1926 lines
69 KiB
Nix
1926 lines
69 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 {
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inherit R;
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inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation;
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inherit (pkgs) gettext gfortran;
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};
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# Generates package templates given per-repository settings
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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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mkDerive = {mkHomepage, mkUrls}: args:
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# XXX: not ideal ("2.2" would match "2.22") but sufficient
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assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R));
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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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inherit sha256;
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urls = mkUrls (args // { inherit name version; });
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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 = mkHomepage (args // { inherit 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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# Templates for generating Bioconductor, CRAN and IRkernel packages
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# from the name, version, sha256, and optional per-package arguments above
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#
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deriveBioc = mkDerive {
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mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html";
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mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveBiocAnn = mkDerive {
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mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveBiocExp = mkDerive {
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mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveCran = mkDerive {
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mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
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mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveIRkernel = mkDerive {
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mkHomepage = {name}: "https://irkernel.github.io/";
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mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ];
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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 ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
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import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } //
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import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } //
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import ./cran-packages.nix { inherit self; derive = deriveCran; } //
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import ./irkernel-packages.nix { inherit self; derive = deriveIRkernel; };
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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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pander = [ self.codetools ];
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};
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packagesWithNativeBuildInputs = {
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abn = [ pkgs.gsl_1 ];
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adimpro = [ pkgs.imagemagick ];
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audio = [ pkgs.portaudio ];
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BayesSAE = [ pkgs.gsl_1 ];
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BayesVarSel = [ pkgs.gsl_1 ];
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BayesXsrc = [ pkgs.readline pkgs.ncurses ];
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bigGP = [ pkgs.openmpi ];
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BiocCheck = [ pkgs.which ];
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Biostrings = [ pkgs.zlib ];
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bnpmr = [ pkgs.gsl_1 ];
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BNSP = [ pkgs.gsl_1 ];
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cairoDevice = [ pkgs.gtk2 ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
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Cardinal = [ pkgs.which ];
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chebpol = [ pkgs.fftw ];
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ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
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cit = [ pkgs.gsl_1 ];
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curl = [ pkgs.curl.dev ];
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devEMF = [ pkgs.xorg.libXft ];
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diversitree = [ pkgs.gsl_1 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_1 ];
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git2r = [ pkgs.zlib pkgs.openssl ];
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GLAD = [ pkgs.gsl_1 ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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gmp = [ pkgs.gmp ];
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graphscan = [ pkgs.gsl_1 ];
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gsl = [ pkgs.gsl_1 ];
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h5 = [ pkgs.hdf5-cpp pkgs.which ];
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h5vc = [ pkgs.zlib.dev ];
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HiCseg = [ pkgs.gsl_1 ];
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iBMQ = [ pkgs.gsl_1 ];
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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_1 ];
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kza = [ pkgs.fftw ];
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libamtrack = [ pkgs.gsl_1 ];
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mixcat = [ pkgs.gsl_1 ];
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mvabund = [ pkgs.gsl_1 ];
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mwaved = [ pkgs.fftw ];
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ncdf4 = [ pkgs.netcdf ];
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nloptr = [ pkgs.nlopt ];
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openssl = [ pkgs.openssl.dev ];
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outbreaker = [ pkgs.gsl_1 ];
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pander = [ pkgs.pandoc pkgs.which ];
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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_1 ];
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R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
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RAppArmor = [ pkgs.libapparmor ];
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rapportools = [ pkgs.which ];
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rapport = [ pkgs.which ];
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rbamtools = [ pkgs.zlib ];
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rcdd = [ pkgs.gmp ];
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RcppCNPy = [ pkgs.zlib ];
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RcppGSL = [ pkgs.gsl_1 ];
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RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
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RcppZiggurat = [ pkgs.gsl_1 ];
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rgdal = [ pkgs.proj pkgs.gdal ];
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rgeos = [ pkgs.geos ];
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rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
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rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
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Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2 ];
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rhdf5 = [ pkgs.zlib ];
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Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
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Rhtslib = [ pkgs.zlib ];
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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_1 ];
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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.lib ];
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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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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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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_1 ];
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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_1 ];
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stringi = [ pkgs.icu.dev ];
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survSNP = [ pkgs.gsl_1 ];
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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_1 ];
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|
tkrplot = [ pkgs.xorg.libX11 ];
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|
topicmodels = [ pkgs.gsl_1 ];
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|
udunits2 = [ pkgs.udunits pkgs.expat ];
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|
V8 = [ pkgs.v8 ];
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|
VBLPCM = [ pkgs.gsl_1 ];
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VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
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|
WhopGenome = [ pkgs.zlib ];
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|
XBRL = [ pkgs.zlib pkgs.libxml2 ];
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|
xml2 = [ pkgs.libxml2 ];
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|
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
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|
affyPLM = [ pkgs.zlib ];
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|
bamsignals = [ pkgs.zlib ];
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|
BitSeq = [ pkgs.zlib ];
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|
DiffBind = [ pkgs.zlib ];
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|
ShortRead = [ pkgs.zlib.dev ];
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|
oligo = [ pkgs.zlib ];
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|
gmapR = [ pkgs.zlib ];
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|
Rsubread = [ pkgs.zlib ];
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|
XVector = [ pkgs.zlib.dev ];
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|
Rsamtools = [ pkgs.zlib.dev ];
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|
rtracklayer = [ pkgs.zlib ];
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|
affyio = [ pkgs.zlib ];
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|
VariantAnnotation = [ pkgs.zlib ];
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|
snpStats = [ pkgs.zlib ];
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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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|
RCurl = [ pkgs.curl.dev ];
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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 ];
|
|
Cairo = [ pkgs.pkgconfig ];
|
|
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
qtutils = [ pkgs.qt4 ];
|
|
ecoretriever = [ pkgs.which ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
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|
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
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|
rPython = [ pkgs.which ];
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|
gridGraphics = [ pkgs.which ];
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|
gputools = [ 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 ];
|
|
mzR = [ pkgs.netcdf ];
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|
};
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|
|
|
packagesRequireingX = [
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"accrual"
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|
"ade4TkGUI"
|
|
"adehabitat"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
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|
"AnthropMMD"
|
|
"aplpack"
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|
"aqfig"
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|
"arf3DS4"
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|
"asbio"
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|
"AtelieR"
|
|
"BAT"
|
|
"bayesDem"
|
|
"BCA"
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|
"BEQI2"
|
|
"betapart"
|
|
"betaper"
|
|
"BiodiversityR"
|
|
"BioGeoBEARS"
|
|
"bio_infer"
|
|
"bipartite"
|
|
"biplotbootGUI"
|
|
"blender"
|
|
"cairoDevice"
|
|
"CCTpack"
|
|
"cncaGUI"
|
|
"cocorresp"
|
|
"CommunityCorrelogram"
|
|
"confidence"
|
|
"constrainedKriging"
|
|
"ConvergenceConcepts"
|
|
"cpa"
|
|
"DALY"
|
|
"dave"
|
|
"debug"
|
|
"Deducer"
|
|
"DeducerExtras"
|
|
"DeducerPlugInExample"
|
|
"DeducerPlugInScaling"
|
|
"DeducerSpatial"
|
|
"DeducerSurvival"
|
|
"DeducerText"
|
|
"Demerelate"
|
|
"DescTools"
|
|
"detrendeR"
|
|
"dgmb"
|
|
"DivMelt"
|
|
"dpa"
|
|
"DSpat"
|
|
"dynamicGraph"
|
|
"dynBiplotGUI"
|
|
"EasyqpcR"
|
|
"EcoVirtual"
|
|
"ENiRG"
|
|
"EnQuireR"
|
|
"eVenn"
|
|
"exactLoglinTest"
|
|
"FAiR"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"FD"
|
|
"feature"
|
|
"FeedbackTS"
|
|
"FFD"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"fit4NM"
|
|
"forams"
|
|
"forensim"
|
|
"FreeSortR"
|
|
"fscaret"
|
|
"fSRM"
|
|
"gcmr"
|
|
"Geneland"
|
|
"GeoGenetix"
|
|
"geomorph"
|
|
"geoR"
|
|
"geoRglm"
|
|
"georob"
|
|
"GeoXp"
|
|
"GGEBiplotGUI"
|
|
"gnm"
|
|
"GPCSIV"
|
|
"GrammR"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"gsubfn"
|
|
"GUniFrac"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"HH"
|
|
"HiveR"
|
|
"HomoPolymer"
|
|
"iBUGS"
|
|
"ic50"
|
|
"iDynoR"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"likeLTD"
|
|
"logmult"
|
|
"LS2Wstat"
|
|
"MAR1"
|
|
"MareyMap"
|
|
"memgene"
|
|
"MergeGUI"
|
|
"metacom"
|
|
"Meth27QC"
|
|
"MetSizeR"
|
|
"MicroStrategyR"
|
|
"migui"
|
|
"miniGUI"
|
|
"MissingDataGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"MplusAutomation"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"MTurkR"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"OligoSpecificitySystem"
|
|
"onemap"
|
|
"OpenRepGrid"
|
|
"palaeoSig"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"PKgraph"
|
|
"playwith"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"pmg"
|
|
"PopGenReport"
|
|
"poppr"
|
|
"powerpkg"
|
|
"PredictABEL"
|
|
"prefmod"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"QCAGUI"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"qtutils"
|
|
"R2STATS"
|
|
"r4ss"
|
|
"RandomFields"
|
|
"rareNMtests"
|
|
"rAverage"
|
|
"Rcmdr"
|
|
"RcmdrPlugin_BCA"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_depthTools"
|
|
"RcmdrPlugin_DoE"
|
|
"RcmdrPlugin_doex"
|
|
"RcmdrPlugin_EACSPIR"
|
|
"RcmdrPlugin_EBM"
|
|
"RcmdrPlugin_EcoVirtual"
|
|
"RcmdrPlugin_epack"
|
|
"RcmdrPlugin_EZR"
|
|
"RcmdrPlugin_FactoMineR"
|
|
"RcmdrPlugin_HH"
|
|
"RcmdrPlugin_IPSUR"
|
|
"RcmdrPlugin_KMggplot2"
|
|
"RcmdrPlugin_lfstat"
|
|
"RcmdrPlugin_MA"
|
|
"RcmdrPlugin_mosaic"
|
|
"RcmdrPlugin_MPAStats"
|
|
"RcmdrPlugin_orloca"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_qual"
|
|
"RcmdrPlugin_ROC"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_SM"
|
|
"RcmdrPlugin_sos"
|
|
"RcmdrPlugin_steepness"
|
|
"RcmdrPlugin_survival"
|
|
"RcmdrPlugin_TeachingDemos"
|
|
"RcmdrPlugin_temis"
|
|
"RcmdrPlugin_UCA"
|
|
"recluster"
|
|
"relax"
|
|
"relimp"
|
|
"RenextGUI"
|
|
"reportRx"
|
|
"reshapeGUI"
|
|
"rgl"
|
|
"RHRV"
|
|
"rich"
|
|
"rioja"
|
|
"ripa"
|
|
"rite"
|
|
"rnbn"
|
|
"RNCEP"
|
|
"RQDA"
|
|
"RSDA"
|
|
"rsgcc"
|
|
"RSurvey"
|
|
"RunuranGUI"
|
|
"sdcMicroGUI"
|
|
"sharpshootR"
|
|
"simba"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"SOLOMON"
|
|
"soundecology"
|
|
"SPACECAP"
|
|
"spacodiR"
|
|
"spatsurv"
|
|
"sqldf"
|
|
"SRRS"
|
|
"SSDforR"
|
|
"statcheck"
|
|
"StatDA"
|
|
"STEPCAM"
|
|
"stosim"
|
|
"strvalidator"
|
|
"stylo"
|
|
"svDialogstcltk"
|
|
"svIDE"
|
|
"svSocket"
|
|
"svWidgets"
|
|
"SYNCSA"
|
|
"SyNet"
|
|
"tcltk2"
|
|
"TDMR"
|
|
"TED"
|
|
"TestScorer"
|
|
"TIMP"
|
|
"titan"
|
|
"tkrgl"
|
|
"tkrplot"
|
|
"tmap"
|
|
"tspmeta"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"twiddler"
|
|
"vcdExtra"
|
|
"VecStatGraphs3D"
|
|
"vegan"
|
|
"vegan3d"
|
|
"vegclust"
|
|
"VIMGUI"
|
|
"WMCapacity"
|
|
"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 = [
|
|
"TED" # depends on broken package animation
|
|
"streamMOA" # depends on broken package animation
|
|
"stream" # depends on broken package animation
|
|
"spdynmod" # depends on broken package animation
|
|
"treeplyr" # depends on broken package animation
|
|
"recluster" # depends on broken package animation
|
|
"geomorph" # depends on broken package animation
|
|
"phytools" # depends on broken package animation
|
|
"animation" # broken build
|
|
"srd" # broken build
|
|
"paleotree" # broken build
|
|
"ndtv" # broken build
|
|
"mvMORPH" # broken build
|
|
"mptools" # broken build
|
|
"monogeneaGM" # broken build
|
|
"molaR" # broken build
|
|
"idm" # broken build
|
|
"hisse" # broken build
|
|
"gfcanalysis" # broken build
|
|
"evolqg" # broken build
|
|
"evobiR" # broken build
|
|
"convevol" # broken build
|
|
"bayou" # broken build
|
|
"anim_plots" # broken build
|
|
"TKF" # broken build
|
|
"Rphylopars" # broken build
|
|
"RAM" # broken build
|
|
"PhySortR" # broken build
|
|
"MonoPhy" # broken build
|
|
"Momocs" # broken build
|
|
"Evomorph" # broken build
|
|
"PBD" # depends on broken package DDD
|
|
"DDD" # broken build
|
|
"BMhyd" # broken build
|
|
"rscala" # broken build
|
|
"rgpui" # depends on broken package rgp
|
|
"rgp" # broken build
|
|
"qcmetrics" # broken build
|
|
"lfe" # broken build
|
|
"interactiveDisplay" # depends on broken package interactiveDisplayBase
|
|
"RefNet" # depends on broken package interactiveDisplayBase
|
|
"pwOmics" # depends on broken package interactiveDisplayBase
|
|
"grasp2db" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Mmusculus_v75" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Hsapiens_v79" # depends on broken package interactiveDisplayBase
|
|
"EnsDb_Hsapiens_v75" # depends on broken package interactiveDisplayBase
|
|
"ensembldb" # depends on broken package interactiveDisplayBase
|
|
"AnnotationHubData" # depends on broken package interactiveDisplayBase
|
|
"AnnotationHub" # depends on broken package interactiveDisplayBase
|
|
"interactiveDisplayBase" # broken build
|
|
"h2o" # broken build
|
|
"funModeling" # broken build
|
|
"brr" # broken build
|
|
"bedr" # broken build
|
|
"Sabermetrics" # broken build
|
|
"RKEEL" # depends on broken package RKEELjars
|
|
"RKEELjars" # broken build
|
|
"RapidPolygonLookup" # depends on broken package PBSmapping
|
|
"PBSmapping" # broken build
|
|
"stagePop" # depends on broken package PBSddesolve
|
|
"PBSddesolve" # broken build
|
|
"Metab" # broken build
|
|
"Crossover" # broken build
|
|
"CardinalWorkflows" # broken build
|
|
"spoccutils" # depends on broken package spocc
|
|
"mapr" # depends on broken package spocc
|
|
"vmsbase" # broken build
|
|
"vcfR" # broken build
|
|
"strataG" # broken build
|
|
"SSDM" # broken build
|
|
"SimInf" # broken build
|
|
"shazam" # broken build
|
|
"rsvg" # broken build
|
|
"Rothermel" # broken build
|
|
"rfPermute" # broken build
|
|
"redland" # broken build
|
|
"RAppArmor" # broken build
|
|
"permGPU" # broken build
|
|
"pdftools" # broken build
|
|
"OceanView" # broken build
|
|
"MSeasyTkGUI" # broken build
|
|
"mrMLM" # broken build
|
|
"MonetDBLite" # broken build
|
|
"MixGHD" # broken build
|
|
"LCMCR" # broken build
|
|
"hunspell" # broken build
|
|
"googleformr" # broken build
|
|
"ggseas" # depends on broken package x13binary
|
|
"seasonal" # depends on broken package x13binary
|
|
"gunsales" # depends on broken package x13binary
|
|
"x13binary" # broken build
|
|
"fds" # broken build
|
|
"exifr" # broken build
|
|
"rite" # depends on broken package euroMix
|
|
"MBCB" # depends on broken package euroMix
|
|
"forensim" # depends on broken package euroMix
|
|
"dynBiplotGUI" # depends on broken package euroMix
|
|
"cncaGUI" # depends on broken package euroMix
|
|
"biplotbootGUI" # depends on broken package euroMix
|
|
"AnthropMMD" # depends on broken package euroMix
|
|
"ilc" # depends on broken package demography
|
|
"demography" # broken build
|
|
"webbioc" # depends on broken package limma
|
|
"davidTiling" # depends on broken package limma
|
|
"tilingArray" # depends on broken package limma
|
|
"NAPPA" # depends on broken package limma
|
|
"NanoStringNorm" # depends on broken package limma
|
|
"synapterdata" # depends on broken package limma
|
|
"synapter" # depends on broken package limma
|
|
"RforProteomics" # depends on broken package limma
|
|
"pRolocdata" # depends on broken package limma
|
|
"ProCoNA" # depends on broken package limma
|
|
"Pbase" # depends on broken package limma
|
|
"MSnID" # depends on broken package limma
|
|
"msmsEDA" # depends on broken package limma
|
|
"MSnbase" # depends on broken package limma
|
|
"staRank" # depends on broken package limma
|
|
"phenoDist" # depends on broken package limma
|
|
"imageHTS" # depends on broken package limma
|
|
"Mulder2012" # depends on broken package limma
|
|
"HTSanalyzeR" # depends on broken package limma
|
|
"gespeR" # depends on broken package limma
|
|
"cellHTS2" # depends on broken package limma
|
|
"affyPara" # depends on broken package limma
|
|
"vsn" # depends on broken package limma
|
|
"ttScreening" # depends on broken package limma
|
|
"metaX" # depends on broken package limma
|
|
"SSPA" # depends on broken package limma
|
|
"SQDA" # depends on broken package limma
|
|
"ADaCGH2" # depends on broken package limma
|
|
"snapCGH" # depends on broken package limma
|
|
"Shrinkage" # depends on broken package limma
|
|
"SafeQuant" # depends on broken package limma
|
|
"RTopper" # depends on broken package limma
|
|
"RTCGAToolbox" # depends on broken package limma
|
|
"RPPanalyzer" # depends on broken package limma
|
|
"Rnits" # depends on broken package limma
|
|
"RNAinteractMAPK" # depends on broken package limma
|
|
"RNAinteract" # depends on broken package limma
|
|
"SimBindProfiles" # depends on broken package limma
|
|
"ccTutorial" # depends on broken package limma
|
|
"Ringo" # depends on broken package limma
|
|
"rCGH" # depends on broken package limma
|
|
"qusage" # depends on broken package limma
|
|
"qpcrNorm" # depends on broken package limma
|
|
"prot2D" # depends on broken package limma
|
|
"polyester" # depends on broken package limma
|
|
"plmDE" # depends on broken package limma
|
|
"phenoTest" # depends on broken package limma
|
|
"RANKS" # depends on broken package limma
|
|
"PerfMeas" # depends on broken package limma
|
|
"pepStat" # depends on broken package limma
|
|
"PECA" # depends on broken package limma
|
|
"PADOG" # depends on broken package limma
|
|
"OGSA" # depends on broken package limma
|
|
"nethet" # depends on broken package limma
|
|
"lpNet" # depends on broken package limma
|
|
"nem" # depends on broken package limma
|
|
"monocle" # depends on broken package limma
|
|
"MmPalateMiRNA" # depends on broken package limma
|
|
"miRtest" # depends on broken package limma
|
|
"miRLAB" # depends on broken package limma
|
|
"mGSZ" # depends on broken package limma
|
|
"MAMA" # depends on broken package limma
|
|
"metaMA" # depends on broken package limma
|
|
"msd16s" # depends on broken package limma
|
|
"metagenomeSeq" # depends on broken package limma
|
|
"metabolomics" # depends on broken package limma
|
|
"maSigPro" # depends on broken package limma
|
|
"timecourse" # depends on broken package limma
|
|
"stepNorm" # depends on broken package limma
|
|
"RBM" # depends on broken package limma
|
|
"saps" # depends on broken package limma
|
|
"PharmacoGx" # depends on broken package limma
|
|
"piano" # depends on broken package limma
|
|
"OLINgui" # depends on broken package limma
|
|
"OLIN" # depends on broken package limma
|
|
"nnNorm" # depends on broken package limma
|
|
"ListerEtAlBSseq" # depends on broken package limma
|
|
"compEpiTools" # depends on broken package limma
|
|
"methylPipe" # depends on broken package limma
|
|
"dyebiasexamples" # depends on broken package limma
|
|
"dyebias" # depends on broken package limma
|
|
"CluMix" # depends on broken package limma
|
|
"HCsnip" # depends on broken package limma
|
|
"sigaR" # depends on broken package limma
|
|
"plrs" # depends on broken package limma
|
|
"CGHregions" # depends on broken package limma
|
|
"QDNAseq_mm10" # depends on broken package limma
|
|
"QDNAseq_hg19" # depends on broken package limma
|
|
"QDNAseq" # depends on broken package limma
|
|
"GeneBreak" # depends on broken package limma
|
|
"focalCall" # depends on broken package limma
|
|
"CGHnormaliter" # depends on broken package limma
|
|
"CGHcall" # depends on broken package limma
|
|
"CGHbase" # depends on broken package limma
|
|
"beta7" # depends on broken package limma
|
|
"marray" # depends on broken package limma
|
|
"LVSmiRNA" # depends on broken package limma
|
|
"lmdme" # depends on broken package limma
|
|
"limmaGUI" # depends on broken package limma
|
|
"InPAS" # depends on broken package limma
|
|
"iChip" # depends on broken package limma
|
|
"unifiedWMWqPCR" # depends on broken package limma
|
|
"nondetects" # depends on broken package limma
|
|
"HTqPCR" # depends on broken package limma
|
|
"HD2013SGI" # depends on broken package limma
|
|
"vtpnet" # depends on broken package limma
|
|
"gwascat" # depends on broken package limma
|
|
"gQTLstats" # depends on broken package limma
|
|
"GOsummaries" # depends on broken package limma
|
|
"yri1kgv" # depends on broken package limma
|
|
"hmyriB36" # depends on broken package limma
|
|
"cheung2010" # depends on broken package limma
|
|
"GGtools" # depends on broken package limma
|
|
"GGdata" # depends on broken package limma
|
|
"encoDnaseI" # depends on broken package limma
|
|
"dsQTL" # depends on broken package limma
|
|
"ceuhm3" # depends on broken package limma
|
|
"ceu1kgv" # depends on broken package limma
|
|
"ceu1kg" # depends on broken package limma
|
|
"GGBase" # depends on broken package limma
|
|
"GeneSelector" # depends on broken package limma
|
|
"GeneSelectMMD" # depends on broken package limma
|
|
"gCMAPWeb" # depends on broken package limma
|
|
"gCMAP" # depends on broken package limma
|
|
"flowBin" # depends on broken package limma
|
|
"Fletcher2013a" # depends on broken package limma
|
|
"FEM" # depends on broken package limma
|
|
"explorase" # depends on broken package limma
|
|
"ExiMiR" # depends on broken package limma
|
|
"tweeDEseq" # depends on broken package limma
|
|
"tRanslatome" # depends on broken package limma
|
|
"ToPASeq" # depends on broken package limma
|
|
"timeSeq" # depends on broken package limma
|
|
"TCGAbiolinks" # depends on broken package limma
|
|
"TCC" # depends on broken package limma
|
|
"systemPipeR" # depends on broken package limma
|
|
"STATegRa" # depends on broken package limma
|
|
"ssizeRNA" # depends on broken package limma
|
|
"RUVSeq" # depends on broken package limma
|
|
"RnaSeqSampleSizeData" # depends on broken package limma
|
|
"RnaSeqSampleSize" # depends on broken package limma
|
|
"rnaSeqMap" # depends on broken package limma
|
|
"ReportingTools" # depends on broken package limma
|
|
"QuasiSeq" # depends on broken package limma
|
|
"PROPER" # depends on broken package limma
|
|
"myTAI" # depends on broken package limma
|
|
"msmsTests" # depends on broken package limma
|
|
"methylMnM" # depends on broken package limma
|
|
"metaseqR" # depends on broken package limma
|
|
"MEDIPS" # depends on broken package limma
|
|
"manta" # depends on broken package limma
|
|
"HTSFilter" # depends on broken package limma
|
|
"HTSCluster" # depends on broken package limma
|
|
"GSAgm" # depends on broken package limma
|
|
"fdrDiscreteNull" # depends on broken package limma
|
|
"erccdashboard" # depends on broken package limma
|
|
"EnrichmentBrowser" # depends on broken package limma
|
|
"edgeRun" # depends on broken package limma
|
|
"EDDA" # depends on broken package limma
|
|
"RnaSeqTutorial" # depends on broken package limma
|
|
"easyRNASeq" # depends on broken package limma
|
|
"DEGreport" # depends on broken package limma
|
|
"Imetagene" # depends on broken package limma
|
|
"metagene" # depends on broken package limma
|
|
"DBChIP" # depends on broken package limma
|
|
"babel" # depends on broken package limma
|
|
"apmsWAPP" # depends on broken package limma
|
|
"ampliQueso" # depends on broken package limma
|
|
"edgeR" # depends on broken package limma
|
|
"MMDiff" # depends on broken package limma
|
|
"ChIPQC" # depends on broken package limma
|
|
"DiffBind" # depends on broken package limma
|
|
"DCGL" # depends on broken package limma
|
|
"Prostar" # depends on broken package limma
|
|
"DAPAR" # depends on broken package limma
|
|
"DAAGbio" # depends on broken package limma
|
|
"csaw" # depends on broken package limma
|
|
"cp4p" # depends on broken package limma
|
|
"coRNAi" # depends on broken package limma
|
|
"Cormotif" # depends on broken package limma
|
|
"CORM" # depends on broken package limma
|
|
"TurboNorm" # depends on broken package limma
|
|
"maigesPack" # depends on broken package limma
|
|
"convert" # depends on broken package limma
|
|
"compcodeR" # depends on broken package limma
|
|
"codelink" # depends on broken package limma
|
|
"clippda" # depends on broken package limma
|
|
"REDseq" # depends on broken package limma
|
|
"GUIDEseq" # depends on broken package limma
|
|
"ggtut" # depends on broken package limma
|
|
"FunciSNP" # depends on broken package limma
|
|
"ChIPpeakAnno" # depends on broken package limma
|
|
"ChIPComp" # depends on broken package limma
|
|
"ChimpHumanBrainData" # depends on broken package limma
|
|
"charmData" # depends on broken package limma
|
|
"charm" # depends on broken package limma
|
|
"cghMCR" # depends on broken package limma
|
|
"CCl4" # depends on broken package limma
|
|
"casper" # depends on broken package limma
|
|
"CancerMutationAnalysis" # depends on broken package limma
|
|
"CALIB" # depends on broken package limma
|
|
"quantro" # depends on broken package limma
|
|
"RnBeads" # depends on broken package limma
|
|
"mvoutData" # depends on broken package limma
|
|
"MineICA" # depends on broken package limma
|
|
"methyAnalysis" # depends on broken package limma
|
|
"MAQCsubsetILM" # depends on broken package limma
|
|
"MAQCsubset" # depends on broken package limma
|
|
"lumiRatIDMapping" # depends on broken package limma
|
|
"lumiMouseIDMapping" # depends on broken package limma
|
|
"lumiHumanIDMapping" # depends on broken package limma
|
|
"lumiBarnes" # depends on broken package limma
|
|
"iCheck" # depends on broken package limma
|
|
"ffpeExampleData" # depends on broken package limma
|
|
"arrayMvout" # depends on broken package limma
|
|
"lumi" # depends on broken package limma
|
|
"ffpe" # depends on broken package limma
|
|
"methylumi" # depends on broken package limma
|
|
"shinyMethyl" # depends on broken package limma
|
|
"MethylAidData" # depends on broken package limma
|
|
"MethylAid" # depends on broken package limma
|
|
"IlluminaHumanMethylation450kmanifest" # depends on broken package limma
|
|
"skewr" # depends on broken package limma
|
|
"wateRmelon" # depends on broken package limma
|
|
"missMethyl" # depends on broken package limma
|
|
"minfiData" # depends on broken package limma
|
|
"IlluminaHumanMethylation450kanno_ilmn12_hg19" # depends on broken package limma
|
|
"IlluminaHumanMethylation27kmanifest" # depends on broken package limma
|
|
"FlowSorted_DLPFC_450k" # depends on broken package limma
|
|
"FlowSorted_Blood_450k" # depends on broken package limma
|
|
"ENmix" # depends on broken package limma
|
|
"ELMER" # depends on broken package limma
|
|
"MEAL" # depends on broken package limma
|
|
"DMRcate" # depends on broken package limma
|
|
"CopyNumber450kData" # depends on broken package limma
|
|
"CopyNumber450k" # depends on broken package limma
|
|
"conumee" # depends on broken package limma
|
|
"ChAMP" # depends on broken package limma
|
|
"minfi" # depends on broken package limma
|
|
"regionReport" # depends on broken package limma
|
|
"derfinderPlot" # depends on broken package limma
|
|
"derfinder" # depends on broken package limma
|
|
"bumphunter" # depends on broken package limma
|
|
"birta" # depends on broken package limma
|
|
"betr" # depends on broken package limma
|
|
"beadarrayMSV" # depends on broken package limma
|
|
"RobLoxBioC" # depends on broken package limma
|
|
"maGUI" # depends on broken package limma
|
|
"epigenomix" # depends on broken package limma
|
|
"blima" # depends on broken package limma
|
|
"BeadArrayUseCases" # depends on broken package limma
|
|
"beadarrayFilter" # depends on broken package limma
|
|
"beadarrayExampleData" # depends on broken package limma
|
|
"beadarray" # depends on broken package limma
|
|
"ballgown" # depends on broken package limma
|
|
"attract" # depends on broken package limma
|
|
"ArrayTools" # depends on broken package limma
|
|
"arrayQuality" # depends on broken package limma
|
|
"DrugVsDisease" # depends on broken package limma
|
|
"ArrayExpress" # depends on broken package limma
|
|
"oneChannelGUI" # depends on broken package limma
|
|
"affylmGUI" # depends on broken package limma
|
|
"AffyExpress" # depends on broken package limma
|
|
"AgiMicroRna" # depends on broken package limma
|
|
"affycoretools" # depends on broken package limma
|
|
"ABSSeq" # depends on broken package limma
|
|
"a4" # depends on broken package limma
|
|
"a4Base" # depends on broken package limma
|
|
"limma" # broken build
|
|
"TransView" # broken build
|
|
"Starr" # broken build
|
|
"SICtools" # broken build
|
|
"ReQON" # depends on broken package seqbias
|
|
"seqbias" # broken build
|
|
"Repitools" # broken build
|
|
"QuasR" # broken build
|
|
"qrqc" # broken build
|
|
"ProteomicsAnnotationHubData" # broken build
|
|
"podkat" # broken build
|
|
"PING" # depends on broken package PICS
|
|
"PICS" # broken build
|
|
"mcaGUI" # broken build
|
|
"deepSNV" # broken build
|
|
"motifbreakR" # depends on broken package MotIV
|
|
"LowMACA" # depends on broken package MotIV
|
|
"dagLogo" # depends on broken package MotIV
|
|
"motifStack" # depends on broken package MotIV
|
|
"MotIV" # broken build
|
|
"CNEr" # broken build
|
|
"canceR" # broken build
|
|
"BubbleTree" # broken build
|
|
"arrayQualityMetrics" # broken build
|
|
"ArrayExpressHTS" # broken build
|
|
"TargetSearchData" # depends on broken package TargetSearch
|
|
"TargetSearch" # broken build
|
|
"ptw" # depends on broken package nloptr
|
|
"gpuR" # broken build
|
|
"erma" # broken build
|
|
"MBmca" # depends on broken package chipPCR
|
|
"dpcR" # depends on broken package chipPCR
|
|
"chipPCR" # broken build
|
|
"alsace" # broken build
|
|
"rrlda" # depends on broken package VIM
|
|
"qrfactor" # depends on broken package VIM
|
|
"MVN" # depends on broken package VIM
|
|
"mvoutlier" # depends on broken package VIM
|
|
"robCompositions" # depends on broken package VIM
|
|
"DiagrammeRsvg" # depends on broken package V8
|
|
"dagitty" # depends on broken package V8
|
|
"remoter" # depends on broken package sodium
|
|
"Fletcher2013b" # depends on broken package RTN
|
|
"apaStyle" # depends on broken package ReporteRs
|
|
"categoryCompare" # depends on broken package RCytoscape
|
|
"preseqR" # depends on broken package polynom
|
|
"permutations" # depends on broken package partitions
|
|
"GLMMRR" # depends on broken package lme4
|
|
"replicationInterval" # depends on broken package lme4
|
|
"GWASdata" # depends on broken package GWASTools
|
|
"EnsemblePCReg" # depends on broken package EnsembleBase
|
|
"EnsembleCV" # depends on broken package EnsembleBase
|
|
"cpgen" # depends on broken package pedigreemm
|
|
"mitml" # depends on broken package jomo
|
|
"IlluminaHumanMethylation450k_db" # broken build
|
|
"gahgu95ecdf" # broken build
|
|
"gahgu95dcdf" # broken build
|
|
"gahgu95ccdf" # broken build
|
|
"gahgu95bcdf" # broken build
|
|
"gahgu95av2cdf" # broken build
|
|
"PREDAsampledata" # depends on broken package gahgu133plus2cdf
|
|
"gahgu133plus2cdf" # broken build
|
|
"gahgu133bcdf" # broken build
|
|
"gahgu133acdf" # broken build
|
|
"annmap" # depends on broken package RMySQL
|
|
"choroplethr" # depends on broken package acs
|
|
"acs" # broken build
|
|
"spray" # depends on broken package partitions
|
|
"CNVrd2" # broken build
|
|
"proteoQC" # depends on broken package rTANDEM
|
|
"PGA" # depends on broken package rTANDEM
|
|
"MBESS" # depends on broken package OpenMx
|
|
"DOQTL" # depends on broken package rhdf5
|
|
"DmelSGI" # depends on broken package rhdf5
|
|
"flowDiv" # depends on broken package ncdfFlow
|
|
"ChemmineDrugs" # depends on broken package ChemmineR
|
|
"stpm" # depends on broken package nloptr
|
|
"sjmisc" # depends on broken package nloptr
|
|
"rstanarm" # depends on broken package nloptr
|
|
"glmmsr" # depends on broken package nloptr
|
|
"FDboost" # depends on broken package nloptr
|
|
"faraway" # depends on broken package nloptr
|
|
"interplot" # depends on broken package nloptr
|
|
"VSE" # depends on broken package car
|
|
"VARSEDIG" # depends on broken package car
|
|
"translateSPSS2R" # depends on broken package car
|
|
"tadaatoolbox" # depends on broken package car
|
|
"lavaan_shiny" # depends on broken package car
|
|
"RcmdrPlugin_GWRM" # depends on broken package car
|
|
"TextoMineR" # depends on broken package car
|
|
"pcaBootPlot" # depends on broken package car
|
|
"ClustGeo" # depends on broken package car
|
|
"preproviz" # depends on broken package car
|
|
"hsdar" # depends on broken package car
|
|
"DecisionCurve" # depends on broken package car
|
|
"CONDOP" # depends on broken package car
|
|
"EnsemblePenReg" # depends on broken package car
|
|
"EnsembleBase" # depends on broken package car
|
|
"fullfact" # depends on broken package car
|
|
"clusterSEs" # depends on broken package car
|
|
"ggiraph" # depends on broken package gdtools
|
|
"rvg" # depends on broken package gdtools
|
|
"ggpmisc" # depends on broken package polynom
|
|
"mlt_docreg" # depends on broken package polynom
|
|
"mlt" # depends on broken package polynom
|
|
"basefun" # depends on broken package polynom
|
|
"rtable" # depends on broken package ReporteRs
|
|
"Mediana" # depends on broken package ReporteRs
|
|
"ReporteRs" # broken build
|
|
"abd" # depends on broken package nlopt
|
|
"adabag" # depends on broken package nlopt
|
|
"adhoc" # broken build
|
|
"AER" # depends on broken package nlopt
|
|
"afex" # depends on broken package nlopt
|
|
"agRee" # depends on broken package nlopt
|
|
"aLFQ" # depends on broken package nlopt
|
|
"algstat" # broken build
|
|
"alr3" # depends on broken package nlopt
|
|
"alr4" # depends on broken package nlopt
|
|
"alsace" # depends on broken nloptr
|
|
"anacor" # depends on broken package nlopt
|
|
"aods3" # depends on broken package nlopt
|
|
"apaTables" # depends on broken package car
|
|
"apt" # depends on broken package nlopt
|
|
"ArfimaMLM" # depends on broken package nlopt
|
|
"arm" # depends on broken package nlopt
|
|
"ART" # depends on broken package car
|
|
"ARTool" # depends on broken package nlopt
|
|
"AssetPricing" # broken build
|
|
"AtelieR" # broken build
|
|
"auRoc" # depends on broken package MBESS
|
|
"AutoModel" # depends on broken package car
|
|
"bamdit" # broken build
|
|
"bapred" # depends on broken package lme4
|
|
"bartMachine" # depends on broken package nlopt
|
|
"bayesDem" # depends on broken package nlopt
|
|
"bayesLife" # depends on broken package nlopt
|
|
"BayesMed" # broken build
|
|
"bayesmix" # broken build
|
|
"bayesPop" # depends on broken package nlopt
|
|
"Bayesthresh" # depends on broken package nlopt
|
|
"BaySIC" # broken build
|
|
"BBRecapture" # depends on broken package nlopt
|
|
"BCA" # depends on broken package nlopt
|
|
"bdynsys" # depends on broken package car
|
|
"BEST" # broken build
|
|
"bgmm" # depends on broken package nlopt
|
|
"BIFIEsurvey" # depends on broken package nlopt
|
|
"BiGGR" # depends on broken package rsbml
|
|
"bioassayR" # broken build
|
|
"BiodiversityR" # depends on broken package nlopt
|
|
"biotools" # depends on broken package rpanel
|
|
"birte" # build is broken
|
|
"BLCOP" # depends on broken package Rsymphony
|
|
"blmeco" # depends on broken package nlopt
|
|
"blme" # depends on broken package nlopt
|
|
"bmd" # depends on broken package nlopt
|
|
"bmem" # depends on broken package nlopt
|
|
"bmeta" # depends on broken package R2jags
|
|
"bootnet" # depends on broken package nlopt
|
|
"boral" # broken build
|
|
"BradleyTerry2" # depends on broken package nlopt
|
|
"BrailleR" # broken build
|
|
"brainGraph" # build is broken
|
|
"brms" # build is broken
|
|
"BRugs" # build is broken
|
|
"BTSPAS" # broken build
|
|
"CADFtest" # depends on broken package nlopt
|
|
"cAIC4" # depends on broken package nlopt
|
|
"candisc" # depends on broken package nlopt
|
|
"carcass" # depends on broken package nlopt
|
|
"car" # depends on broken package nlopt
|
|
"caret" # depends on broken package nlopt
|
|
"caretEnsemble" # depends on broken package nlopt
|
|
"CARrampsOcl" # depends on broken package OpenCL
|
|
"Causata" # broken build
|
|
"CCpop" # depends on broken package nlopt
|
|
"CCTpack" # broken build
|
|
"ChainLadder" # depends on broken package nlopt
|
|
"ChemmineR" # Build Is Broken
|
|
"chipenrich" # build is broken
|
|
"chipPCR" # depends on broken nloptr
|
|
"classify" # broken build
|
|
"climwin" # depends on broken package nlopt
|
|
"CLME" # depends on broken package nlopt
|
|
"clpAPI" # build is broken
|
|
"clusterPower" # depends on broken package nlopt
|
|
"clusterSEs" # depends on broken AER
|
|
"ClustGeo" # depends on broken FactoMineR
|
|
"CNORfuzzy" # depends on broken package nlopt
|
|
"CNVPanelizer" # depends on broken cn.mops
|
|
"COHCAP" # build is broken
|
|
"colorscience" # broken build
|
|
"compendiumdb" # broken build
|
|
"conformal" # depends on broken package nlopt
|
|
"corHMM" # depends on broken package nlopt
|
|
"CosmoPhotoz" # depends on broken package nlopt
|
|
"covmat" # depends on broken package VIM
|
|
"cplexAPI" # build is broken
|
|
"cquad" # depends on broken package car
|
|
"CrypticIBDcheck" # depends on broken package nlopt
|
|
"ctsem" # depends on broken package OpenMx
|
|
"cudaBayesreg" # build is broken
|
|
"daff" # depends on broken package V8
|
|
"dagbag" # build is broken
|
|
"DAMisc" # depends on broken package nlopt
|
|
"datafsm" # depends on broken package caret
|
|
"dbConnect" # broken build
|
|
"DBKGrad" # depends on broken package rpanel
|
|
#"dcmle" # broken build
|
|
"ddst" # broken build
|
|
"Deducer" # depends on broken package nlopt
|
|
"DeducerExtras" # depends on broken package nlopt
|
|
"DeducerPlugInExample" # depends on broken package nlopt
|
|
"DeducerPlugInScaling" # depends on broken package nlopt
|
|
"DeducerSpatial" # depends on broken package nlopt
|
|
"DeducerSurvival" # depends on broken package nlopt
|
|
"DeducerText" # depends on broken package nlopt
|
|
"DEGraph" # depends on broken package RCytoscape
|
|
"destiny" # depends on broken package VIM
|
|
"DiagTest3Grp" # depends on broken package nlopt
|
|
"diffHic" # depends on broken package edgeR
|
|
"difR" # depends on broken package nlopt
|
|
"DirichletMultinomial" # Build Is Broken
|
|
"DistatisR" # depends on broken package nlopt
|
|
"diveRsity" # depends on broken package nlopt
|
|
"DJL" # depends on broken package car
|
|
"dpa" # depends on broken package nlopt
|
|
"dpcR" # depends on broken nloptr
|
|
"drc" # depends on broken package nlopt
|
|
"drfit" # depends on broken package nlopt
|
|
"drsmooth" # depends on broken package nlopt
|
|
"dynlm" # depends on broken package nlopt
|
|
"easyanova" # depends on broken package nlopt
|
|
"ecd" # depends on broken package polynom
|
|
"edge" # depends on broken package nlopt
|
|
"edgeR" # broken url
|
|
"eeptools" # depends on broken package nlopt
|
|
"EffectLiteR" # depends on broken package nlopt
|
|
"effects" # depends on broken package nlopt
|
|
"eiR" # depends on broken package ChemmineR
|
|
"EMA" # depends on broken package nlopt
|
|
"embryogrowth" # broken build
|
|
"emg" # broken build
|
|
"EnQuireR" # depends on broken package nlopt
|
|
"episplineDensity" # depends on broken package nlopt
|
|
"epr" # depends on broken package nlopt
|
|
"erer" # depends on broken package nlopt
|
|
"erma" # depends on broken GenomicFiles
|
|
"erpR" # depends on broken package rpanel
|
|
"ESKNN" # depends on broken package caret
|
|
"euroMix" # build is broken
|
|
"extRemes" # depends on broken package nlopt
|
|
"ez" # depends on broken package nlopt
|
|
"ezec" # depends on broken package drc
|
|
"facopy" # depends on broken package nlopt
|
|
"FactoMineR" # depends on broken package nlopt
|
|
"Factoshiny" # depends on broken package nlopt
|
|
"faoutlier" # depends on broken package nlopt
|
|
"fastR" # depends on broken package nlopt
|
|
"FDRreg" # depends on broken package nlopt
|
|
"fishmethods" # depends on broken package lme4
|
|
"flipflop" # broken build
|
|
"flowDensity" # depends on broken package nlopt
|
|
"flowPeaks" # build is broken
|
|
"flowQ" # build is broken
|
|
"flowStats" # depends on broken package ncdfFlow
|
|
"flowVS" # depends on broken package ncdfFlow
|
|
"flowWorkspace" # depends on broken package ncdfFlow
|
|
"fmcsR" # depends on broken package ChemmineR
|
|
"fPortfolio" # depends on broken package Rsymphony
|
|
"fracprolif" # broken build
|
|
"FreeSortR" # broken build
|
|
"freqweights" # depends on broken package nlopt
|
|
"frmqa" # broken build
|
|
"FSA" # depends on broken package car
|
|
"fscaret" # depends on broken package nlopt
|
|
"funcy" # depends on broken package car
|
|
"fxregime" # depends on broken package nlopt
|
|
"gamclass" # depends on broken package nlopt
|
|
"gamlss_demo" # depends on broken package rpanel
|
|
"gamm4" # depends on broken package nlopt
|
|
"gaussquad" # broken build
|
|
"gcmr" # depends on broken package nlopt
|
|
"GDAtools" # depends on broken package nlopt
|
|
"gdtools" # broken build
|
|
"GENESIS" # broken build
|
|
"genridge" # depends on broken package nlopt
|
|
"geojsonio" # depends on broken package V8
|
|
"GEWIST" # depends on broken package nlopt
|
|
"ggtree" # broken build
|
|
"gimme" # depends on broken package nlopt
|
|
"gmatrix" # depends on broken package cudatoolkit
|
|
"gMCP" # build is broken
|
|
"gmum_r" # broken build
|
|
"Goslate" # depends on broken package PythonInR
|
|
"GPC" # broken build
|
|
"gplm" # depends on broken package nlopt
|
|
"gpuR" # depends on GPU-specific header files
|
|
"gputools" # depends on broken package cudatoolkit
|
|
"granova" # depends on broken package nlopt
|
|
"graphicalVAR" # depends on broken package nlopt
|
|
"GraphPAC" # broken build
|
|
"gridGraphics" # build is broken
|
|
"GSCA" # depends on broken package rhdf5
|
|
"GUIDE" # depends on broken package rpanel
|
|
"GWAF" # depends on broken package nlopt
|
|
"GWASTools" # broken build
|
|
"hbsae" # depends on broken package nlopt
|
|
"heplots" # depends on broken package nlopt
|
|
"HiDimMaxStable" # broken build
|
|
"HierO" # Build Is Broken
|
|
"HilbertVisGUI" # Build Is Broken
|
|
"HiPLARM" # Build Is Broken
|
|
"HistDAWass" # depends on broken package nlopt
|
|
"HLMdiag" # depends on broken package nlopt
|
|
"homomorpheR" # broken build
|
|
"hpcwld" # broken build
|
|
"hwwntest" # broken build
|
|
"HydeNet" # broken build
|
|
"hysteresis" # depends on broken package nlopt
|
|
"IATscores" # depends on broken package nlopt
|
|
"ibd" # depends on broken package nlopt
|
|
"iccbeta" # depends on broken package nlopt
|
|
"iClick" # depends on broken package rugarch
|
|
"ifaTools" # depends on broken package OpenMx
|
|
"imager" # broken build
|
|
"immunoClust" # build is broken
|
|
"in2extRemes" # depends on broken package nlopt
|
|
"inferference" # depends on broken package nlopt
|
|
"influence_ME" # depends on broken package nlopt
|
|
"inSilicoMerging" # build is broken
|
|
"INSPEcT" # depends on broken GenomicFeatures
|
|
"interplot" # depends on broken arm
|
|
"IsingFit" # depends on broken package nlopt
|
|
"ITEMAN" # depends on broken package car
|
|
"iteRates" # broken build
|
|
"iterpc" # broken build
|
|
"IUPS" # broken build
|
|
"IVAS" # depends on broken package nlopt
|
|
"ivpack" # depends on broken package nlopt
|
|
"jagsUI" # broken build
|
|
"JAGUAR" # depends on broken package nlopt
|
|
"joda" # depends on broken package nlopt
|
|
"jomo" # build is broken
|
|
"js" # depends on broken package V8
|
|
"KoNLP" # broken build
|
|
"kzft" # broken build
|
|
"LaplaceDeconv" # depends on broken package orthopolynom
|
|
"lawn" # depends on broken package V8
|
|
"ldamatch" # broken build
|
|
"learnstats" # depends on broken package nlopt
|
|
"lefse" # build is broken
|
|
"lessR" # depends on broken package nlopt
|
|
"lgcp" # depends on broken package rpanel
|
|
"Libra" # broken build
|
|
"LinRegInteractive" # depends on broken package rpanel
|
|
"lira" # broken build
|
|
"littler" # broken build
|
|
"lme4" # depends on broken package nlopt
|
|
"LMERConvenienceFunctions" # depends on broken package nlopt
|
|
"lmerTest" # depends on broken package nlopt
|
|
"lmSupport" # depends on broken package nlopt
|
|
"LOGIT" # depends on broken package caret
|
|
"longpower" # depends on broken package nlopt
|
|
"LPTime" # broken build
|
|
"MAIT" # depends on broken package nlopt
|
|
"mAPKL" # build is broken
|
|
"maPredictDSC" # depends on broken package nlopt
|
|
"mar1s" # broken build
|
|
"marked" # depends on broken package nlopt
|
|
"matchingMarkets" # broken build
|
|
"MatrixRider" # depends on broken package DirichletMultinomial
|
|
"MaxPro" # depends on broken package nlopt
|
|
"mbest" # depends on broken package nlopt
|
|
"MBmca" # depends on broken nloptr
|
|
"mBvs" # build is broken
|
|
"meboot" # depends on broken package nlopt
|
|
"medflex" # depends on broken package car
|
|
"mediation" # depends on broken package lme4
|
|
"MEDME" # depends on broken package nlopt
|
|
"MEMSS" # depends on broken package nlopt
|
|
"merTools" # depends on broken package arm
|
|
"meta4diag" # broken build
|
|
"metagear" # build is broken
|
|
"metaheur" # depends on broken package preprocomb
|
|
"metamisc" # broken build
|
|
"metaplus" # depends on broken package nlopt
|
|
"metaSEM" # depends on broken package OpenMx
|
|
"Metatron" # depends on broken package nlopt
|
|
"miceadds" # depends on broken package nlopt
|
|
"micEconAids" # depends on broken package nlopt
|
|
"micEconCES" # depends on broken package nlopt
|
|
"micEconSNQP" # depends on broken package nlopt
|
|
"mi" # depends on broken package nlopt
|
|
"MigClim" # Build Is Broken
|
|
"migui" # depends on broken package nlopt
|
|
"minimist" # depends on broken package V8
|
|
"missMDA" # depends on broken package nlopt
|
|
"mitoODE" # build is broken
|
|
"mixAK" # depends on broken package nlopt
|
|
"MixedPoisson" # broken build
|
|
"mixlm" # depends on broken package nlopt
|
|
"MixMAP" # depends on broken package nlopt
|
|
"mlma" # depends on broken package lme4
|
|
"mlmRev" # depends on broken package nlopt
|
|
"MLSeq" # depends on broken package nlopt
|
|
"mlVAR" # depends on broken package nlopt
|
|
"MM" # broken build
|
|
"mongolite" # build is broken
|
|
"mosaic" # depends on broken package nlopt
|
|
"mpoly" # broken build
|
|
"mRMRe" # broken build
|
|
"msa" # broken build
|
|
"MSGFgui" # depends on broken package MSGFplus
|
|
"MSGFplus" # Build Is Broken
|
|
"MSstats" # depends on broken package nlopt
|
|
"MultiRR" # depends on broken package nlopt
|
|
"muma" # depends on broken package nlopt
|
|
"munsellinterpol" # broken build
|
|
"mutossGUI" # build is broken
|
|
"mvinfluence" # depends on broken package nlopt
|
|
"MXM" # broken build
|
|
"NanoStringDiff" # broken build
|
|
"NanoStringQCPro" # build is broken
|
|
"nCal" # depends on broken package nlopt
|
|
"ncdfFlow" # build is broken
|
|
"NCIgraph" # depends on broken package RCytoscape
|
|
"NHPoisson" # depends on broken package nlopt
|
|
"nloptr" # depends on broken package nlopt
|
|
"nlsem" # broken build
|
|
"nlts" # broken build
|
|
"nonrandom" # depends on broken package nlopt
|
|
"NORRRM" # build is broken
|
|
"npIntFactRep" # depends on broken package nlopt
|
|
"NSM3" # broken build
|
|
"omics" # depends on broken package lme4
|
|
"OmicsMarkeR" # depends on broken package nlopt
|
|
"OPDOE" # broken build
|
|
"OpenCL" # build is broken
|
|
"openCyto" # depends on broken package ncdfFlow
|
|
"OpenMx" # build is broken
|
|
"optBiomarker" # depends on broken package rpanel
|
|
"ora" # depends on broken package ROracle
|
|
"ordBTL" # depends on broken package nlopt
|
|
"ordPens" # depends on broken package lme4
|
|
"orthopolynom" # broken build
|
|
"OUwie" # depends on broken package nlopt
|
|
"oz" # broken build
|
|
"PAA" # broken build
|
|
"pamm" # depends on broken package nlopt
|
|
"panelAR" # depends on broken package nlopt
|
|
"papeR" # depends on broken package nlopt
|
|
"parboost" # depends on broken package nlopt
|
|
"parma" # depends on broken package nlopt
|
|
"partitions" # broken build
|
|
"PatternClass" # build is broken
|
|
"PBImisc" # depends on broken package nlopt
|
|
"pcaBootPlot" # depends on broken FactoMineR
|
|
"pcaL1" # build is broken
|
|
"pcnetmeta" # broken build
|
|
"PDQutils" # broken build
|
|
"pedigreemm" # depends on broken package nlopt
|
|
"pequod" # depends on broken package nlopt
|
|
"pglm" # depends on broken package car
|
|
"PhenStat" # depends on broken package nlopt
|
|
"phia" # depends on broken package nlopt
|
|
"phylocurve" # depends on broken package nlopt
|
|
"piecewiseSEM" # depends on broken package lme4
|
|
"plateCore" # depends on broken package ncdfFlow
|
|
"plfMA" # broken build
|
|
"plm" # depends on broken package car
|
|
"plsRbeta" # depends on broken package nlopt
|
|
"plsRcox" # depends on broken package nlopt
|
|
"plsRglm" # depends on broken package nlopt
|
|
"pmm" # depends on broken package nlopt
|
|
"polynom" # broken build
|
|
"pomp" # depends on broken package nlopt
|
|
"predictmeans" # depends on broken package nlopt
|
|
"preprocomb" # depends on broken package caret
|
|
"prevalence" # broken build
|
|
"prLogistic" # depends on broken package nlopt
|
|
"pRoloc" # depends on broken package nlopt
|
|
"pRolocGUI" # depends on broken package nlopt
|
|
"PSAboot" # depends on broken package nlopt
|
|
"ptw" # depends on broken nloptr
|
|
"PurBayes" # broken build
|
|
"pvca" # depends on broken package nlopt
|
|
"PythonInR" # broken build
|
|
"QFRM" # broken build
|
|
"qgraph" # depends on broken package nlopt
|
|
"qtbase" # build is broken
|
|
"qtlnet" # depends on broken package nlopt
|
|
"qtpaint" # depends on broken package qtbase
|
|
"qtutils" # depends on broken package qtbase
|
|
"QUALIFIER" # depends on broken package ncdfFlow
|
|
"quantification" # depends on broken package nlopt
|
|
"QuartPAC" # broken build
|
|
"R2jags" # broken build
|
|
"R2STATS" # depends on broken package nlopt
|
|
"rain" # broken build
|
|
"raincpc" # build is broken
|
|
"rainfreq" # build is broken
|
|
"RamiGO" # depends on broken package RCytoscape
|
|
"RareVariantVis" # depends on broken VariantAnnotation
|
|
"rasclass" # depends on broken package nlopt
|
|
"rationalfun" # broken build
|
|
"RBerkeley" # broken build
|
|
"RbioRXN" # depends on broken package ChemmineR
|
|
"Rblpapi" # broken build
|
|
"Rchemcpp" # depends on broken package ChemmineR
|
|
"rchess" # depends on broken package V8
|
|
"Rchoice" # depends on broken package car
|
|
"Rcmdr" # depends on broken package nlopt
|
|
"RcmdrMisc" # depends on broken package nlopt
|
|
"RcmdrPlugin_BCA" # depends on broken package nlopt
|
|
"RcmdrPlugin_coin" # depends on broken package nlopt
|
|
"RcmdrPlugin_depthTools" # depends on broken package nlopt
|
|
"RcmdrPlugin_DoE" # depends on broken package nlopt
|
|
"RcmdrPlugin_doex" # depends on broken package nlopt
|
|
"RcmdrPlugin_EACSPIR" # depends on broken package nlopt
|
|
"RcmdrPlugin_EBM" # depends on broken package nlopt
|
|
"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt
|
|
"RcmdrPlugin_epack" # depends on broken package nlopt
|
|
"RcmdrPlugin_Export" # depends on broken package Rcmdr
|
|
"RcmdrPlugin_EZR" # depends on broken package nlopt
|
|
"RcmdrPlugin_FactoMineR" # depends on broken package nlopt
|
|
"RcmdrPlugin_HH" # depends on broken package nlopt
|
|
"RcmdrPlugin_IPSUR" # depends on broken package nlopt
|
|
"RcmdrPlugin_KMggplot2" # depends on broken package nlopt
|
|
"RcmdrPlugin_lfstat" # depends on broken package nlopt
|
|
"RcmdrPlugin_MA" # depends on broken package nlopt
|
|
"RcmdrPlugin_mosaic" # depends on broken package nlopt
|
|
"RcmdrPlugin_MPAStats" # depends on broken package nlopt
|
|
"RcmdrPlugin_NMBU" # depends on broken package nlopt
|
|
"RcmdrPlugin_orloca" # depends on broken package nlopt
|
|
"RcmdrPlugin_plotByGroup" # depends on broken package nlopt
|
|
"RcmdrPlugin_pointG" # depends on broken package nlopt
|
|
"RcmdrPlugin_qual" # depends on broken package nlopt
|
|
"RcmdrPlugin_RMTCJags" # depends on broken package nlopt
|
|
"RcmdrPlugin_ROC" # depends on broken package nlopt
|
|
"RcmdrPlugin_sampling" # depends on broken package nlopt
|
|
"RcmdrPlugin_SCDA" # depends on broken package nlopt
|
|
"RcmdrPlugin_seeg" # depends on broken package nlopt
|
|
"RcmdrPlugin_SLC" # depends on broken package nlopt
|
|
"RcmdrPlugin_SM" # depends on broken package nlopt
|
|
"RcmdrPlugin_sos" # depends on broken package nlopt
|
|
"RcmdrPlugin_steepness" # depends on broken package nlopt
|
|
"RcmdrPlugin_survival" # depends on broken package nlopt
|
|
"RcmdrPlugin_TeachingDemos" # depends on broken package nlopt
|
|
"RcmdrPlugin_temis" # depends on broken package nlopt
|
|
"RcmdrPlugin_UCA" # depends on broken package nlopt
|
|
"Rcpi" # depends on broken package ChemmineR
|
|
"Rcplex" # Build Is Broken
|
|
"RcppAPT" # Build Is Broken
|
|
"RcppRedis" # build is broken
|
|
"rcrypt" # broken build
|
|
"RCytoscape" # Build Is Broken
|
|
"rdd" # depends on broken package nlopt
|
|
"rddtools" # depends on broken package AER
|
|
"rDEA" # build is broken
|
|
"RDieHarder" # build is broken
|
|
"REBayes" # depends on broken package Rmosek
|
|
"referenceIntervals" # depends on broken package nlopt
|
|
"refund" # depends on broken package nlopt
|
|
"refund_shiny" # depends on broken package refund
|
|
"REndo" # depends on broken package AER
|
|
"repijson" # depends on broken package V8
|
|
"REST" # depends on broken package nlopt
|
|
"rgbif" # depends on broken package V8
|
|
"Rgnuplot" # broken build
|
|
"rjade" # depends on broken package V8
|
|
"rJPSGCS" # build is broken
|
|
"rLindo" # build is broken
|
|
"RLRsim" # depends on broken package lme4
|
|
"RMallow" # broken build
|
|
"rMAT" # build is broken
|
|
"rmgarch" # depends on broken package nlopt
|
|
"rminer" # depends on broken package nlopt
|
|
"Rmosek" # build is broken
|
|
"RMySQL" # broken build
|
|
"RNAither" # depends on broken package nlopt
|
|
"RnavGraph" # build is broken
|
|
"rnetcarto" # broken build
|
|
"robustlmm" # depends on broken package nlopt
|
|
"rockchalk" # depends on broken package nlopt
|
|
"ROI_plugin_symphony" # depends on broken package Rsymphony
|
|
"rols" # build is broken
|
|
"ROracle" # Build Is Broken
|
|
"rpanel" # build is broken
|
|
"Rpoppler" # broken build
|
|
"rpubchem" # depends on broken package nlopt
|
|
"RQuantLib" # build is broken
|
|
"rr" # depends on broken package nlopt
|
|
"RRreg" # depends on broken package lme4
|
|
"RSAP" # build is broken
|
|
"rsbml" # build is broken
|
|
"RSDA" # depends on broken package nlopt
|
|
"Rsomoclu" # broken build
|
|
"RStoolbox" # depends on broken package caret
|
|
"Rsymphony" # build is broken
|
|
"rTableICC" # broken build
|
|
"rTANDEM" # build is broken
|
|
"RTN" # depends on broken package nlopt
|
|
"rugarch" # depends on broken package nlopt
|
|
"rUnemploymentData" # broken build
|
|
"RVAideMemoire" # depends on broken package nlopt
|
|
"RVFam" # depends on broken package nlopt
|
|
"RVideoPoker" # depends on broken package rpanel
|
|
"RWebServices" # broken build
|
|
"ryouready" # depends on broken package nlopt
|
|
"sadists" # broken build
|
|
"sampleSelection" # depends on broken package nlopt
|
|
"sapFinder" # depends on broken package rTANDEM
|
|
"sdcMicro" # depends on broken package nlopt
|
|
"sdcMicroGUI" # depends on broken package nlopt
|
|
"SDD" # depends on broken package rpanel
|
|
"seeg" # depends on broken package nlopt
|
|
"Sejong" # broken build
|
|
"sem" # depends on broken package nlopt
|
|
"semdiag" # depends on broken package nlopt
|
|
"semGOF" # depends on broken package nlopt
|
|
"semPlot" # depends on broken package nlopt
|
|
"SensMixed" # depends on broken package lme4
|
|
"SensoMineR" # depends on broken package nlopt
|
|
"seqCNA" # build is broken
|
|
"SeqFeatR" # broken build
|
|
"SeqGrapheR" # Build Is Broken
|
|
"seqHMM" # depends on broken package nloptr
|
|
"seqTools" # build is broken
|
|
"SharpeR" # broken build
|
|
"shinyTANDEM" # depends on broken package rTANDEM
|
|
"SIBER" # broken build
|
|
"simPop" # depends on broken package VIM
|
|
"simr" # depends on broken package lme4
|
|
"SJava" # broken build
|
|
"sjPlot" # depends on broken package nlopt
|
|
"smacof" # broken build
|
|
"SNAGEE" # build is broken
|
|
"snm" # depends on broken package nlopt
|
|
"SOD" # depends on broken package cudatoolkit
|
|
"sodium" # broken build
|
|
"soilphysics" # depends on broken package rpanel
|
|
"sortinghat" # broken build
|
|
"SoyNAM" # depends on broken package lme4
|
|
"spacom" # depends on broken package nlopt
|
|
"SparseLearner" # depends on broken package qgraph
|
|
"specificity" # depends on broken package nlopt
|
|
"specmine" # depends on broken package caret
|
|
"splm" # depends on broken package car
|
|
"spocc" # depends on broken package V8
|
|
"spoccutils" # depends on broken spocc
|
|
"ssmrob" # depends on broken package nlopt
|
|
"StatMethRank" # broken build
|
|
"stepp" # depends on broken package nlopt
|
|
"stringgaussnet" # build is broken
|
|
"Surrogate" # depends on broken package nlopt
|
|
"svglite" # depends on broken package gdtools
|
|
"sybilSBML" # build is broken
|
|
"systemfit" # depends on broken package nlopt
|
|
"TcGSA" # depends on broken package nlopt
|
|
"TDMR" # depends on broken package nlopt
|
|
"TextoMineR" # depends on broken package FactoMineR
|
|
"TFBSTools" # depends on broken package DirichletMultinomial
|
|
"tigerstats" # depends on broken package nlopt
|
|
"TLBC" # depends on broken package caret
|
|
"tmle" # broken build
|
|
"tnam" # depends on broken package lme4
|
|
"tolBasis" # depends on broken package polynom
|
|
"translateSPSS2R" # depends on broken car
|
|
"TriMatch" # depends on broken package nlopt
|
|
"TSMySQL" # broken build
|
|
"tsoutliers" # broken build
|
|
"UBCRM" # broken build
|
|
"umx" # depends on broken package OpenMx
|
|
"uniftest" # broken build
|
|
"untb" # broken build
|
|
"userfriendlyscience" # depends on broken package nlopt
|
|
"V8" # build is broken
|
|
"varComp" # depends on broken package lme4
|
|
"varian" # build is broken
|
|
"variancePartition" # depends on broken package lme4
|
|
"VBmix" # broken build
|
|
"VIM" # depends on broken package nlopt
|
|
"VIMGUI" # depends on broken package nlopt
|
|
"vows" # depends on broken package nlopt
|
|
"webp" # build is broken
|
|
"wfe" # depends on broken package nlopt
|
|
"wordbankr" # depends on broken package RMySQL
|
|
"xergm" # depends on broken package nlopt
|
|
"xps" # build is broken
|
|
"ZeligChoice" # depends on broken package AER
|
|
"Zelig" # depends on broken package AER
|
|
"zetadiv" # depends on broken package nlopt
|
|
"zoib" # broken build
|
|
];
|
|
|
|
otherOverrides = old: new: {
|
|
stringi = old.stringi.overrideDerivation (attrs: {
|
|
postInstall = let
|
|
icuName = "icudt52l";
|
|
icuSrc = pkgs.fetchzip {
|
|
url = "http://static.rexamine.com/packages/${icuName}.zip";
|
|
sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
|
|
stripRoot = false;
|
|
};
|
|
in ''
|
|
${attrs.postInstall or ""}
|
|
cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
|
|
'';
|
|
});
|
|
|
|
xml2 = old.xml2.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
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${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr.dev}/include"
|
|
];
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/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.lib}";
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
gputools = old.gputools.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gputools.patch ];
|
|
CUDA_HOME = "${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 = "${pkgs.cudatoolkit}/include";
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
OPENSSL_INCLUDES = "${pkgs.openssl.dev}/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'"
|
|
];
|
|
});
|
|
|
|
V8 = old.V8.overrideDerivation (attrs: {
|
|
preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
|
|
});
|
|
|
|
};
|
|
in
|
|
self
|