
"TDMR"
|
|
"TED"
|
|
"TIMP"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"TestScorer"
|
|
"VIMGUI"
|
|
"VecStatGraphs3D"
|
|
"WMCapacity"
|
|
"accrual"
|
|
"ade4TkGUI"
|
|
"adehabitat"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"aplpack"
|
|
"aqfig"
|
|
"arf3DS4"
|
|
"asbio"
|
|
"bayesDem"
|
|
"betapart"
|
|
"betaper"
|
|
"bio_infer"
|
|
"bipartite"
|
|
"biplotbootGUI"
|
|
"blender"
|
|
"cairoDevice"
|
|
"cncaGUI"
|
|
"cocorresp"
|
|
"confidence"
|
|
"constrainedKriging"
|
|
"cpa"
|
|
"dave"
|
|
"debug"
|
|
"detrendeR"
|
|
"dgmb"
|
|
"dpa"
|
|
"dynBiplotGUI"
|
|
"dynamicGraph"
|
|
"eVenn"
|
|
"exactLoglinTest"
|
|
"fSRM"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"feature"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"fit4NM"
|
|
"forams"
|
|
"forensim"
|
|
"fscaret"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"gcmr"
|
|
"geoR"
|
|
"geoRglm"
|
|
"geomorph"
|
|
"georob"
|
|
"gnm"
|
|
"gsubfn"
|
|
"iBUGS"
|
|
"iDynoR"
|
|
"ic50"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"likeLTD"
|
|
"loe"
|
|
"logmult"
|
|
"memgene"
|
|
"metacom"
|
|
"migui"
|
|
"miniGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"onemap"
|
|
"palaeoSig"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"playwith"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"pmg"
|
|
"poppr"
|
|
"powerpkg"
|
|
"prefmod"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"qtutils"
|
|
"r4ss"
|
|
"rAverage"
|
|
"rareNMtests"
|
|
"recluster"
|
|
"relax"
|
|
"relimp"
|
|
"reportRx"
|
|
"reshapeGUI"
|
|
"rgl"
|
|
"rich"
|
|
"ringscale"
|
|
"rioja"
|
|
"ripa"
|
|
"rite"
|
|
"rnbn"
|
|
"rsgcc"
|
|
"sdcMicroGUI"
|
|
"sharpshootR"
|
|
"simba"
|
|
"soundecology"
|
|
"spacodiR"
|
|
"spatsurv"
|
|
"sqldf"
|
|
"statcheck"
|
|
"stosim"
|
|
"strvalidator"
|
|
"stylo"
|
|
"svDialogstcltk"
|
|
"svIDE"
|
|
"svSocket"
|
|
"svWidgets"
|
|
"tcltk2"
|
|
"titan"
|
|
"tkrgl"
|
|
"tkrplot"
|
|
"tmap"
|
|
"tspmeta"
|
|
"twiddler"
|
|
"vcdExtra"
|
|
"vegan"
|
|
"vegan3d"
|
|
"vegclust"
|
|
"x12GUI"
|
|
"xergm"
|
|
];
|
|
|
|
packagesToSkipCheck = [
|
|
"Rmpi" # tries to run MPI processes
|
|
"gmatrix" # requires CUDA runtime
|
|
"sprint" # tries to run MPI processes
|
|
"pbdMPI" # tries to run MPI processes
|
|
];
|
|
|
|
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
|
brokenPackages = [
|
|
"ACNE" # requires aroma_affymetrix
|
|
"Actigraphy" # SDMTools.so: undefined symbol: X
|
|
"adaptsmoFMRI" # requires spatstat
|
|
"ads" # requires spatstat
|
|
"agridat" # requires pcaMethods
|
|
"aLFQ" # requires protiq
|
|
"AntWeb" # requires leafletR
|
|
"aoristic" # requires spatstat
|
|
"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
|
|
"aroma_affymetrix" # requires aroma_core
|
|
"aroma_cn" # requires PSCBS
|
|
"aroma_core" # requires PSCBS
|
|
"ArrayBin" # requires SAGx
|
|
"babel" # requires edgeR
|
|
"BACA" # requires RDAVIDWebService
|
|
"BcDiag" # requires fabia
|
|
"bdvis" # requres taxize
|
|
"beadarrayFilter" # requires beadarray
|
|
"bigGP" # requires MPI running. HELP WANTED!
|
|
"bigpca" # requires NCmisc
|
|
"Biograph" # requires mvna
|
|
"biotools" # requires rpanel
|
|
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
|
|
"BLCOP" # depends on broken fPortfolio
|
|
"bmrm" # requires clpAPI
|
|
"branchLars" # requires Rgraphviz
|
|
"BRugs" # requires OpenBUGS
|
|
"calmate" # requires aroma_core
|
|
"CARrampsOcl" # depends on OpenCL
|
|
"CHAT" # requires DNAcopy
|
|
"ChemoSpec" # depends on broken speaq
|
|
"classGraph" # requires graph, and Rgraphviz
|
|
"clpAPI" # requires clp
|
|
"compendiumdb" # requires Biobase
|
|
"CORM" # requires limma
|
|
"cplexAPI" # requires CPLEX
|
|
"crmn" # requires pcaMethods, and Biobase
|
|
"CrypticIBDcheck" # requires rJPSGCS
|
|
"cudaBayesreg" # requres Rmath
|
|
"curvHDR" # requires flowCore
|
|
"D2C" # requires gRbase
|
|
"DAAGbio" # requires limma
|
|
"daff" # requires V8 to build
|
|
"dagbag" # requires Rlapack
|
|
"DBKGrad" # requires SDD
|
|
"dbmss" # requires spatstat
|
|
"DCGL" # requires limma
|
|
"dcGOR" # requires dnet
|
|
"demi" # requires affy, affxparser, and oligo
|
|
"DepthProc" # requires samr
|
|
"DiagrammeR" # requires V8 to build
|
|
"Digiroo2" # requires spatstat
|
|
"dixon" # requires spatstat
|
|
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
|
|
"doMPI" # requires MPI running. HELP WANTED!
|
|
"dpcR" # requires spatstat
|
|
"DSpat" # requires spatstat
|
|
"ecespa" # requires spatstat
|
|
"ecoengine" # requires leafletR
|
|
"ecospat" # requires spatstat
|
|
"edgeRun" # requires edgeR
|
|
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
|
|
"EMDomics" # requires BiocParallel
|
|
"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
|
|
"epoc" # requires graph, and Rgraphviz
|
|
"erpR" # requires rpanel
|
|
"ETAS" # requires spatstat
|
|
"eulerian" # requires graph
|
|
"evobiR" # requres taxiz
|
|
"evora" # requires qvalue
|
|
"ExomeDepth" # requires GenomicRanges, and Rsamtools
|
|
"FAMT" # requires impute
|
|
"fdrDiscreteNull" # requires edgeR
|
|
"FHtest" # requires interval
|
|
"flexCWM" # depends on broken mixture
|
|
"fPortfolio" # requires rneos
|
|
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
|
|
"gamlss_demo" # requires rpanel
|
|
"GeneticTools" # requires snpStats
|
|
"GExMap" # requires Biobase and multtest
|
|
"gitter" # requires EBImage
|
|
"glmgraph" # test suite says: "undefined symbol: dgemv_"
|
|
"gmatrix" # depends on proprietary cudatoolkit
|
|
"GOGANPA" # requires WGCNA
|
|
"gputools" # depends on proprietary cudatoolkit
|
|
"gRain" # requires gRbase
|
|
"gRapHD" # requires graph
|
|
"gRbase" # requires RBGL, and graph
|
|
"gRc" # requires gRbase
|
|
"gridDebug" # requires gridGraphviz
|
|
"gridGraphviz" # requires graph, and Rgraphviz
|
|
"GriegSmith" # requires spatstat
|
|
"gRim" # requires gRbase
|
|
"GSAgm" # requires edgeR
|
|
"GUIDE" # requires rpanel
|
|
"h2o" # tries to download some h2o.jar during its build
|
|
"hasseDiagram" # requires Rgraphviz
|
|
"hddplot" # requires multtest
|
|
"HierO" # requires rneos
|
|
"HiPLARM" # requires MAGMA or PLASMA
|
|
"hpoPlot" # requires Rgraphviz
|
|
"HTSCluster" # requires edgeR
|
|
"iFes" # depends on proprietary cudatoolkit
|
|
"imputeLCMD" # requires pcaMethods, and impute
|
|
"intamapInteractive" # requires spatstat
|
|
"interval" # requires Icens
|
|
"ionflows" # requires Biostrings
|
|
"iRefR" # requires graph, and RBGL
|
|
"IsoGene" # requires Biobase, and affy
|
|
"isva" # requires qvalue
|
|
"jomo" # linking errors
|
|
"js" # requires broken V8
|
|
"KANT" # requires affy, and Biobase
|
|
"ktspair" # requires Biobase
|
|
"latticeDensity" # requires spatstat
|
|
"leapp" # requires sva
|
|
"lefse" # SDMTools.so: undefined symbol: X
|
|
"lgcp" # requires rpanel
|
|
"LinRegInteractive" # requires Rpanel
|
|
"LogisticDx" # requires gRbase
|
|
"LOST" # requires pcaMethods
|
|
"ltsk" # requires Rlapack and Rblas
|
|
"magma" # requires MAGMA
|
|
"MAMA" # requires metaMA
|
|
"MEET" # requires pcaMethods, and seqLogo
|
|
"metabolomics" # depends on broken crmn
|
|
"MetaDE" # requires impute, and Biobase
|
|
"MetaLandSim" # requires Biobase
|
|
"metaMA" # requires limma
|
|
"metaMix" # requires MPI running. HELP WANTED!
|
|
"mGSZ" # requires Biobase, and limma
|
|
"MigClim" # SDMTools.So: Undefined Symbol: X
|
|
"minimist" # requires broken V8
|
|
"miRtest" # requires globaltest, GlobalAncova, and limma
|
|
"mixture" # mixture.so: undefined symbol: dtrmm_
|
|
"moduleColor" # requires impute
|
|
"msarc" # requires AnnotationDbi
|
|
"MSeasy" # requires mzR, and xcms
|
|
"MSeasyTkGUI" # requires MSeasyTkGUI
|
|
"MSIseq" # requires IRanges
|
|
"msSurv" # requires graph
|
|
"multiDimBio" # requires pcaMethods
|
|
"mutossGUI" # requires mutoss
|
|
"mutoss" # requires multtest
|
|
"MXM" # depends on broken gRbase
|
|
"NBPSeq" # requires qvalue
|
|
"NCmisc" # requires BiocInstaller
|
|
"netClass" # requires samr
|
|
"nettools" # requires WGCNA
|
|
"NORRRM" # can't load SDMTools properly
|
|
"netweavers" # requires BiocGenerics, Biobase, and limma
|
|
"NLPutils" # requires qdap
|
|
"NSA" # requires aroma_core
|
|
"OpenCL" # FIXME: requires CL/opencl.h
|
|
"optBiomarker" # requires rpanel
|
|
"ora" # requires ROracle
|
|
"orQA" # requires genefilter
|
|
"PBSmapping" # fails its test suite for unclear reasons
|
|
"PairViz" # requires graph
|
|
"PANDA" # requires GO.db
|
|
"ParDNAcopy" # requires DNAcopy
|
|
"pathClass" # requires affy, and Biobase
|
|
"PatternClass" # SDMTools.So: Undefined Symbol: X
|
|
"pbdBASE" # requires pbdMPI
|
|
"pbdDEMO" # requires pbdMPI
|
|
"pbdDMAT" # requires pbdMPI
|
|
"pbdSLAP" # requires pbdMPI
|
|
"pcaL1" # requires clp
|
|
"pcalg" # requires graph, and RBGL
|
|
"PCGSE" # requires safe
|
|
"PCS" # requires multtest
|
|
"PepPrep" # requires biomaRt
|
|
"PerfMeas" # requires limma, graph, and RBGL
|
|
"permGPU" # requires Biobase
|
|
"PhViD" # requires LBE
|
|
"pi0" # requires qvalue
|
|
"plmDE" # requires limma
|
|
"plsRcox" # requires survcomp
|
|
"PMA" # requires impute
|
|
"pmcgd" # depends on broken mixture
|
|
"pmclust" # requires MPI running. HELP WANTED!
|
|
"polyCub" # requires spatstat
|
|
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
|
|
"propOverlap" # requires Biobase
|
|
"protiq" # requires graph, and RBGL
|
|
"PSCBS" # requires DNAcopy
|
|
"pubmed_mineR" # requires SSOAP
|
|
"PubMedWordcloud" # requires GOsummaries
|
|
"qdap" # requires gender
|
|
"qtlnet" # requires pcalg
|
|
"qtpaint" # can't find QtCore libraries
|
|
"QuACN" # requires graph, RBGL
|
|
"QuasiSeq" # requires edgeR
|
|
"RADami" # requires Biostrings
|
|
"raincpc" # SDMTools.so: undefined symbol: X
|
|
"rainfreq" # SDMTools.so: undefined symbol: X
|
|
"RAM" # requires Heatplus
|
|
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
|
|
"RapidPolygonLookup" # depends on broken PBSmapping
|
|
"RbioRXN" # requires fmcsR, and KEGGREST
|
|
"RcppAPT" # configure script depends on /bin/sh
|
|
"RcmdrPlugin_seeg" # requires seeg
|
|
"Rcplex" # requires cplexAPI
|
|
"RcppRedis" # requires Hiredis
|
|
"rDEA" # no such file or directory
|
|
"RDieHarder" # requires libdieharder
|
|
"reader" # requires NCmisc
|
|
"REBayes" # requires Rmosek
|
|
"RefFreeEWAS" # requires isva
|
|
"retistruct" # depends on broken RImageJROI
|
|
"RImageJROI" # requires spatstat
|
|
"rjade" # requires V8 to build
|
|
"rJPSGCS" # requires chopsticks
|
|
"rLindo" # requires LINDO API
|
|
"Rmosek" # requires mosek
|
|
"RnavGraph" # requires graph, and RBGL
|
|
"rneos" # requires XMLRPC
|
|
"RNeXML" # requres taxize
|
|
"RobLoxBioC" # requires Biobase
|
|
"RobLox" # requires Biobase
|
|
"RockFab" # requires EBImage
|
|
"ROI_plugin_symphony" # depends on broken Rsymphony
|
|
"ROracle" # requires OCI
|
|
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
|
|
"RQuantLib" # requires QuantLib
|
|
"RSAP" # requires SAPNWRFCSDK
|
|
"RSeed" # requires RBGL, and graph
|
|
"rsig" # requires survcomp
|
|
"RSNPset" # requires qvalue
|
|
"rsprng" # requres sprng
|
|
"Rsymphony" # FIXME: requires SYMPHONY
|
|
"RVideoPoker" # requires Rpanel
|
|
"rysgran" # requires soiltexture
|
|
"samr" # requires impute
|
|
"saps" # requires piano, and survcomp
|
|
"SDD" # requires rpanel
|
|
"seeg" # requires spatstat
|
|
"selectspm" # depends on broken ecespa
|
|
"semiArtificial" # requires RSNNS
|
|
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
|
|
"sequenza" # requires copynumber
|
|
"SGCS" # requires spatstat
|
|
"siar" # requires spatstat
|
|
"SID" # requires pcalg
|
|
"SimRAD" # requires Biostrings, and ShortRead
|
|
"SimSeq" # requires edgeR
|
|
"siplab" # requires spatstat
|
|
"smart" # requires PMA
|
|
"snpEnrichment" # requires snpStats
|
|
"snplist" # requires biomaRt
|
|
"snpStatsWriter" # requires snpStats
|
|
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
|
|
"SOD" # depends on proprietary cudatoolkit
|
|
"soilphysics" # requires rpanel
|
|
"sparr" # requires spatstat
|
|
"spatialsegregation" # requires spatstat
|
|
"SpatialVx" # requires spatstat
|
|
"speaq" # requires MassSpecWavelet
|
|
"spocc" # requires leafletR
|
|
"SQDA" # requires limma
|
|
"Statomica" # requires Biobase, multtest
|
|
"stpp" # requires spatstat
|
|
"structSSI" # requires multtest
|
|
"strum" # requires Rgraphviz
|
|
"superbiclust" # requires fabia
|
|
"surveillance" # requires polyCub
|
|
"swamp" # requires impute
|
|
"sybilSBML" # requires libSBML
|
|
"taxize" # requres bold
|
|
"TcGSA" # requires multtest
|
|
"topologyGSA" # requires gRbase
|
|
"TR8" # requres taxize
|
|
"trip" # requires spatstat
|
|
"ttScreening" # requires sva, and limma
|
|
"V8" # compilation error
|
|
"vows" # requires rpanel
|
|
"vmsbase" # depends on broken PBSmapping
|
|
"WGCNA" # requires impute
|
|
"wgsea" # requires snpStats
|
|
"WideLM" # depends on proprietary cudatoolkit
|
|
"x_ent" # requires opencpu
|
|
"zoib" # tarball is invalid on server
|
|
];
|
|
|
|
otherOverrides = old: new: {
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl";
|
|
});
|
|
|
|
iFes = old.iFes.overrideDerivation (attrs: {
|
|
patches = [ ./patches/iFes.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
rpf = old.rpf.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesXsrc.patch ];
|
|
});
|
|
|
|
rJava = old.rJava.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
JavaGD = old.JavaGD.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
Mposterior = old.Mposterior.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr}/include"
|
|
];
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
|
|
];
|
|
});
|
|
|
|
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RAppArmor.patch ];
|
|
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
|
|
});
|
|
|
|
RMySQL = old.RMySQL.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RMySQL.patch ];
|
|
MYSQL_DIR="${pkgs.mysql}";
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft";
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
gputools = old.gputools.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gputools.patch ];
|
|
CUDA_HOME = "${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";
|
|
R_INC_PATH = "${pkgs.R}/lib/R/include";
|
|
CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_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 ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
OPENSSL_INCLUDES = "${pkgs.openssl}/include";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
nloptr = old.nloptr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
|
|
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
|
|
];
|
|
});
|
|
|
|
};
|
|
in
|
|
self
|