1387 lines
58 KiB
Nix
1387 lines
58 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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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 and CRAN 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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# 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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# 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.dev pkgs.ncurses ];
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bigGP = [ pkgs.openmpi ];
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bio3d = [ pkgs.zlib ];
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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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cairoDevice = [ pkgs.gtk2.dev ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
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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.dev pkgs.x11 ];
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diversitree = [ pkgs.gsl_1 pkgs.fftw ];
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EMCluster = [ pkgs.liblapack ];
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fftw = [ pkgs.fftw.dev ];
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fftwtools = [ pkgs.fftw.dev ];
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Formula = [ pkgs.gmp ];
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geoCount = [ pkgs.gsl_1 ];
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git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
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GLAD = [ pkgs.gsl_1 ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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gmp = [ pkgs.gmp.dev ];
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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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imager = [ pkgs.x11 ];
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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.dev ];
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KFKSDS = [ pkgs.gsl_1 ];
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kza = [ pkgs.fftw.dev ];
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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.dev ];
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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.dev ];
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png = [ pkgs.libpng.dev ];
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PopGenome = [ pkgs.zlib.dev ];
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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.dev ];
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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.dev ];
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rcdd = [ pkgs.gmp.dev ];
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RcppCNPy = [ pkgs.zlib.dev ];
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RcppGSL = [ pkgs.gsl_1 ];
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RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev 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.dev pkgs.libxml2.dev ];
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rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
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Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2.dev ];
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rhdf5 = [ pkgs.zlib ];
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Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
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Rhtslib = [ pkgs.zlib.dev ];
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RJaCGH = [ pkgs.zlib.dev ];
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rjags = [ pkgs.jags ];
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rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
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Rlibeemd = [ pkgs.gsl_1 ];
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rmatio = [ pkgs.zlib.dev ];
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Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
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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.dev 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.dev ];
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Rserve = [ pkgs.openssl ];
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Rssa = [ pkgs.fftw.dev ];
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rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
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rtiff = [ pkgs.libtiff.dev ];
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runjags = [ pkgs.jags ];
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RVowpalWabbit = [ pkgs.zlib.dev 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.dev pkgs.libsndfile.dev ];
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seqinr = [ pkgs.zlib.dev ];
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seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
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showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
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simplexreg = [ pkgs.gsl_1 ];
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SOD = [ pkgs.opencl-headers ];
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spate = [ pkgs.fftw.dev ];
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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.dev ];
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|
TAQMNGR = [ pkgs.zlib.dev ];
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|
tiff = [ pkgs.libtiff.dev ];
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|
TKF = [ pkgs.gsl_1 ];
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|
tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
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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.dev ];
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|
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
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|
xml2 = [ pkgs.libxml2.dev ];
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|
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
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|
affyPLM = [ pkgs.zlib.dev ];
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|
bamsignals = [ pkgs.zlib.dev ];
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|
BitSeq = [ pkgs.zlib.dev ];
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|
DiffBind = [ pkgs.zlib ];
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|
ShortRead = [ pkgs.zlib.dev ];
|
|
oligo = [ pkgs.zlib.dev ];
|
|
gmapR = [ pkgs.zlib.dev ];
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|
Rsubread = [ pkgs.zlib.dev ];
|
|
XVector = [ pkgs.zlib.dev ];
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|
Rsamtools = [ pkgs.zlib.dev ];
|
|
rtracklayer = [ pkgs.zlib.dev ];
|
|
affyio = [ pkgs.zlib.dev ];
|
|
VariantAnnotation = [ pkgs.zlib.dev ];
|
|
snpStats = [ pkgs.zlib.dev ];
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|
gputools = [ pkgs.pcre.dev pkgs.lzma.dev pkgs.zlib.dev pkgs.bzip2.dev pkgs.icu.dev ];
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|
};
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|
|
|
packagesWithBuildInputs = {
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|
# sort -t '=' -k 2
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|
svKomodo = [ pkgs.which ];
|
|
nat = [ pkgs.which ];
|
|
nat_nblast = [ pkgs.which ];
|
|
nat_templatebrains = [ pkgs.which ];
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|
RMark = [ pkgs.which ];
|
|
RPushbullet = [ pkgs.which ];
|
|
qtpaint = [ pkgs.cmake ];
|
|
qtbase = [ pkgs.cmake pkgs.perl ];
|
|
gmatrix = [ pkgs.cudatoolkit pkgs.which ];
|
|
RCurl = [ pkgs.curl.dev ];
|
|
R2SWF = [ pkgs.pkgconfig ];
|
|
rggobi = [ pkgs.pkgconfig ];
|
|
RGtk2 = [ pkgs.pkgconfig ];
|
|
RProtoBuf = [ pkgs.pkgconfig ];
|
|
Rpoppler = [ pkgs.pkgconfig ];
|
|
VBmix = [ pkgs.pkgconfig ];
|
|
XML = [ pkgs.pkgconfig ];
|
|
cairoDevice = [ pkgs.pkgconfig ];
|
|
chebpol = [ pkgs.pkgconfig ];
|
|
fftw = [ pkgs.pkgconfig ];
|
|
geoCount = [ pkgs.pkgconfig ];
|
|
kza = [ pkgs.pkgconfig ];
|
|
mwaved = [ pkgs.pkgconfig ];
|
|
showtext = [ pkgs.pkgconfig ];
|
|
spate = [ pkgs.pkgconfig ];
|
|
stringi = [ pkgs.pkgconfig ];
|
|
sysfonts = [ pkgs.pkgconfig ];
|
|
Cairo = [ pkgs.pkgconfig ];
|
|
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
qtutils = [ pkgs.qt4 ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
|
|
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
|
|
rPython = [ pkgs.which ];
|
|
gridGraphics = [ pkgs.which ];
|
|
gputools = [ pkgs.which pkgs.cudatoolkit ];
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|
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
|
|
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
mzR = [ pkgs.netcdf ];
|
|
};
|
|
|
|
packagesRequireingX = [
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|
"accrual"
|
|
"ade4TkGUI"
|
|
"adehabitat"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"AnthropMMD"
|
|
"aplpack"
|
|
"aqfig"
|
|
"arf3DS4"
|
|
"asbio"
|
|
"AtelieR"
|
|
"BAT"
|
|
"bayesDem"
|
|
"BCA"
|
|
"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"
|
|
"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"
|
|
"RNCEP"
|
|
"RQDA"
|
|
"RSDA"
|
|
"rsgcc"
|
|
"RSurvey"
|
|
"RunuranGUI"
|
|
"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"
|
|
"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
|
|
"gputools" # 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 = [
|
|
"acs" # build is broken
|
|
"agRee" # depends on broken package BRugs-0.8-6
|
|
"aLFQ" # depends on broken package bio3d-2.3-1
|
|
"anamiR" # depends on broken package RMySQL-0.10.11
|
|
"AneuFinder" # depends on broken package Rhtslib-1.6.0
|
|
"animation" # build is broken
|
|
"anim_plots" # depends on broken package animation-2.4
|
|
"annmap" # depends on broken package RMySQL-0.10.9
|
|
"apaStyle" # depends on broken package gdtools-0.1.3
|
|
"apaTables" # depends on broken package OpenMx-2.7.4
|
|
"aptg" # depends on broken package brranching-0.2.0
|
|
"ArrayExpressHTS" # build is broken
|
|
"arrayQualityMetrics" # build is broken
|
|
"auRoc" # depends on broken package OpenMx-2.7.4
|
|
"bamsignals" # depends on broken package Rhtslib-1.6.0
|
|
"BatchQC" # build is broken
|
|
"bayesCL" # build is broken
|
|
"bayou" # depends on broken package animation-2.4
|
|
"bedr" # build is broken
|
|
"BETS" # build is broken
|
|
"BiGGR" # depends on broken package rsbml-2.30.0
|
|
"bio3d" # build is broken
|
|
"bioassayR" # depends on broken package ChemmineR-2.24.2
|
|
"bioCancer" # depends on broken package covr-2.2.2
|
|
"biomformat" # depends on broken package r-rhdf5-2.16.0
|
|
"biotools" # depends on broken package rpanel-1.1-3
|
|
"birte" # build is broken
|
|
"BiSEp" # build is broken
|
|
"BLCOP" # depends on broken package Rsymphony-0.1-26
|
|
"BMhyd" # depends on broken package animation-2.4
|
|
"BNSP" # build is broken
|
|
"BPEC" # depends on broken package animation-2.4
|
|
"BrailleR" # depends on broken package gridGraphics-0.1-5
|
|
"brainGraph" # build is broken
|
|
"brranching" # depends on broken package animation-2.4
|
|
"brr" # build is broken
|
|
"BRugs" # build is broken
|
|
"CADStat" # build is broken
|
|
"CampaR1" # depends on broken package r-bio3d-2.3-1
|
|
"canceR" # build is broken
|
|
"CardinalWorkflows" # build is broken
|
|
"CARrampsOcl" # depends on broken package OpenCL-0.1-3
|
|
"categoryCompare" # depends on broken package RCytoscape-1.21.1
|
|
"Causata" # depends on broken package RMySQL-0.10.9
|
|
"cdcfluview" # depends on broken package V8-1.2
|
|
"CexoR" # depends on broken package Rhtslib-1.6.0
|
|
"ChAMP" # depends on broken package goseq-1.26.0
|
|
"ChemmineDrugs" # depends on broken package ChemmineR-2.24.2
|
|
"ChemmineR" # build is broken
|
|
"chinese_misc" # build is broken
|
|
"ChIPQC" # depends on broken package r-DiffBind-2.0.9
|
|
"ChIPXpress" # build is broken
|
|
"ChIPXpressData" # build is broken
|
|
"choroplethr" # depends on broken package acs-2.0
|
|
"CHRONOS" # build is broken
|
|
"cleanEHR" # build is broken
|
|
"clickR" # depends on broken package gdtools-0.1.3
|
|
"clpAPI" # build is broken
|
|
"CNEr" # build is broken
|
|
"colormap" # depends on broken package V8-1.2
|
|
"colorscience" # build is broken
|
|
"compendiumdb" # depends on broken package RMySQL-0.10.9
|
|
"CONFESS" # depends on broken package r-flowCore-1.38.2
|
|
"CONS" # build is broken
|
|
"convevol" # depends on broken package animation-2.4
|
|
"CountClust" # build is broken
|
|
"CountsEPPM" # build is broken
|
|
"COUSCOus" # depends on broken package r-bio3d-2.3-1
|
|
"covr" # build is broken
|
|
"cplexAPI" # build is broken
|
|
"Crossover" # build is broken
|
|
"CrypticIBDcheck" # build is broken
|
|
"csaw" # build is broken
|
|
"ctsem" # depends on broken package OpenMx-2.7.4
|
|
"cudaBayesreg" # build is broken
|
|
"cytofkit" # depends on broken package flowCore-1.38.2
|
|
"CytoML" # depends on broken package flowCore-1.40.6
|
|
"daff" # depends on broken package V8-1.2
|
|
"dagbag" # build is broken
|
|
"dagitty" # depends on broken package V8-1.2
|
|
"dagLogo" # depends on broken package MotIV-1.28.0
|
|
"DAISIE" # depends on broken package animation-2.4
|
|
"DataEntry" # build is broken
|
|
"dataMaid" # build is broken
|
|
"dataone" # build is broken
|
|
"datapack" # build is broken
|
|
"dbConnect" # depends on broken package RMySQL-0.10.9
|
|
"DBKGrad" # depends on broken package rpanel-1.1-3
|
|
"DCM" # build is broken
|
|
"DDD" # depends on broken package animation-2.4
|
|
"deBInfer" # depends on broken package PBSddesolve-1.12.2
|
|
"debrowser" # depends on broken package V8-1.4
|
|
"DecisionCurve" # build is broken
|
|
"DeepBlueR" # build is broken
|
|
"deepSNV" # build is broken
|
|
"DEGraph" # depends on broken package RCytoscape-1.21.1
|
|
"DEploid" # build is broken
|
|
"DiagrammeRsvg" # depends on broken package V8-1.2
|
|
"DiffBind" # build is broken
|
|
"diffHic" # depends on broken package r-csaw-1.6.1
|
|
"DirichletMultinomial" # build is broken
|
|
"diveRsity" # build is broken
|
|
"DmelSGI" # depends on broken package r-rhdf5-2.16.0
|
|
"docxtools" # build is broken
|
|
"DOQTL" # depends on broken package r-rhdf5-2.16.0
|
|
"DOT" # depends on broken package V8-1.2
|
|
"dynr" # build is broken
|
|
"ecospat" # depends on broken package MigClim-1.6
|
|
"EGAD" # depends on broken package arrayQualityMetrics-3.28.2
|
|
"eiR" # depends on broken package ChemmineR-2.24.2
|
|
"emg" # build is broken
|
|
"envlpaster" # build is broken
|
|
"erpR" # depends on broken package rpanel-1.1-3
|
|
"euroMix" # build is broken
|
|
"evobiR" # depends on broken package animation-2.4
|
|
"exifr" # build is broken
|
|
"ExperimentHubData" # build is broken
|
|
"exprso" # build is broken
|
|
"fastR" # build is broken
|
|
"fCCAC" # depends on broken package Rhtslib-1.6.0
|
|
"fdq" # depends on broken package gdtools-0.1.3
|
|
"Fgmutils" # depends on broken package gdtools-0.1.3
|
|
"flan" # build is broken
|
|
"flextable" # depends on broken package gdtools-0.1.4
|
|
"flowAI" # depends on broken package r-flowCore-1.38.2
|
|
"flowBeads" # depends on broken package r-flowCore-1.38.2
|
|
"flowBin" # depends on broken package r-flowCore-1.38.2
|
|
"flowCHIC" # depends on broken package r-flowCore-1.38.2
|
|
"flowClean" # depends on broken package r-flowCore-1.38.2
|
|
"flowClust" # depends on broken package r-flowCore-1.38.2
|
|
"flowCore" # build is broken
|
|
"flowDensity" # depends on broken package flowCore-1.38.2
|
|
"flowDiv" # depends on broken package r-flowCore-1.38.2
|
|
"flowFit" # depends on broken package r-flowCore-1.38.2
|
|
"flowFitExampleData" # depends on broken package r-flowCore-1.38.2
|
|
"flowFP" # depends on broken package r-flowCore-1.38.2
|
|
"flowMatch" # depends on broken package r-flowCore-1.38.2
|
|
"flowMeans" # depends on broken package r-flowCore-1.38.2
|
|
"flowMerge" # depends on broken package r-flowCore-1.38.2
|
|
"flowPeaks" # build is broken
|
|
"flowPloidy" # depends on broken package flowCore-1.40.6
|
|
"flowQB" # depends on broken package r-flowCore-1.38.2
|
|
"flowQ" # depends on broken package flowCore-1.38.2
|
|
"FlowSOM" # depends on broken package r-flowCore-1.38.2
|
|
"flowStats" # depends on broken package r-flowCore-1.38.2
|
|
"flowTrans" # depends on broken package r-flowCore-1.38.2
|
|
"flowType" # depends on broken package r-flowCore-1.38.2
|
|
"flowUtils" # depends on broken package r-flowCore-1.38.2
|
|
"flowViz" # depends on broken package r-flowCore-1.38.2
|
|
"flowVS" # depends on broken package r-flowCore-1.38.2
|
|
"flowWorkspace" # depends on broken package r-flowCore-1.38.2
|
|
"fmcsR" # depends on broken package ChemmineR-2.24.2
|
|
"fPortfolio" # depends on broken package Rsymphony-0.1-26
|
|
"fracprolif" # build is broken
|
|
"funModeling" # build is broken
|
|
"gahgu133acdf" # build is broken
|
|
"gahgu133bcdf" # build is broken
|
|
"gahgu133plus2cdf" # build is broken
|
|
"gahgu95av2cdf" # build is broken
|
|
"gahgu95bcdf" # build is broken
|
|
"gahgu95ccdf" # build is broken
|
|
"gahgu95dcdf" # build is broken
|
|
"gahgu95ecdf" # build is broken
|
|
"gamlss_demo" # depends on broken package rpanel-1.1-3
|
|
"gazepath" # build is broken
|
|
"gdtools" # build is broken
|
|
"GENE_E" # depends on broken package r-rhdf5-2.16.0
|
|
"GenoGAM" # build is broken
|
|
"genomation" # depends on broken package Rhtslib-1.6.0
|
|
"geojson" # depends on broken package r-protolite-1.5
|
|
"geojsonio" # depends on broken package V8-1.2
|
|
"geojsonlint" # depends on broken package V8-1.2
|
|
"gfcanalysis" # depends on broken package animation-2.4
|
|
"gfer" # depends on broken package V8-1.2
|
|
"ggcyto" # depends on broken package r-flowCore-1.38.2
|
|
"ggghost" # depends on broken package animation-2.4
|
|
"ggimage" # depends on broken package gridGraphics-0.1-5
|
|
"ggiraph" # depends on broken package gdtools-0.1.3
|
|
"ggiraphExtra" # depends on broken package gdtools-0.1.3
|
|
"ggseas" # build is broken
|
|
"gmapR" # build is broken
|
|
"gmatrix" # depends on broken package cudatoolkit-8.0.61
|
|
"gMCP" # build is broken
|
|
"gmDatabase" # depends on broken package RMySQL-0.10.9
|
|
"gmum_r" # build is broken
|
|
"googleformr" # build is broken
|
|
"goseq" # build is broken
|
|
"gpg" # build is broken
|
|
"gpuR" # build is broken
|
|
"gputools" # depends on broken package cudatoolkit-8.0.61
|
|
"GraphPAC" # build is broken
|
|
"greengenes13_5MgDb" # build is broken
|
|
"gridGraphics" # build is broken
|
|
"GSCA" # depends on broken package r-rhdf5-2.16.0
|
|
"GUIDE" # depends on broken package rpanel-1.1-3
|
|
"gunsales" # build is broken
|
|
"h2o" # build is broken
|
|
"h5vc" # depends on broken package r-rhdf5-2.16.0
|
|
"harrietr" # build is broken
|
|
"HDF5Array" # depends on broken package r-rhdf5-2.16.0
|
|
"healthyFlowData" # depends on broken package r-flowCore-1.38.2
|
|
"hexSticker" # depends on broken package gridGraphics-0.1-5
|
|
"HierO" # build is broken
|
|
"HilbertVisGUI" # build is broken
|
|
"HiPLARM" # build is broken
|
|
"hisse" # depends on broken package animation-2.4
|
|
"hoardeR" # depends on broken package Rhtslib-1.6.0
|
|
"homomorpheR" # depends on broken package sodium-0.4
|
|
"HTSeqGenie" # depends on broken package gmapR-1.16.0
|
|
"HTSSIP" # depends on broken package r-rhdf5-2.16.0
|
|
"idm" # depends on broken package animation-2.4
|
|
"ifaTools" # depends on broken package OpenMx-2.7.4
|
|
"IHW" # depends on broken package r-lpsymphony-1.0.2
|
|
"IHWpaper" # depends on broken package r-lpsymphony-1.0.2
|
|
"IlluminaHumanMethylation450k_db" # build is broken
|
|
"immunoClust" # depends on broken package r-flowCore-1.38.2
|
|
"imputeR" # depends on broken package ridge-2.2
|
|
"intansv" # build is broken
|
|
"interactiveDisplay" # build is broken
|
|
"ionicons" # depends on broken package rsvg-1.0
|
|
"IONiseR" # depends on broken package r-rhdf5-2.16.0
|
|
"ITGM" # depends on broken package gdtools-0.1.3
|
|
"jpmesh" # depends on broken package V8-1.2
|
|
"js" # depends on broken package V8-1.2
|
|
"jsonld" # depends on broken package V8-1.2
|
|
"jsonvalidate" # depends on broken package V8-1.2
|
|
"KoNLP" # build is broken
|
|
"largeList" # build is broken
|
|
"largeVis" # build is broken
|
|
"lavaan_shiny" # depends on broken package OpenMx-2.7.10
|
|
"lawn" # depends on broken package V8-1.2
|
|
"LCMCR" # build is broken
|
|
"LeArEst" # depends on broken package opencpu-1.6.1
|
|
"lefse" # build is broken
|
|
"lfe" # build is broken
|
|
"lgcp" # depends on broken package rpanel-1.1-3
|
|
"Libra" # build is broken
|
|
"libsoc" # build is broken
|
|
"link2GI" # depends on broken package r-sf-0.3-4
|
|
"LinRegInteractive" # depends on broken package rpanel-1.1-3
|
|
"liquidSVM" # build is broken
|
|
"littler" # build is broken
|
|
"LowMACA" # depends on broken package MotIV-1.28.0
|
|
"lpsymphony" # build is broken
|
|
"lvnet" # depends on broken package OpenMx-2.7.4
|
|
"MafDb_1Kgenomes_phase3_hs37d5" # build is broken
|
|
"mafs" # build is broken
|
|
"magick" # build is broken
|
|
"maGUI" # build is broken
|
|
"mapr" # depends on broken package V8-1.2
|
|
"mar1s" # build is broken
|
|
"MatrixRider" # depends on broken package CNEr-1.8.3
|
|
"MBESS" # depends on broken package OpenMx-2.7.4
|
|
"mBvs" # build is broken
|
|
"mcaGUI" # build is broken
|
|
"mcPAFit" # build is broken
|
|
"mdsr" # depends on broken package RMySQL-0.10.9
|
|
"Mediana" # depends on broken package gdtools-0.1.3
|
|
"melviewr" # build is broken
|
|
"MeSH_Hsa_eg_db" # build is broken
|
|
"MeSH_Mmu_eg_db" # build is broken
|
|
"meshr" # depends on broken package r-MeSH.Hsa.eg.db-1.6.0
|
|
"Metab" # build is broken
|
|
"metagear" # build is broken
|
|
"MetaIntegrator" # depends on broken package RMySQL-0.10.9
|
|
"metaSEM" # depends on broken package OpenMx-2.7.4
|
|
"methylKit" # depends on broken package Rhtslib-1.6.0
|
|
"MigClim" # build is broken
|
|
"minimist" # depends on broken package V8-1.2
|
|
"miscF" # depends on broken package BRugs-0.8-6
|
|
"mixlink" # build is broken
|
|
"MLSeq" # build is broken
|
|
"mmnet" # build is broken
|
|
"MODIStsp" # build is broken
|
|
"MonetDBLite" # build is broken
|
|
"mongolite" # build is broken
|
|
"monogeneaGM" # depends on broken package animation-2.4
|
|
"MonoPhy" # depends on broken package animation-2.4
|
|
"motifbreakR" # depends on broken package MotIV-1.28.0
|
|
"motifStack" # depends on broken package MotIV-1.28.0
|
|
"MotIV" # build is broken
|
|
"mptools" # depends on broken package animation-2.4
|
|
"mrMLM" # build is broken
|
|
"mRMRe" # build is broken
|
|
"mscstexta4r" # build is broken
|
|
"mscsweblm4r" # build is broken
|
|
"MSeasyTkGUI" # build is broken
|
|
"MSGFgui" # depends on broken package MSGFplus-1.6.2
|
|
"MSGFplus" # build is broken
|
|
"multiDimBio" # depends on broken package gridGraphics-0.1-5
|
|
"multipanelfigure" # depends on broken package gridGraphics-0.1-5
|
|
"munsellinterpol" # build is broken
|
|
"mutossGUI" # build is broken
|
|
"mvMORPH" # depends on broken package animation-2.4
|
|
"mvst" # build is broken
|
|
"ncdfFlow" # depends on broken package r-flowCore-1.38.2
|
|
"NCIgraph" # depends on broken package RCytoscape-1.21.1
|
|
"ndjson" # build is broken
|
|
"ndtv" # depends on broken package animation-2.4
|
|
"NetRep" # depends on broken package r-RhpcBLASctl-0.15-148
|
|
"networkBMA" # build is broken
|
|
"nlts" # build is broken
|
|
"normr" # depends on broken package Rhtslib-1.6.0
|
|
"NORRRM" # build is broken
|
|
"odbc" # build is broken
|
|
"officer" # depends on broken package gdtools-0.1.3
|
|
"OpenCL" # build is broken
|
|
"opencpu" # depends on broken package r-protolite-1.5
|
|
"openCyto" # depends on broken package r-flowCore-1.38.2
|
|
"OpenMx" # build is broken
|
|
"optbdmaeAT" # build is broken
|
|
"optBiomarker" # depends on broken package rpanel-1.1-3
|
|
"optrcdmaeAT" # build is broken
|
|
"ora" # depends on broken package ROracle-1.3-1
|
|
"OUwie" # depends on broken package animation-2.4
|
|
"PAA" # build is broken
|
|
"paleotree" # depends on broken package animation-2.4
|
|
"PathoStat" # depends on broken package BatchQC-1.2.1
|
|
"PathSelectMP" # build is broken
|
|
"PatternClass" # build is broken
|
|
"PBD" # depends on broken package animation-2.4
|
|
"PBSddesolve" # build is broken
|
|
"PBSmapping" # build is broken
|
|
"pcadapt" # depends on broken package vcfR-1.4.0
|
|
"pcaL1" # build is broken
|
|
"pcaPA" # build is broken
|
|
"pcrsim" # build is broken
|
|
"pdfsearch" # build is broken
|
|
"pdftools" # build is broken
|
|
"pd_genomewidesnp_6" # build is broken
|
|
"permGPU" # build is broken
|
|
"PGA" # build is broken
|
|
"PGPC" # depends on broken package ChemmineR-2.24.2
|
|
"ph2bye" # depends on broken package animation-2.4
|
|
"PharmacoGx" # build is broken
|
|
"PhyInformR" # depends on broken package animation-2.4
|
|
"phylocurve" # depends on broken package animation-2.4
|
|
"phyloseq" # depends on broken package r-rhdf5-2.16.0
|
|
"PhySortR" # depends on broken package animation-2.4
|
|
"phytools" # depends on broken package animation-2.4
|
|
"PICS" # build is broken
|
|
"PING" # depends on broken package PICS-2.16.0
|
|
"plateCore" # depends on broken package r-flowCore-1.38.2
|
|
"plfMA" # build is broken
|
|
"plink" # build is broken
|
|
"podkat" # build is broken
|
|
"PottsUtils" # depends on broken package BRugs-0.8-6
|
|
"powell" # build is broken
|
|
"pqsfinder" # depends on broken package r-flowCore-1.38.2
|
|
"prebs" # depends on broken package r-rhdf5-2.16.0
|
|
"PREDAsampledata" # depends on broken package gahgu133plus2cdf-2.2.1
|
|
"predictionInterval" # depends on broken package OpenMx-2.7.4
|
|
"pRoloc" # build is broken
|
|
"pRolocGUI" # build is broken
|
|
"proteoQC" # build is broken
|
|
"protolite" # build is broken
|
|
"prototest" # build is broken
|
|
"PSAboot" # build is broken
|
|
"psbcGroup" # build is broken
|
|
"PythonInR" # build is broken
|
|
"qcmetrics" # build is broken
|
|
"QFRM" # build is broken
|
|
"qrqc" # build is broken
|
|
"qtbase" # build is broken
|
|
"qtpaint" # build is broken
|
|
"qtutils" # build is broken
|
|
"QUALIFIER" # depends on broken package r-flowCore-1.38.2
|
|
"QuartPAC" # build is broken
|
|
"QuasR" # build is broken
|
|
"QUBIC" # build is broken
|
|
"QVM" # build is broken
|
|
"raincpc" # build is broken
|
|
"rainfreq" # build is broken
|
|
"RAM" # depends on broken package animation-2.4
|
|
"RamiGO" # depends on broken package RCytoscape-1.21.1
|
|
"randomcoloR" # depends on broken package V8-1.2
|
|
"randstr" # build is broken
|
|
"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
|
|
"RAppArmor" # build is broken
|
|
"raptr" # depends on broken package PBSmapping-2.69.76
|
|
"RbioRXN" # depends on broken package ChemmineR-2.24.2
|
|
"Rblpapi" # build is broken
|
|
"RCAS" # depends on broken package Rhtslib-1.6.0
|
|
"Rchemcpp" # depends on broken package ChemmineR-2.24.2
|
|
"rchess" # depends on broken package V8-1.2
|
|
"RchivalTag" # depends on broken package PBSmapping-2.69.76
|
|
"RchyOptimyx" # depends on broken package r-flowCore-1.38.2
|
|
"RcmdrPlugin_FuzzyClust" # build is broken
|
|
"RcmdrPlugin_PcaRobust" # build is broken
|
|
"Rcpi" # depends on broken package ChemmineR-2.24.2
|
|
"Rcplex" # build is broken
|
|
"RcppAPT" # build is broken
|
|
"RcppGetconf" # build is broken
|
|
"RcppOctave" # build is broken
|
|
"RcppRedis" # build is broken
|
|
"rcqp" # build is broken
|
|
"rcrypt" # build is broken
|
|
"RCytoscape" # build is broken
|
|
"rdataretriever" # build is broken
|
|
"rDEA" # build is broken
|
|
"RDieHarder" # build is broken
|
|
"REBayes" # depends on broken package Rmosek-1.2.5.1
|
|
"recluster" # depends on broken package animation-2.4
|
|
"redland" # build is broken
|
|
"remoter" # build is broken
|
|
"repijson" # depends on broken package V8-1.2
|
|
"replicationInterval" # depends on broken package OpenMx-2.7.4
|
|
"ReporteRs" # depends on broken package gdtools-0.1.3
|
|
"ReQON" # depends on broken package seqbias-1.20.0
|
|
"RforProteomics" # depends on broken package interactiveDisplay-1.10.2
|
|
"rgbif" # depends on broken package V8-1.2
|
|
"Rgnuplot" # build is broken
|
|
"rgp" # build is broken
|
|
"rgpui" # depends on broken package rgp-0.4-1
|
|
"rgsepd" # depends on broken package goseq-1.26.0
|
|
"rhdf5" # build is broken
|
|
"RhpcBLASctl" # build is broken
|
|
"Rhtslib" # build is broken
|
|
"ridge" # build is broken
|
|
"rjade" # depends on broken package V8-1.2
|
|
"rJPSGCS" # build is broken
|
|
"RKEEL" # depends on broken package RKEELjars-1.0.15
|
|
"RKEELjars" # build is broken
|
|
"Rknots" # depends on broken package r-bio3d-2.3-1
|
|
"rLindo" # build is broken
|
|
"rlo" # depends on broken package PythonInR-0.1-3
|
|
"RMallow" # build is broken
|
|
"rmapshaper" # depends on broken package V8-1.2
|
|
"rMAT" # build is broken
|
|
"Rmosek" # build is broken
|
|
"rmumps" # build is broken
|
|
"RMySQL" # build is broken
|
|
"rnaturalearth" # depends on broken package sf-0.4-1
|
|
"RnavGraph" # build is broken
|
|
"rnetcarto" # build is broken
|
|
"ROI_plugin_clp" # depends on broken package clpAPI-1.2.7
|
|
"ROI_plugin_cplex" # depends on broken package Rcplex-0.3-3
|
|
"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-26
|
|
"ROracle" # build is broken
|
|
"RPA" # depends on broken package r-rhdf5-2.16.0
|
|
"RPANDA" # depends on broken package animation-2.4
|
|
"rpanel" # build is broken
|
|
"rpg" # build is broken
|
|
"Rphylopars" # depends on broken package animation-2.4
|
|
"Rpoppler" # build is broken
|
|
"RQuantLib" # build is broken
|
|
"Rsampletrees" # build is broken
|
|
"RSAP" # build is broken
|
|
"rsbml" # build is broken
|
|
"RSCABS" # build is broken
|
|
"rscala" # build is broken
|
|
"Rsomoclu" # build is broken
|
|
"rsparkling" # depends on broken package h2o-3.10.3.6
|
|
"rsvg" # build is broken
|
|
"Rsymphony" # build is broken
|
|
"rtable" # depends on broken package gdtools-0.1.3
|
|
"rTANDEM" # build is broken
|
|
"Rtextrankr" # build is broken
|
|
"rUnemploymentData" # depends on broken package acs-2.0
|
|
"rvg" # depends on broken package gdtools-0.1.3
|
|
"RVideoPoker" # depends on broken package rpanel-1.1-3
|
|
"rzmq" # build is broken
|
|
"s2" # build is broken
|
|
"sapFinder" # build is broken
|
|
"sbrl" # build is broken
|
|
"SC3" # depends on broken package scater-1.2.0
|
|
"scater" # depends on broken package r-rhdf5-2.16.0
|
|
"scran" # depends on broken package r-rhdf5-2.16.0
|
|
"SDD" # depends on broken package rpanel-1.1-3
|
|
"seasonal" # build is broken
|
|
"seasonalview" # build is broken
|
|
"Sejong" # build is broken
|
|
"SemiCompRisks" # build is broken
|
|
"semPlot" # depends on broken package OpenMx-2.7.10
|
|
"semtree" # depends on broken package OpenMx-2.7.4
|
|
"seqbias" # build is broken
|
|
"SeqGrapheR" # build is broken
|
|
"seqTools" # build is broken
|
|
"sf" # build is broken
|
|
"shazam" # build is broken
|
|
"shinyTANDEM" # build is broken
|
|
"SICtools" # build is broken
|
|
"SigTree" # depends on broken package r-rhdf5-2.16.0
|
|
"SimInf" # build is broken
|
|
"simsalapar" # build is broken
|
|
"smapr" # depends on broken package r-rhdf5-2.16.0
|
|
"SMITE" # depends on broken package goseq-1.26.0
|
|
"SnakeCharmR" # build is broken
|
|
"sodium" # build is broken
|
|
"soilphysics" # depends on broken package rpanel-1.1-3
|
|
"sortinghat" # build is broken
|
|
"spdynmod" # depends on broken package animation-2.4
|
|
"spocc" # depends on broken package V8-1.2
|
|
"spongecake" # build is broken
|
|
"srd" # depends on broken package animation-2.4
|
|
"SSDM" # build is broken
|
|
"stagePop" # depends on broken package PBSddesolve-1.12.2
|
|
"Starr" # build is broken
|
|
"stream" # depends on broken package animation-2.4
|
|
"streamMOA" # depends on broken package animation-2.4
|
|
"stremr" # build is broken
|
|
"subspaceMOA" # depends on broken package animation-2.4
|
|
"svglite" # depends on broken package gdtools-0.1.3
|
|
"sybilSBML" # build is broken
|
|
"SymTS" # build is broken
|
|
"synthACS" # depends on broken package acs-2.0
|
|
"tcpl" # depends on broken package RMySQL-0.10.9
|
|
"TDA" # build is broken
|
|
"TED" # depends on broken package animation-2.4
|
|
"tesseract" # build is broken
|
|
"texPreview" # depends on broken package magick-0.4
|
|
"textreadr" # build is broken
|
|
"textTinyR" # build is broken
|
|
"TFBSTools" # depends on broken package CNEr-1.8.3
|
|
"tilegramsR" # depends on broken package sf-0.4-1
|
|
"TKF" # depends on broken package animation-2.4
|
|
"tmap" # depends on broken package V8-1.2
|
|
"tmaptools" # depends on broken package V8-1.2
|
|
"tofsims" # build is broken
|
|
"toxboot" # depends on broken package RMySQL-0.10.9
|
|
"TransView" # build is broken
|
|
"treatSens" # build is broken
|
|
"treeplyr" # depends on broken package animation-2.4
|
|
"TSMySQL" # depends on broken package RMySQL-0.10.9
|
|
"uaparserjs" # depends on broken package V8-1.2
|
|
"UBCRM" # build is broken
|
|
"uHMM" # build is broken
|
|
"umx" # depends on broken package OpenMx-2.7.4
|
|
"userfriendlyscience" # depends on broken package OpenMx-2.7.4
|
|
"V8" # build is broken
|
|
"VariantTools" # depends on broken package gmapR-1.16.0
|
|
"VBmix" # build is broken
|
|
"vcfR" # build is broken
|
|
"vdiffr" # depends on broken package gdtools-0.1.3
|
|
"vmsbase" # depends on broken package PBSmapping-2.69.76
|
|
"wallace" # depends on broken package V8-1.2
|
|
"wand" # build is broken
|
|
"WebGestaltR" # depends on broken package PythonInR-0.1-3
|
|
"webp" # build is broken
|
|
"wordbankr" # depends on broken package RMySQL-0.10.9
|
|
"x13binary" # build is broken
|
|
"x_ent" # depends on broken package r-protolite-1.5
|
|
"xps" # build is broken
|
|
"xslt" # build is broken
|
|
"zoon" # build is broken
|
|
];
|
|
|
|
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
|
|
'';
|
|
});
|
|
|
|
Cairo = old.Cairo.overrideDerivation (attrs: {
|
|
NIX_LDFLAGS = "-lfontconfig";
|
|
});
|
|
|
|
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${pkgs.xorg.libXft.out}/lib -lXft";
|
|
NIX_LDFLAGS = "-lX11";
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
OPENSSL_INCLUDES = "${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
|