6dba41fbcb
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
{
mpi = super.mpich;
}
All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
955 lines
27 KiB
Nix
955 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/${name}/${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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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.mpi ];
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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.pkg-config ];
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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.lapack ];
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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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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.pkg-config ];
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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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|
gert = [ pkgs.libgit2 ];
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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 ];
|
|
JavaGD = [ pkgs.jdk ];
|
|
jpeg = [ pkgs.libjpeg.dev ];
|
|
jqr = [ pkgs.jq.dev ];
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|
KFKSDS = [ pkgs.gsl_1 ];
|
|
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 ];
|
|
ncdf4 = [ pkgs.netcdf ];
|
|
nloptr = [ pkgs.nlopt pkgs.pkg-config ];
|
|
n1qn1 = [ pkgs.gfortran ];
|
|
odbc = [ pkgs.unixODBC ];
|
|
pander = [ pkgs.pandoc pkgs.which ];
|
|
pbdMPI = [ pkgs.mpi ];
|
|
pbdPROF = [ pkgs.mpi ];
|
|
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
|
|
pdftools = [ pkgs.poppler.dev ];
|
|
phytools = [ pkgs.which ];
|
|
PKI = [ pkgs.openssl.dev ];
|
|
png = [ pkgs.libpng.dev ];
|
|
proj4 = [ pkgs.proj ];
|
|
protolite = [ pkgs.protobuf ];
|
|
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
|
|
RAppArmor = [ pkgs.libapparmor ];
|
|
rapportools = [ pkgs.which ];
|
|
rapport = [ pkgs.which ];
|
|
readxl = [ pkgs.libiconv ];
|
|
rcdd = [ pkgs.gmp.dev ];
|
|
RcppCNPy = [ pkgs.zlib.dev ];
|
|
RcppGSL = [ pkgs.gsl_1 ];
|
|
RcppZiggurat = [ pkgs.gsl_1 ];
|
|
reprex = [ pkgs.which ];
|
|
rgdal = [ pkgs.proj.dev pkgs.gdal ];
|
|
rgeos = [ pkgs.geos ];
|
|
Rglpk = [ pkgs.glpk ];
|
|
RGtk2 = [ pkgs.gtk2.dev ];
|
|
rhdf5 = [ pkgs.zlib ];
|
|
Rhdf5lib = [ pkgs.zlib ];
|
|
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.mpi pkgs.pcre.dev ];
|
|
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ];
|
|
rjags = [ pkgs.jags ];
|
|
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
|
|
Rlibeemd = [ pkgs.gsl_1 ];
|
|
rmatio = [ pkgs.zlib.dev ];
|
|
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
|
|
Rmpi = [ pkgs.mpi ];
|
|
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
|
|
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
|
|
RODBC = [ pkgs.libiodbc ];
|
|
rpanel = [ pkgs.bwidget ];
|
|
rpg = [ pkgs.postgresql ];
|
|
Rpoppler = [ pkgs.poppler ];
|
|
RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
|
|
RProtoBuf = [ pkgs.protobuf ];
|
|
RSclient = [ pkgs.openssl.dev ];
|
|
Rserve = [ pkgs.openssl ];
|
|
Rssa = [ pkgs.fftw.dev ];
|
|
rtiff = [ pkgs.libtiff.dev ];
|
|
runjags = [ pkgs.jags ];
|
|
RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
|
|
rzmq = [ pkgs.zeromq pkgs.pkg-config ];
|
|
clustermq = [ pkgs.zeromq ];
|
|
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
|
|
sdcTable = [ pkgs.gmp pkgs.glpk ];
|
|
seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
|
|
seqinr = [ pkgs.zlib.dev ];
|
|
seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
|
|
sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
|
|
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
|
|
simplexreg = [ pkgs.gsl_1 ];
|
|
spate = [ pkgs.fftw.dev ];
|
|
ssanv = [ pkgs.proj ];
|
|
stsm = [ pkgs.gsl_1 ];
|
|
stringi = [ pkgs.icu.dev ];
|
|
survSNP = [ pkgs.gsl_1 ];
|
|
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
|
|
systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ];
|
|
TAQMNGR = [ pkgs.zlib.dev ];
|
|
tesseract = [ pkgs.tesseract pkgs.leptonica ];
|
|
tiff = [ pkgs.libtiff.dev ];
|
|
tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
|
|
topicmodels = [ pkgs.gsl_1 ];
|
|
udunits2 = [ pkgs.udunits pkgs.expat ];
|
|
units = [ pkgs.udunits ];
|
|
V8 = [ pkgs.v8 ];
|
|
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 ];
|
|
ShortRead = [ pkgs.zlib.dev ];
|
|
oligo = [ pkgs.zlib.dev ];
|
|
gmapR = [ pkgs.zlib.dev ];
|
|
Rsubread = [ pkgs.zlib.dev ];
|
|
XVector = [ pkgs.zlib.dev ];
|
|
Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ];
|
|
rtracklayer = [ pkgs.zlib.dev ];
|
|
affyio = [ pkgs.zlib.dev ];
|
|
VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ];
|
|
snpStats = [ pkgs.zlib.dev ];
|
|
};
|
|
|
|
packagesWithBuildInputs = {
|
|
# sort -t '=' -k 2
|
|
gam = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
quantreg = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
hexbin = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
|
|
svKomodo = [ pkgs.which ];
|
|
nat = [ pkgs.which ];
|
|
nat_templatebrains = [ pkgs.which ];
|
|
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
|
|
clustermq = [ pkgs.pkg-config ];
|
|
RMark = [ pkgs.which ];
|
|
RPushbullet = [ pkgs.which ];
|
|
RcppEigen = [ pkgs.libiconv ];
|
|
RCurl = [ pkgs.curl.dev ];
|
|
R2SWF = [ pkgs.pkg-config ];
|
|
rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ];
|
|
RGtk2 = [ pkgs.pkg-config ];
|
|
RProtoBuf = [ pkgs.pkg-config ];
|
|
Rpoppler = [ pkgs.pkg-config ];
|
|
XML = [ pkgs.pkg-config ];
|
|
cairoDevice = [ pkgs.pkg-config ];
|
|
chebpol = [ pkgs.pkg-config ];
|
|
fftw = [ pkgs.pkg-config ];
|
|
gdtools = [ pkgs.pkg-config ];
|
|
jqr = [ pkgs.jq.lib ];
|
|
kza = [ pkgs.pkg-config ];
|
|
magick = [ pkgs.pkg-config ];
|
|
mwaved = [ pkgs.pkg-config ];
|
|
odbc = [ pkgs.pkg-config ];
|
|
openssl = [ pkgs.pkg-config ];
|
|
pdftools = [ pkgs.pkg-config ];
|
|
sf = [ pkgs.pkg-config pkgs.sqlite.dev pkgs.proj.dev ];
|
|
showtext = [ pkgs.pkg-config ];
|
|
spate = [ pkgs.pkg-config ];
|
|
stringi = [ pkgs.pkg-config ];
|
|
sysfonts = [ pkgs.pkg-config ];
|
|
systemfonts = [ pkgs.pkg-config ];
|
|
tesseract = [ pkgs.pkg-config ];
|
|
Cairo = [ pkgs.pkg-config ];
|
|
CLVTools = [ pkgs.gsl ];
|
|
JMcmprsk = [ pkgs.gsl ];
|
|
mashr = [ pkgs.gsl ];
|
|
hadron = [ pkgs.gsl ];
|
|
AMOUNTAIN = [ pkgs.gsl ];
|
|
Rsymphony = [ pkgs.pkg-config pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
|
|
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
|
|
gridGraphics = [ pkgs.which ];
|
|
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
|
|
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 ];
|
|
mvtnorm = [ pkgs.libiconv ];
|
|
statmod = [ pkgs.libiconv ];
|
|
};
|
|
|
|
packagesRequireingX = [
|
|
"accrual"
|
|
"ade4TkGUI"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"AnthropMMD"
|
|
"aplpack"
|
|
"asbio"
|
|
"BAT"
|
|
"BCA"
|
|
"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"
|
|
"dpa"
|
|
"DSpat"
|
|
"dynamicGraph"
|
|
"dynBiplotGUI"
|
|
"EasyqpcR"
|
|
"EcoVirtual"
|
|
"exactLoglinTest"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"FD"
|
|
"feature"
|
|
"FeedbackTS"
|
|
"FFD"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"forams"
|
|
"forensim"
|
|
"FreeSortR"
|
|
"fscaret"
|
|
"gcmr"
|
|
"geomorph"
|
|
"geoR"
|
|
"georob"
|
|
"GGEBiplotGUI"
|
|
"gnm"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"gsubfn"
|
|
"GUniFrac"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"HH"
|
|
"HiveR"
|
|
"ic50"
|
|
"iDynoR"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"likeLTD"
|
|
"logmult"
|
|
"LS2Wstat"
|
|
"MareyMap"
|
|
"memgene"
|
|
"metacom"
|
|
"Meth27QC"
|
|
"migui"
|
|
"miniGUI"
|
|
"mixsep"
|
|
"MplusAutomation"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"OligoSpecificitySystem"
|
|
"onemap"
|
|
"OpenRepGrid"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"PopGenReport"
|
|
"poppr"
|
|
"powerpkg"
|
|
"PredictABEL"
|
|
"prefmod"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"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_MPAStats"
|
|
"RcmdrPlugin_orloca"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_ROC"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_sos"
|
|
"RcmdrPlugin_steepness"
|
|
"RcmdrPlugin_survival"
|
|
"RcmdrPlugin_TeachingDemos"
|
|
"RcmdrPlugin_temis"
|
|
"RcmdrPlugin_UCA"
|
|
"recluster"
|
|
"relimp"
|
|
"rgl"
|
|
"RHRV"
|
|
"rich"
|
|
"RNCEP"
|
|
"RSDA"
|
|
"RSurvey"
|
|
"simba"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"SOLOMON"
|
|
"soundecology"
|
|
"spatsurv"
|
|
"sqldf"
|
|
"SSDforR"
|
|
"statcheck"
|
|
"StatDA"
|
|
"STEPCAM"
|
|
"stosim"
|
|
"strvalidator"
|
|
"stylo"
|
|
"svDialogstcltk"
|
|
"svIDE"
|
|
"svSocket"
|
|
"svWidgets"
|
|
"SYNCSA"
|
|
"SyNet"
|
|
"tcltk2"
|
|
"TestScorer"
|
|
"TIMP"
|
|
"tkrplot"
|
|
"tmap"
|
|
"tspmeta"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"twiddler"
|
|
"vcdExtra"
|
|
"VecStatGraphs3D"
|
|
"vegan"
|
|
"vegan3d"
|
|
"vegclust"
|
|
"x12GUI"
|
|
];
|
|
|
|
packagesToSkipCheck = [
|
|
"Rmpi" # tries to run MPI processes
|
|
"pbdMPI" # tries to run MPI processes
|
|
"data_table" # fails to rename shared library before check
|
|
];
|
|
|
|
# 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
|
|
'';
|
|
});
|
|
|
|
rzmq = old.rzmq.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
clustermq = old.clustermq.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
Cairo = old.Cairo.overrideDerivation (attrs: {
|
|
NIX_LDFLAGS = "-lfontconfig";
|
|
});
|
|
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
RcppParallel = old.RcppParallel.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
ggbio = old.ggbio.overrideDerivation (attrs: {
|
|
patches = [
|
|
(pkgs.fetchpatch {
|
|
url = "https://github.com/tengfei/ggbio/commit/b04a9840cf5c0bd0514db2536f2e610bbd364727.patch";
|
|
sha256 = "blwtObyIYo1UBWz4nlmcJ8Nyw/n0qwmJrtwFWuoUyMg=";
|
|
})
|
|
];
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
data_table = old.data_table.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp";
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
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}
|
|
'';
|
|
});
|
|
|
|
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' $file
|
|
done
|
|
'';
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${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${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
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: {
|
|
postPatch = ''
|
|
substituteInPlace configure \
|
|
--replace " -lv8_libplatform" ""
|
|
'';
|
|
|
|
preConfigure = ''
|
|
export INCLUDE_DIR=${pkgs.v8}/include
|
|
export LIB_DIR=${pkgs.v8}/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
|
|
'';
|
|
});
|
|
|
|
libgeos = old.libgeos.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
|