983 lines
27 KiB
Nix
983 lines
27 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) cacert 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, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html";
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mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
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"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ];
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};
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deriveBiocAnn = mkDerive {
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mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveBiocExp = mkDerive {
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mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/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 = { inherit buildRPackage; } //
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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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animation = [ pkgs.which ];
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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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data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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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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gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
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git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkgconfig ];
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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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haven = [ pkgs.libiconv pkgs.zlib.dev ];
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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 pkgs.libxml2.dev ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg.dev ];
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jqr = [ pkgs.jq.dev ];
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KFKSDS = [ pkgs.gsl_1 ];
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kza = [ pkgs.fftw.dev ];
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magick = [ pkgs.imagemagick.dev ];
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ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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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 pkgs.pkgconfig ];
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odbc = [ pkgs.unixODBC ];
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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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pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
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pdftools = [ pkgs.poppler.dev ];
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phytools = [ pkgs.which ];
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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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protolite = [ pkgs.protobuf ];
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qtbase = [ pkgs.qt4 ];
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qtpaint = [ pkgs.qt4 ];
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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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readxl = [ pkgs.libiconv ];
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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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RcppZiggurat = [ pkgs.gsl_1 ];
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reprex = [ pkgs.which ];
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rgdal = [ pkgs.proj.dev 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.libGLU pkgs.libGL 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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Rhdf5lib = [ 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 pkgs.automake pkgs.autoconf ];
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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.libmysqlclient pkgs.openssl.dev ];
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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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rpanel = [ pkgs.bwidget ];
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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 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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|
sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
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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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|
spate = [ pkgs.fftw.dev ];
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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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|
systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ];
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|
TAQMNGR = [ pkgs.zlib.dev ];
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|
tesseract = [ pkgs.tesseract pkgs.leptonica ];
|
|
tiff = [ pkgs.libtiff.dev ];
|
|
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 ];
|
|
units = [ pkgs.udunits ];
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|
V8 = [ pkgs.v8_3_14 ];
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|
VBLPCM = [ pkgs.gsl_1 ];
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|
WhopGenome = [ pkgs.zlib.dev ];
|
|
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
|
|
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
|
|
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
|
|
affyPLM = [ pkgs.zlib.dev ];
|
|
bamsignals = [ pkgs.zlib.dev ];
|
|
BitSeq = [ pkgs.zlib.dev ];
|
|
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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|
};
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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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|
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
|
|
RMark = [ pkgs.which ];
|
|
RPushbullet = [ pkgs.which ];
|
|
qtpaint = [ pkgs.cmake ];
|
|
qtbase = [ pkgs.cmake pkgs.perl ];
|
|
RcppEigen = [ pkgs.libiconv ];
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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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|
XML = [ pkgs.pkgconfig ];
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|
cairoDevice = [ pkgs.pkgconfig ];
|
|
chebpol = [ pkgs.pkgconfig ];
|
|
fftw = [ pkgs.pkgconfig ];
|
|
geoCount = [ pkgs.pkgconfig ];
|
|
gdtools = [ pkgs.pkgconfig ];
|
|
JuniperKernel = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
|
|
jqr = [ pkgs.jq.lib ];
|
|
kza = [ pkgs.pkgconfig ];
|
|
magick = [ pkgs.pkgconfig ];
|
|
mwaved = [ pkgs.pkgconfig ];
|
|
odbc = [ pkgs.pkgconfig ];
|
|
openssl = [ pkgs.pkgconfig ];
|
|
pdftools = [ pkgs.pkgconfig ];
|
|
sf = [ pkgs.pkgconfig pkgs.sqlite.dev pkgs.proj.dev ];
|
|
showtext = [ pkgs.pkgconfig ];
|
|
spate = [ pkgs.pkgconfig ];
|
|
stringi = [ pkgs.pkgconfig ];
|
|
sysfonts = [ pkgs.pkgconfig ];
|
|
systemfonts = [ pkgs.pkgconfig ];
|
|
tesseract = [ pkgs.pkgconfig ];
|
|
Cairo = [ pkgs.pkgconfig ];
|
|
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
|
|
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
|
|
rPython = [ pkgs.which ];
|
|
gridGraphics = [ pkgs.which ];
|
|
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 ];
|
|
cluster = [ pkgs.libiconv ];
|
|
KernSmooth = [ pkgs.libiconv ];
|
|
nlme = [ pkgs.libiconv ];
|
|
Matrix = [ pkgs.libiconv ];
|
|
mgcv = [ pkgs.libiconv ];
|
|
minqa = [ pkgs.libiconv ];
|
|
igraph = [ pkgs.libiconv ];
|
|
ape = [ pkgs.libiconv ];
|
|
expm = [ pkgs.libiconv ];
|
|
mnormt = [ pkgs.libiconv ];
|
|
pan = [ pkgs.libiconv ];
|
|
phangorn = [ pkgs.libiconv ];
|
|
quadprog = [ pkgs.libiconv ];
|
|
randomForest = [ pkgs.libiconv ];
|
|
sundialr = [ pkgs.libiconv ];
|
|
ucminf = [ pkgs.libiconv ];
|
|
glmnet = [ pkgs.libiconv ];
|
|
};
|
|
|
|
packagesRequireingX = [
|
|
"accrual"
|
|
"ade4TkGUI"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"AnthropMMD"
|
|
"aplpack"
|
|
"aqfig"
|
|
"arf3DS4"
|
|
"asbio"
|
|
"AtelieR"
|
|
"BAT"
|
|
"bayesDem"
|
|
"BCA"
|
|
"BEQI2"
|
|
"betapart"
|
|
"BiodiversityR"
|
|
"bio_infer"
|
|
"bipartite"
|
|
"biplotbootGUI"
|
|
"blender"
|
|
"cairoDevice"
|
|
"CCTpack"
|
|
"cncaGUI"
|
|
"cocorresp"
|
|
"CommunityCorrelogram"
|
|
"confidence"
|
|
"constrainedKriging"
|
|
"ConvergenceConcepts"
|
|
"cpa"
|
|
"DALY"
|
|
"dave"
|
|
"Deducer"
|
|
"DeducerPlugInExample"
|
|
"DeducerPlugInScaling"
|
|
"DeducerSpatial"
|
|
"DeducerSurvival"
|
|
"DeducerText"
|
|
"Demerelate"
|
|
"detrendeR"
|
|
"dgmb"
|
|
"DivMelt"
|
|
"dpa"
|
|
"DSpat"
|
|
"dynamicGraph"
|
|
"dynBiplotGUI"
|
|
"EasyqpcR"
|
|
"EcoVirtual"
|
|
"ENiRG"
|
|
"exactLoglinTest"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"FD"
|
|
"feature"
|
|
"FeedbackTS"
|
|
"FFD"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"fit4NM"
|
|
"forams"
|
|
"forensim"
|
|
"FreeSortR"
|
|
"fscaret"
|
|
"fSRM"
|
|
"gcmr"
|
|
"GeoGenetix"
|
|
"geomorph"
|
|
"geoR"
|
|
"geoRglm"
|
|
"georob"
|
|
"GGEBiplotGUI"
|
|
"gnm"
|
|
"GPCSIV"
|
|
"GrammR"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"gsubfn"
|
|
"GUniFrac"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"HH"
|
|
"HiveR"
|
|
"ic50"
|
|
"iDynoR"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"likeLTD"
|
|
"logmult"
|
|
"LS2Wstat"
|
|
"MareyMap"
|
|
"memgene"
|
|
"MergeGUI"
|
|
"metacom"
|
|
"Meth27QC"
|
|
"MetSizeR"
|
|
"MicroStrategyR"
|
|
"migui"
|
|
"miniGUI"
|
|
"MissingDataGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"MplusAutomation"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"OligoSpecificitySystem"
|
|
"onemap"
|
|
"OpenRepGrid"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"PKgraph"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"PopGenReport"
|
|
"poppr"
|
|
"powerpkg"
|
|
"PredictABEL"
|
|
"prefmod"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"r4ss"
|
|
"RandomFields"
|
|
"rareNMtests"
|
|
"rAverage"
|
|
"Rcmdr"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_depthTools"
|
|
"RcmdrPlugin_DoE"
|
|
"RcmdrPlugin_EACSPIR"
|
|
"RcmdrPlugin_EBM"
|
|
"RcmdrPlugin_EcoVirtual"
|
|
"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_sos"
|
|
"RcmdrPlugin_steepness"
|
|
"RcmdrPlugin_survival"
|
|
"RcmdrPlugin_TeachingDemos"
|
|
"RcmdrPlugin_temis"
|
|
"RcmdrPlugin_UCA"
|
|
"recluster"
|
|
"relimp"
|
|
"RenextGUI"
|
|
"reportRx"
|
|
"reshapeGUI"
|
|
"rgl"
|
|
"RHRV"
|
|
"rich"
|
|
"RNCEP"
|
|
"RQDA"
|
|
"RSDA"
|
|
"rsgcc"
|
|
"RSurvey"
|
|
"RunuranGUI"
|
|
"sharpshootR"
|
|
"simba"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"SOLOMON"
|
|
"soundecology"
|
|
"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
|
|
"pbdMPI" # tries to run MPI processes
|
|
];
|
|
|
|
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
|
brokenPackages = [
|
|
];
|
|
|
|
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";
|
|
});
|
|
|
|
data_table = old.data_table.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
|
|
+ lib.optionalString stdenv.isDarwin " -fopenmp";
|
|
});
|
|
|
|
ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
|
|
+ lib.optionalString stdenv.isDarwin " -fopenmp";
|
|
});
|
|
|
|
rpf = old.rpf.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesXsrc.patch ];
|
|
});
|
|
|
|
Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rhdf5lib.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}
|
|
'';
|
|
});
|
|
|
|
JuniperKernel = old.JuniperKernel.overrideDerivation (attrs: {
|
|
postPatch = lib.optionalString stdenv.isDarwin ''
|
|
for file in {R,src}/*.R; do
|
|
sed -i 's#system("which \(otool\|install_name_tool\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
|
|
done
|
|
'';
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
jqr = old.jqr.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: {
|
|
postPatch = lib.optionalString stdenv.isDarwin ''
|
|
for file in R/*.{r,r.in}; do
|
|
sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
|
|
done
|
|
'';
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${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: {
|
|
MYSQL_DIR="${pkgs.libmysqlclient}";
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${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 ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
|
|
});
|
|
|
|
websocket = old.websocket.overrideDerivation (attrs: {
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
nloptr = old.nloptr.overrideDerivation (attrs: {
|
|
# Drop bundled nlopt source code. Probably unnecessary, but I want to be
|
|
# sure we're using the system library, not this one.
|
|
preConfigure = "rm -r src/nlopt_src";
|
|
});
|
|
|
|
V8 = old.V8.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export INCLUDE_DIR=${pkgs.v8_3_14}/include
|
|
export LIB_DIR=${pkgs.v8_3_14}/lib
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
acs = old.acs.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
gdtools = old.gdtools.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
NIX_LDFLAGS = "-lfontconfig -lfreetype";
|
|
});
|
|
|
|
magick = old.magick.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
protolite = old.protolite.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
rpanel = old.rpanel.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
|
|
'';
|
|
TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
|
|
});
|
|
|
|
RPostgres = old.RPostgres.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export INCLUDE_DIR=${pkgs.postgresql}/include
|
|
export LIB_DIR=${pkgs.postgresql.lib}/lib
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
OpenMx = old.OpenMx.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
odbc = old.odbc.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
x13binary = old.x13binary.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
geojsonio = old.geojsonio.overrideDerivation (attrs: {
|
|
buildInputs = [ cacert ] ++ attrs.buildInputs;
|
|
});
|
|
|
|
rstan = old.rstan.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
|
|
});
|
|
|
|
mongolite = old.mongolite.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
|
|
});
|
|
|
|
ps = old.ps.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
rlang = old.rlang.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
systemfonts = old.systemfonts.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
littler = old.littler.overrideAttrs (attrs: with pkgs; {
|
|
buildInputs = [ pcre lzma zlib bzip2 icu which ] ++ attrs.buildInputs;
|
|
postInstall = ''
|
|
install -d $out/bin $out/share/man/man1
|
|
ln -s ../library/littler/bin/r $out/bin/r
|
|
ln -s ../library/littler/bin/r $out/bin/lr
|
|
ln -s ../../../library/littler/man-page/r.1 $out/share/man/man1
|
|
# these won't run without special provisions, so better remove them
|
|
rm -r $out/library/littler/script-tests
|
|
'';
|
|
});
|
|
|
|
};
|
|
in
|
|
self
|