1828 lines
57 KiB
Nix
1828 lines
57 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, hydraPlatforms ? null}: args:
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let hydraPlatforms' = hydraPlatforms; in
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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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platforms ? R.meta.platforms,
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hydraPlatforms ? if hydraPlatforms' != null then hydraPlatforms' else platforms,
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maintainers ? []
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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 = platforms;
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meta.hydraPlatforms = hydraPlatforms;
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meta.broken = broken;
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meta.maintainers = maintainers;
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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}: [
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"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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};
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deriveBiocAnn = mkDerive {
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mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, biocVersion}: [
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"mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz"
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];
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hydraPlatforms = [];
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};
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deriveBiocExp = mkDerive {
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mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
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mkUrls = {name, version, biocVersion}: [
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"mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz"
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];
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hydraPlatforms = [];
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};
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deriveCran = mkDerive {
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mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/";
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mkUrls = {name, version}: [
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"mirror://cran/${name}_${version}.tar.gz"
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"mirror://cran/Archive/${name}/${name}_${version}.tar.gz"
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];
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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.overrideAttrs (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).overrideAttrs (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.overrideAttrs (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).overrideAttrs (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 maintainers.
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# For example,
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#
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# overrideMaintainers {
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# foo = [ lib.maintainers.jsmith ]
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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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# maintainers = [ lib.maintainers.jsmith ];
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# };
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# }
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overrideMaintainers = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).override {
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maintainers = value;
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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.overrideAttrs (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).overrideAttrs (attrs: {
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nativeBuildInputs = (attrs.nativeBuildInputs or []) ++ value;
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propagatedNativeBuildInputs = (attrs.propagatedNativeBuildInputs or []) ++ 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 requiring a home directory to install or to
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# run tests.
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# For example,
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#
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# overrideRequireHome [
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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.overrideAttrs (oldAttrs: {
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# preInstall = ''
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# ${oldAttrs.preInstall or ""}
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# export HOME=$(mktemp -d)
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# '';
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# });
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# }
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overrideRequireHome = 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).overrideAttrs (oldAttrs: {
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preInstall = ''
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${oldAttrs.preInstall or ""}
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export HOME=$(mktemp -d)
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'';
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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 packagesRequiringX old0);
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old2 = old1 // (overrideRequireHome packagesRequiringHome old1);
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old3 = old2 // (overrideSkipCheck packagesToSkipCheck old2);
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old4 = old3 // (overrideRDepends packagesWithRDepends old3);
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old5 = old4 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old4);
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old6 = old5 // (overrideBuildInputs packagesWithBuildInputs old5);
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old7 = old6 // (overrideBroken brokenPackages old6);
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old8 = old7 // (overrideMaintainers packagesWithMaintainers old7);
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old = old8;
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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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packagesWithMaintainers = with lib.maintainers; {
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data_table = [ jbedo ];
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BiocManager = [ jbedo ];
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ggplot2 = [ jbedo ];
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svaNUMT = [ jbedo ];
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svaRetro = [ jbedo ];
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StructuralVariantAnnotation = [ jbedo ];
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};
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packagesWithRDepends = {
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spectralGraphTopology = [ self.CVXR ];
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FactoMineR = [ self.car ];
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pander = [ self.codetools ];
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rmsb = [ self.rstantools ];
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gastempt = [ self.rstantools ];
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interactiveDisplay = [ self.BiocManager ];
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disbayes = [ self.rstantools ];
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tipsae = [ self.rstantools ];
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TriDimRegression = [ self.rstantools ];
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bbmix = [ self.rstantools ];
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};
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packagesWithNativeBuildInputs = {
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adbcpostgresql = [ pkgs.postgresql ];
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adimpro = [ pkgs.imagemagick ];
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animation = [ pkgs.which ];
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Apollonius = with pkgs; [ pkg-config gmp.dev mpfr.dev ];
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arrow = with pkgs; [ pkg-config cmake ] ++ lib.optionals stdenv.isDarwin [ intltool ];
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audio = [ pkgs.portaudio ];
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BayesSAE = [ pkgs.gsl ];
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BayesVarSel = [ pkgs.gsl ];
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BayesXsrc = with pkgs; [ readline.dev ncurses gsl ];
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bioacoustics = [ pkgs.fftw.dev pkgs.cmake ];
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bigGP = [ pkgs.mpi ];
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bigrquerystorage = with pkgs; [ grpc protobuf which ];
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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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CellBarcode = [ pkgs.zlib ];
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cld3 = [ pkgs.protobuf ];
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bnpmr = [ pkgs.gsl ];
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caviarpd = [ pkgs.cargo ];
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cairoDevice = [ pkgs.gtk2.dev ];
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Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ];
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Cardinal = [ pkgs.which ];
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chebpol = [ pkgs.fftw.dev ];
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ChemmineOB = [ pkgs.pkg-config ];
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interpolation = [ pkgs.pkg-config ];
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clarabel = [ pkgs.cargo ];
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curl = [ pkgs.curl.dev ];
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CytoML = [ pkgs.libxml2.dev ];
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data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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devEMF = with pkgs; [ xorg.libXft.dev ];
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diversitree = with pkgs; [ gsl fftw ];
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exactextractr = [ pkgs.geos ];
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EMCluster = [ pkgs.lapack ];
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fangs = [ pkgs.cargo ];
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fcl = [ pkgs.cargo ];
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fftw = [ pkgs.fftw.dev ];
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fftwtools = with pkgs; [ fftw.dev pkg-config ];
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fingerPro = [ pkgs.gsl ];
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Formula = [ pkgs.gmp ];
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frailtyMMpen = [ pkgs.gsl ];
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gamstransfer = [ pkgs.zlib ];
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gdalraster = [ pkgs.pkg-config ];
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gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ];
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GeneralizedWendland = [ pkgs.gsl ];
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ggiraph = with pkgs; [ pkgs.libpng.dev ];
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git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ];
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GLAD = [ pkgs.gsl ];
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glpkAPI = with pkgs; [ gmp glpk ];
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gmp = [ pkgs.gmp.dev ];
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GPBayes = [ pkgs.gsl ];
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graphscan = [ pkgs.gsl ];
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gsl = [ pkgs.gsl ];
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gslnls = [ pkgs.gsl ];
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gert = [ pkgs.libgit2 ];
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haven = with pkgs; [ zlib.dev ];
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hellorust = [ pkgs.cargo ];
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hgwrr = [ pkgs.gsl ];
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h5vc = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
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yyjsonr = with pkgs; [ zlib.dev ];
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RNifti = with pkgs; [ zlib.dev ];
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RNiftyReg = with pkgs; [ zlib.dev ];
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highs = [ pkgs.which pkgs.cmake ];
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crc32c = [ pkgs.which pkgs.cmake ];
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rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ];
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HiCseg = [ pkgs.gsl ];
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imager = [ pkgs.xorg.libX11.dev ];
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imbibe = [ pkgs.zlib.dev ];
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image_CannyEdges = with pkgs; [ fftw.dev libpng.dev ];
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iBMQ = [ pkgs.gsl ];
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|
jack = [ pkgs.pkg-config ];
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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 ];
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KSgeneral = with pkgs; [ pkg-config ];
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kza = [ pkgs.fftw.dev ];
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|
leidenAlg = [ pkgs.gmp.dev ];
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Libra = [ pkgs.gsl ];
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|
libstable4u = [ pkgs.gsl ];
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heck = [ pkgs.cargo ];
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|
LOMAR = [ pkgs.gmp.dev ];
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|
littler = [ pkgs.libdeflate ];
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|
lpsymphony = with pkgs; [ pkg-config gfortran gettext ];
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|
lwgeom = with pkgs; [ proj geos gdal ];
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|
rsbml = [ pkgs.pkg-config ];
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|
rvg = [ pkgs.libpng.dev ];
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|
MAGEE = [ pkgs.zlib.dev pkgs.bzip2.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 ];
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|
mwaved = [ pkgs.fftw.dev ];
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|
mzR = with pkgs; [ zlib netcdf ];
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|
nanonext = with pkgs; [ mbedtls nng ];
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|
ncdf4 = [ pkgs.netcdf ];
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|
neojags = [ pkgs.jags ];
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|
nloptr = with pkgs; [ nlopt pkg-config ];
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|
n1qn1 = [ pkgs.gfortran ];
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|
odbc = [ pkgs.unixODBC ];
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|
opencv = [ pkgs.pkg-config ];
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|
pak = [ pkgs.curl.dev ];
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|
pander = with pkgs; [ pandoc which ];
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|
pbdMPI = [ pkgs.mpi ];
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|
pbdPROF = [ pkgs.mpi ];
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|
pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.isDarwin [ pkgs.which ];
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|
pcaL1 = [ pkgs.pkg-config pkgs.clp ];
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|
pdftools = [ pkgs.poppler.dev ];
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|
PEPBVS = [ pkgs.gsl ];
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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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|
protolite = [ pkgs.protobuf ];
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|
R2SWF = with pkgs; [ zlib libpng freetype.dev ];
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|
RAppArmor = [ pkgs.libapparmor ];
|
|
rapportools = [ pkgs.which ];
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|
rapport = [ pkgs.which ];
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|
rcdd = [ pkgs.gmp.dev ];
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|
RcppCNPy = [ pkgs.zlib.dev ];
|
|
RcppGSL = [ pkgs.gsl ];
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|
RcppZiggurat = [ pkgs.gsl ];
|
|
reprex = [ pkgs.which ];
|
|
rgdal = with pkgs; [ proj.dev gdal ];
|
|
Rhisat2 = [ pkgs.which pkgs.hostname ];
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|
gdalcubes = [ pkgs.pkg-config ];
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|
rgeos = [ pkgs.geos ];
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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 = with pkgs; [ zlib.dev ];
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|
Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
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|
Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
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|
rjags = [ pkgs.jags ];
|
|
rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip libdeflate ];
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|
Rlibeemd = [ pkgs.gsl ];
|
|
rmatio = [ pkgs.zlib.dev pkgs.pkg-config ];
|
|
Rmpfr = with pkgs; [ gmp mpfr.dev ];
|
|
Rmpi = [ pkgs.mpi ];
|
|
RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ];
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|
RNetCDF = with pkgs; [ netcdf udunits ];
|
|
RODBC = [ pkgs.libiodbc ];
|
|
rpanel = [ pkgs.bwidget ];
|
|
Rpoppler = [ pkgs.poppler ];
|
|
RPostgreSQL = with pkgs; [ postgresql postgresql ];
|
|
RProtoBuf = [ pkgs.protobuf ];
|
|
RSclient = [ pkgs.openssl.dev ];
|
|
Rserve = [ pkgs.openssl ];
|
|
Rssa = [ pkgs.fftw.dev ];
|
|
rsvg = [ pkgs.pkg-config ];
|
|
runjags = [ pkgs.jags ];
|
|
xslt = [ pkgs.pkg-config ];
|
|
RVowpalWabbit = with pkgs; [ zlib.dev boost ];
|
|
rzmq = with pkgs; [ zeromq pkg-config ];
|
|
httpuv = [ pkgs.zlib.dev ];
|
|
clustermq = [ pkgs.zeromq ];
|
|
SAVE = with pkgs; [ zlib bzip2 icu xz pcre ];
|
|
salso = [ pkgs.cargo ];
|
|
ymd = [ pkgs.cargo ];
|
|
arcpbf = [ pkgs.cargo ];
|
|
sdcTable = with pkgs; [ gmp glpk ];
|
|
seewave = with pkgs; [ fftw.dev libsndfile.dev ];
|
|
seqinr = [ pkgs.zlib.dev ];
|
|
smcryptoR = with pkgs; [ cargo rustc which ];
|
|
webp = [ pkgs.pkg-config ];
|
|
seqminer = with pkgs; [ zlib.dev bzip2 ];
|
|
sf = with pkgs; [ gdal proj geos libtiff curl ];
|
|
strawr = with pkgs; [ curl.dev ];
|
|
string2path = [ pkgs.cargo ];
|
|
terra = with pkgs; [ gdal proj geos ];
|
|
tok = [ pkgs.cargo ];
|
|
rshift = [ pkgs.cargo ];
|
|
arcgisutils = with pkgs; [ cargo rustc ];
|
|
arcgisgeocode = with pkgs; [ cargo rustc ];
|
|
arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ];
|
|
apcf = with pkgs; [ geos ];
|
|
SemiCompRisks = [ pkgs.gsl ];
|
|
showtext = with pkgs; [ zlib libpng icu freetype.dev ];
|
|
simplexreg = [ pkgs.gsl ];
|
|
spate = [ pkgs.fftw.dev ];
|
|
ssanv = [ pkgs.proj ];
|
|
stsm = [ pkgs.gsl ];
|
|
stringi = [ pkgs.icu.dev ];
|
|
survSNP = [ pkgs.gsl ];
|
|
svglite = [ pkgs.libpng.dev ];
|
|
sysfonts = with pkgs; [ zlib libpng freetype.dev ];
|
|
systemfonts = with pkgs; [ fontconfig.dev freetype.dev ];
|
|
TAQMNGR = [ pkgs.zlib.dev ];
|
|
TDA = [ pkgs.gmp ];
|
|
tesseract = with pkgs; [ tesseract leptonica ];
|
|
tiff = [ pkgs.libtiff.dev ];
|
|
tkrplot = with pkgs; [ xorg.libX11 tk.dev ];
|
|
topicmodels = [ pkgs.gsl ];
|
|
udunits2 = with pkgs; [ udunits expat ];
|
|
units = [ pkgs.udunits ];
|
|
unigd = [ pkgs.pkg-config ];
|
|
vdiffr = [ pkgs.libpng.dev ];
|
|
V8 = [ pkgs.nodejs.libv8 ];
|
|
XBRL = with pkgs; [ zlib libxml2.dev ];
|
|
XLConnect = [ pkgs.jdk ];
|
|
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
|
|
XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ];
|
|
affyPLM = [ pkgs.zlib.dev ];
|
|
BitSeq = [ pkgs.zlib.dev ];
|
|
DiffBind = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
|
|
ShortRead = [ pkgs.zlib.dev ];
|
|
oligo = [ pkgs.zlib.dev ];
|
|
gmapR = [ pkgs.zlib.dev ];
|
|
Rsubread = [ pkgs.zlib.dev ];
|
|
XVector = [ pkgs.zlib.dev ];
|
|
Rsamtools = with pkgs; [ zlib.dev curl.dev bzip2 xz ];
|
|
rtracklayer = with pkgs; [ zlib.dev curl.dev ];
|
|
affyio = [ pkgs.zlib.dev ];
|
|
snpStats = [ pkgs.zlib.dev ];
|
|
vcfppR = [ pkgs.curl.dev pkgs.bzip2 pkgs.zlib.dev pkgs.xz];
|
|
httpgd = with pkgs; [ cairo.dev ];
|
|
SymTS = [ pkgs.gsl ];
|
|
VBLPCM = [ pkgs.gsl ];
|
|
dynr = [ pkgs.gsl ];
|
|
mixlink = [ pkgs.gsl ];
|
|
ridge = [ pkgs.gsl ];
|
|
smam = [ pkgs.gsl ];
|
|
rnetcarto = [ pkgs.gsl ];
|
|
rGEDI = [ pkgs.gsl ];
|
|
mmpca = [ pkgs.gsl ];
|
|
monoreg = [ pkgs.gsl ];
|
|
mvst = [ pkgs.gsl ];
|
|
mixture = [ pkgs.gsl ];
|
|
jSDM = [ pkgs.gsl ];
|
|
immunoClust = [ pkgs.gsl ];
|
|
hSDM = [ pkgs.gsl ];
|
|
flowPeaks = [ pkgs.gsl ];
|
|
fRLR = [ pkgs.gsl ];
|
|
eaf = [ pkgs.gsl ];
|
|
diseq = [ pkgs.gsl ];
|
|
cit = [ pkgs.gsl ];
|
|
abn = [ pkgs.gsl ];
|
|
SimInf = [ pkgs.gsl ];
|
|
RJMCMCNucleosomes = [ pkgs.gsl ];
|
|
RDieHarder = [ pkgs.gsl ];
|
|
QF = [ pkgs.gsl ];
|
|
PICS = [ pkgs.gsl ];
|
|
RationalMatrix = [ pkgs.pkg-config pkgs.gmp.dev];
|
|
RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ];
|
|
redux = [ pkgs.pkg-config ];
|
|
rswipl = with pkgs; [ cmake pkg-config ];
|
|
rrd = [ pkgs.pkg-config ];
|
|
surveyvoi = [ pkgs.pkg-config ];
|
|
Rbwa = [ pkgs.zlib.dev ];
|
|
trackViewer = [ pkgs.zlib.dev ];
|
|
themetagenomics = [ pkgs.zlib.dev ];
|
|
Rsymphony = [ pkgs.pkg-config ];
|
|
NanoMethViz = [ pkgs.zlib.dev ];
|
|
RcppMeCab = [ pkgs.pkg-config ];
|
|
HilbertVisGUI = with pkgs; [ pkg-config which ];
|
|
textshaping = [ pkgs.pkg-config ];
|
|
ragg = [ pkgs.pkg-config ];
|
|
qqconf = [ pkgs.pkg-config ];
|
|
qspray = [ pkgs.pkg-config ];
|
|
ratioOfQsprays = [ pkgs.pkg-config ];
|
|
symbolicQspray = [ pkgs.pkg-config ];
|
|
sphereTessellation = [ pkgs.pkg-config ];
|
|
vapour = [ pkgs.pkg-config ];
|
|
};
|
|
|
|
packagesWithBuildInputs = {
|
|
# sort -t '=' -k 2
|
|
asciicast = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
|
|
island = [ pkgs.gsl.dev ];
|
|
svKomodo = [ pkgs.which ];
|
|
ulid = [ pkgs.zlib.dev ];
|
|
unrtf = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
|
|
nat = [ pkgs.which ];
|
|
nat_templatebrains = [ pkgs.which ];
|
|
pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
|
|
bigmemory = lib.optionals stdenv.isLinux [ pkgs.libuuid.dev ];
|
|
bayesWatch = [ pkgs.boost.dev ];
|
|
clustermq = [ pkgs.pkg-config ];
|
|
coga = [ pkgs.gsl.dev ];
|
|
mBvs = [ pkgs.gsl.dev ];
|
|
rcontroll = [ pkgs.gsl.dev ];
|
|
deepSNV = with pkgs; [ xz.dev bzip2.dev zlib.dev ];
|
|
epialleleR = with pkgs; [ xz.dev bzip2.dev zlib.dev ];
|
|
gdalraster = with pkgs; [ gdal proj.dev sqlite.dev ];
|
|
mitoClone2 = with pkgs; [ xz.dev bzip2.dev zlib.dev ];
|
|
gpg = [ pkgs.gpgme ];
|
|
webp = [ pkgs.libwebp ];
|
|
RMark = [ pkgs.which ];
|
|
RPushbullet = [ pkgs.which ];
|
|
stpphawkes = [ pkgs.gsl ];
|
|
registr = with pkgs; [ icu.dev zlib.dev bzip2.dev xz.dev libdeflate ];
|
|
RCurl = [ pkgs.curl.dev ];
|
|
R2SWF = [ pkgs.pkg-config ];
|
|
rDEA = [ pkgs.glpk ];
|
|
rgl = with pkgs; [ libGLU libGLU.dev libGL xorg.libX11.dev freetype.dev libpng.dev ];
|
|
RGtk2 = [ pkgs.pkg-config ];
|
|
RProtoBuf = [ pkgs.pkg-config ];
|
|
Rpoppler = [ pkgs.pkg-config ];
|
|
XML = [ pkgs.pkg-config ];
|
|
apsimx = [ pkgs.which ];
|
|
cairoDevice = [ pkgs.pkg-config ];
|
|
chebpol = [ pkgs.pkg-config ];
|
|
eds = [ pkgs.zlib.dev ];
|
|
pgenlibr = [ pkgs.zlib.dev ];
|
|
fftw = [ pkgs.pkg-config ];
|
|
gdtools = [ pkgs.pkg-config ];
|
|
archive = [ pkgs.libarchive];
|
|
gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ];
|
|
rsbml = [ pkgs.libsbml ];
|
|
SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev];
|
|
specklestar = [ pkgs.fftw.dev ];
|
|
cartogramR = [ pkgs.fftw.dev ];
|
|
jqr = [ pkgs.jq.lib ];
|
|
kza = [ pkgs.pkg-config ];
|
|
igraph = with pkgs; [ gmp libxml2.dev glpk ];
|
|
interpolation = [ pkgs.gmp ];
|
|
image_textlinedetector = with pkgs; [ pkg-config opencv ];
|
|
lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ];
|
|
magick = [ pkgs.pkg-config ];
|
|
mwaved = [ pkgs.pkg-config ];
|
|
odbc = [ pkgs.pkg-config ];
|
|
openssl = [ pkgs.pkg-config ];
|
|
pdftools = [ pkgs.pkg-config ];
|
|
qckitfastq = [ pkgs.zlib.dev ];
|
|
raer = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
|
|
RQuantLib = with pkgs; [ quantlib.dev boost.dev ];
|
|
sf = with pkgs; [ pkg-config sqlite.dev proj.dev ];
|
|
terra = with pkgs; [ pkg-config sqlite.dev 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 ];
|
|
excursions = [ pkgs.gsl ];
|
|
gpuMagic = [ pkgs.ocl-icd ];
|
|
JMcmprsk = [ pkgs.gsl ];
|
|
KSgeneral = [ pkgs.fftw.dev ];
|
|
mashr = [ pkgs.gsl ];
|
|
hadron = [ pkgs.gsl ];
|
|
AMOUNTAIN = [ pkgs.gsl ];
|
|
Rsymphony = with pkgs; [ symphony doxygen graphviz subversion cgl clp];
|
|
tcltk2 = with pkgs; [ tcl tk ];
|
|
rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ];
|
|
GrafGen = [ pkgs.zlib ];
|
|
tikzDevice = with pkgs; [ which texliveMedium ];
|
|
gridGraphics = [ pkgs.which ];
|
|
adimpro = with pkgs; [ which xorg.xdpyinfo ];
|
|
tfevents = [ pkgs.protobuf ];
|
|
rsvg = [ pkgs.librsvg.dev ];
|
|
ssh = with pkgs; [ libssh ];
|
|
s2 = [ pkgs.openssl.dev ];
|
|
ArrayExpressHTS = with pkgs; [ zlib.dev curl.dev which ];
|
|
bbl = with pkgs; [ gsl ];
|
|
diffHic = with pkgs; [ xz.dev bzip2.dev ];
|
|
writexl = with pkgs; [ zlib.dev ];
|
|
xslt = with pkgs; [ libxslt libxml2 ];
|
|
qpdf = with pkgs; [ libjpeg.dev zlib.dev ];
|
|
vcfR = with pkgs; [ zlib.dev ];
|
|
bio3d = with pkgs; [ zlib.dev ];
|
|
arrangements = with pkgs; [ gmp.dev ];
|
|
gfilogisreg = [ pkgs.gmp.dev ];
|
|
spp = with pkgs; [ zlib.dev ];
|
|
bamsignals = with pkgs; [ zlib.dev xz.dev bzip2 ];
|
|
Rbowtie = with pkgs; [ zlib.dev ];
|
|
gaston = with pkgs; [ zlib.dev ];
|
|
csaw = with pkgs; [ zlib.dev xz.dev bzip2.dev curl ];
|
|
DirichletMultinomial = with pkgs; [ gsl ];
|
|
DiffBind = with pkgs; [ zlib.dev ];
|
|
CNEr = with pkgs; [ zlib ];
|
|
GMMAT = with pkgs; [ zlib.dev bzip2.dev ];
|
|
rmumps = with pkgs; [ zlib.dev ];
|
|
HiCDCPlus = [ pkgs.zlib.dev ];
|
|
PopGenome = [ pkgs.zlib.dev ];
|
|
QuasR = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
|
|
Rarr = [ pkgs.zlib.dev ];
|
|
Rbowtie2 = [ pkgs.zlib.dev ];
|
|
Rfastp = with pkgs; [ xz.dev bzip2.dev zlib.dev ];
|
|
maftools = with pkgs; [ zlib.dev bzip2 xz.dev ];
|
|
Rmmquant = [ pkgs.zlib.dev ];
|
|
SICtools = with pkgs; [ zlib.dev ncurses.dev ];
|
|
Signac = [ pkgs.zlib.dev ];
|
|
TransView = with pkgs; [ xz.dev bzip2.dev zlib.dev ];
|
|
bigsnpr = [ pkgs.zlib.dev ];
|
|
zlib = [ pkgs.zlib.dev ];
|
|
divest = [ pkgs.zlib.dev ];
|
|
hipread = [ pkgs.zlib.dev ];
|
|
jack = with pkgs; [ gmp.dev mpfr.dev ];
|
|
jackalope = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
|
|
largeList = [ pkgs.zlib.dev ];
|
|
mappoly = [ pkgs.zlib.dev ];
|
|
VariantAnnotation = with pkgs; [ zlib.dev curl.dev bzip2.dev xz.dev ];
|
|
matchingMarkets = [ pkgs.zlib.dev ];
|
|
methylKit = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
|
|
ndjson = [ pkgs.zlib.dev ];
|
|
podkat = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
|
|
qrqc = [ pkgs.zlib.dev ];
|
|
rJPSGCS = [ pkgs.zlib.dev ];
|
|
rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ];
|
|
symengine = with pkgs; [ mpfr symengine flint ];
|
|
rtk = [ pkgs.zlib.dev ];
|
|
scPipe = with pkgs; [ bzip2.dev xz.dev zlib.dev ];
|
|
seqTools = [ pkgs.zlib.dev ];
|
|
seqbias = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
|
|
sparkwarc = [ pkgs.zlib.dev ];
|
|
RoBMA = [ pkgs.jags ];
|
|
RoBSA = [ pkgs.jags ];
|
|
pexm = [ pkgs.jags ];
|
|
rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ];
|
|
rawrr = [ pkgs.mono ];
|
|
HDF5Array = [ pkgs.zlib.dev ];
|
|
FLAMES = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
|
|
ncdfFlow = [ pkgs.zlib.dev ];
|
|
proj4 = [ pkgs.proj.dev ];
|
|
rtmpt = [ pkgs.gsl ];
|
|
mixcat = [ pkgs.gsl ];
|
|
libstableR = [ pkgs.gsl ];
|
|
landsepi = [ pkgs.gsl ];
|
|
flan = [ pkgs.gsl ];
|
|
econetwork = [ pkgs.gsl ];
|
|
crandep = [ pkgs.gsl ];
|
|
catSurv = [ pkgs.gsl ];
|
|
ccfindR = [ pkgs.gsl ];
|
|
screenCounter = [ pkgs.zlib.dev ];
|
|
SPARSEMODr = [ pkgs.gsl ];
|
|
RKHSMetaMod = [ pkgs.gsl ];
|
|
LCMCR = [ pkgs.gsl ];
|
|
BNSP = [ pkgs.gsl ];
|
|
scModels = [ pkgs.mpfr.dev ];
|
|
multibridge = with pkgs; [ pkg-config mpfr.dev ];
|
|
RcppCWB = with pkgs; [ pcre.dev glib.dev ];
|
|
redux = [ pkgs.hiredis ];
|
|
RmecabKo = [ pkgs.mecab ];
|
|
markets = [ pkgs.gsl ];
|
|
PoissonBinomial = [ pkgs.fftw.dev ];
|
|
poisbinom = [ pkgs.fftw.dev ];
|
|
PoissonMultinomial = [ pkgs.fftw.dev ];
|
|
psbcGroup = [ pkgs.gsl.dev ];
|
|
rrd = [ pkgs.rrdtool ];
|
|
flowWorkspace = [ pkgs.zlib.dev ];
|
|
RITCH = [ pkgs.zlib.dev ];
|
|
RcppMeCab = [ pkgs.mecab ];
|
|
PING = [ pkgs.gsl ];
|
|
PROJ = [ pkgs.proj.dev ];
|
|
RcppAlgos = [ pkgs.gmp.dev ];
|
|
RcppBigIntAlgos = [ pkgs.gmp.dev ];
|
|
spaMM = [ pkgs.gsl ];
|
|
shrinkTVP = [ pkgs.gsl ];
|
|
sbrl = with pkgs; [ gsl gmp.dev ];
|
|
surveyvoi = with pkgs; [ gmp.dev mpfr.dev ];
|
|
unigd = with pkgs; [ cairo.dev libpng.dev ];
|
|
HilbertVisGUI = [ pkgs.gtkmm2.dev ];
|
|
textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ];
|
|
DropletUtils = [ pkgs.zlib.dev ];
|
|
RMariaDB = [ pkgs.libmysqlclient.dev ];
|
|
ijtiff = [ pkgs.libtiff ];
|
|
ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.isDarwin lerc.dev;
|
|
qqconf = [ pkgs.fftw.dev ];
|
|
spFW = [ pkgs.fftw.dev ];
|
|
qspray = with pkgs; [ gmp.dev mpfr.dev ];
|
|
ratioOfQsprays = with pkgs; [ gmp.dev mpfr.dev ];
|
|
symbolicQspray = with pkgs; [ gmp.dev mpfr.dev ];
|
|
sphereTessellation = with pkgs; [ gmp.dev mpfr.dev ];
|
|
vapour = with pkgs; [ proj.dev gdal ];
|
|
MedianaDesigner = [ pkgs.zlib.dev ];
|
|
ChemmineOB = [ pkgs.eigen ];
|
|
};
|
|
|
|
packagesRequiringX = [
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"asbio"
|
|
"BCA"
|
|
"biplotbootGUI"
|
|
"cairoDevice"
|
|
"cncaGUI"
|
|
"CommunityCorrelogram"
|
|
"dave"
|
|
"DeducerPlugInExample"
|
|
"DeducerPlugInScaling"
|
|
"DeducerSpatial"
|
|
"DeducerSurvival"
|
|
"DeducerText"
|
|
"Demerelate"
|
|
"diveR"
|
|
"dpa"
|
|
"dynamicGraph"
|
|
"EasyqpcR"
|
|
"exactLoglinTest"
|
|
"fisheyeR"
|
|
"forams"
|
|
"forensim"
|
|
"GGEBiplotGUI"
|
|
"gsubfn"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"HiveR"
|
|
"ic50"
|
|
"iDynoR"
|
|
"iplots"
|
|
"likeLTD"
|
|
"loon"
|
|
"loon_ggplot"
|
|
"loon_shiny"
|
|
"loon_tourr"
|
|
"Meth27QC"
|
|
"mixsep"
|
|
"multibiplotGUI"
|
|
"OligoSpecificitySystem"
|
|
"optbdmaeAT"
|
|
"optrcdmaeAT"
|
|
"paleoMAS"
|
|
"RandomFields"
|
|
"rfviz"
|
|
"RclusTool"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_FuzzyClust"
|
|
"RcmdrPlugin_IPSUR"
|
|
"RcmdrPlugin_lfstat"
|
|
"RcmdrPlugin_PcaRobust"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_steepness"
|
|
"rich"
|
|
"RSurvey"
|
|
"simba"
|
|
"SimpleTable"
|
|
"SOLOMON"
|
|
"soptdmaeA"
|
|
"strvalidator"
|
|
"stylo"
|
|
"SyNet"
|
|
"switchboard"
|
|
"tkImgR"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"twiddler"
|
|
"uHMM"
|
|
"VecStatGraphs3D"
|
|
];
|
|
|
|
packagesRequiringHome = [
|
|
"aroma_affymetrix"
|
|
"aroma_cn"
|
|
"aroma_core"
|
|
"avotrex"
|
|
"beer"
|
|
"ceramic"
|
|
"connections"
|
|
"covidmx"
|
|
"csodata"
|
|
"DiceView"
|
|
"facmodTS"
|
|
"gasanalyzer"
|
|
"margaret"
|
|
"MSnID"
|
|
"OmnipathR"
|
|
"precommit"
|
|
"protGear"
|
|
"PCRA"
|
|
"PSCBS"
|
|
"iemisc"
|
|
"repmis"
|
|
"R_cache"
|
|
"R_filesets"
|
|
"RKorAPClient"
|
|
"R_rsp"
|
|
"salso"
|
|
"scholar"
|
|
"SpatialDecon"
|
|
"stepR"
|
|
"styler"
|
|
"teal_code"
|
|
"TreeTools"
|
|
"TreeSearch"
|
|
"ACNE"
|
|
"APAlyzer"
|
|
"EstMix"
|
|
"Patterns"
|
|
"PECA"
|
|
"Quartet"
|
|
"ShinyQuickStarter"
|
|
"TIN"
|
|
"cfdnakit"
|
|
"CaDrA"
|
|
"GNOSIS"
|
|
"TotalCopheneticIndex"
|
|
"TreeDist"
|
|
"biocthis"
|
|
"calmate"
|
|
"fgga"
|
|
"fulltext"
|
|
"immuneSIM"
|
|
"mastif"
|
|
"shinymeta"
|
|
"shinyobjects"
|
|
"wppi"
|
|
"pins"
|
|
"CoTiMA"
|
|
"TBRDist"
|
|
"Rogue"
|
|
"fixest"
|
|
"paxtoolsr"
|
|
"systemPipeShiny"
|
|
"matlab2r"
|
|
"GNOSIS"
|
|
];
|
|
|
|
packagesToSkipCheck = [
|
|
"MsDataHub" # tries to connect to ExperimentHub
|
|
"Rmpi" # tries to run MPI processes
|
|
"ReactomeContentService4R" # tries to connect to Reactome
|
|
"PhIPData" # tries to download something from a DB
|
|
"RBioFormats" # tries to download jar during load test
|
|
"pbdMPI" # tries to run MPI processes
|
|
"CTdata" # tries to connect to ExperimentHub
|
|
"rfaRm" # tries to connect to Ebi
|
|
"data_table" # fails to rename shared library before check
|
|
"coMethDMR" # tries to connect to ExperimentHub
|
|
"multiMiR" # tries to connect to DB
|
|
"snapcount" # tries to connect to snaptron.cs.jhu.edu
|
|
];
|
|
|
|
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
|
brokenPackages = [
|
|
"av"
|
|
"NetLogoR"
|
|
"valse"
|
|
"HierO"
|
|
"HIBAG"
|
|
"HiveR"
|
|
|
|
# Impure network access during build
|
|
"waddR"
|
|
"tiledb"
|
|
"x13binary"
|
|
"switchr"
|
|
|
|
# ExperimentHub dependents, require net access during build
|
|
"DuoClustering2018"
|
|
"FieldEffectCrc"
|
|
"GenomicDistributionsData"
|
|
"hpar"
|
|
"HDCytoData"
|
|
"HMP16SData"
|
|
"PANTHER_db"
|
|
"RNAmodR_Data"
|
|
"SCATEData"
|
|
"SingleMoleculeFootprintingData"
|
|
"TabulaMurisData"
|
|
"benchmarkfdrData2019"
|
|
"bodymapRat"
|
|
"clustifyrdatahub"
|
|
"CTexploreR"
|
|
"depmap"
|
|
"emtdata"
|
|
"metaboliteIDmapping"
|
|
"msigdb"
|
|
"muscData"
|
|
"org_Mxanthus_db"
|
|
"scpdata"
|
|
"signatureSearch"
|
|
"nullrangesData"
|
|
];
|
|
|
|
otherOverrides = old: new: {
|
|
# it can happen that the major version of arrow-cpp is ahead of the
|
|
# rPackages.arrow that would be built from CRAN sources; therefore, to avoid
|
|
# build failures and manual updates of the hash, we use the R source at
|
|
# the GitHub release state of libarrow (arrow-cpp) in Nixpkgs. This may
|
|
# not exactly represent the CRAN sources, but because patching of the
|
|
# CRAN R package is mostly done to meet special CRAN build requirements,
|
|
# this is a straightforward approach. Example where patching was necessary
|
|
# -> arrow 14.0.0.2 on CRAN; was lagging behind libarrow release:
|
|
# https://github.com/apache/arrow/issues/39698 )
|
|
|
|
vegan3d = old.vegan3d.overrideAttrs (attrs: {
|
|
RGL_USE_NULL = "true";
|
|
});
|
|
|
|
arrow = old.arrow.overrideAttrs (attrs: {
|
|
src = pkgs.arrow-cpp.src;
|
|
name = "r-arrow-${pkgs.arrow-cpp.version}";
|
|
prePatch = "cd r";
|
|
postPatch = ''
|
|
patchShebangs configure
|
|
'';
|
|
buildInputs = attrs.buildInputs ++ [
|
|
pkgs.arrow-cpp
|
|
];
|
|
});
|
|
|
|
gifski = old.gifski.overrideAttrs (attrs: {
|
|
cargoDeps = pkgs.rustPlatform.fetchCargoTarball {
|
|
src = attrs.src;
|
|
sourceRoot = "gifski/src/myrustlib";
|
|
hash = "sha256-e6nuiQU22GiO2I+bu0muyICGrdkCLSZUDHDz2mM2hz0=";
|
|
};
|
|
|
|
cargoRoot = "src/myrustlib";
|
|
|
|
nativeBuildInputs = attrs.nativeBuildInputs ++ [
|
|
pkgs.rustPlatform.cargoSetupHook
|
|
pkgs.cargo
|
|
pkgs.rustc
|
|
];
|
|
});
|
|
|
|
timeless = old.timeless.overrideAttrs (attrs: {
|
|
cargoDeps = pkgs.rustPlatform.fetchCargoTarball {
|
|
src = attrs.src;
|
|
sourceRoot = "timeless/src/rust";
|
|
hash = "sha256-n0/52CV3NzWe7T3N6VoaURMxWrnqeYaUMPKkUy+LRQs=";
|
|
};
|
|
|
|
cargoRoot = "src/rust";
|
|
|
|
nativeBuildInputs = attrs.nativeBuildInputs ++ [
|
|
pkgs.rustPlatform.cargoSetupHook
|
|
pkgs.cargo
|
|
];
|
|
});
|
|
|
|
stringi = old.stringi.overrideAttrs (attrs: {
|
|
postInstall = let
|
|
icuName = "icudt52l";
|
|
icuSrc = pkgs.fetchzip {
|
|
url = "http://static.rexamine.com/packages/${icuName}.zip";
|
|
sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
|
|
stripRoot = false;
|
|
};
|
|
in ''
|
|
${attrs.postInstall or ""}
|
|
cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
|
|
'';
|
|
});
|
|
|
|
xml2 = old.xml2.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
rzmq = old.rzmq.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
clustermq = old.clustermq.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
Cairo = old.Cairo.overrideAttrs (attrs: {
|
|
NIX_LDFLAGS = "-lfontconfig";
|
|
});
|
|
|
|
curl = old.curl.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
Cyclops = old.Cyclops.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
RcppParallel = old.RcppParallel.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
Colossus = old.Colossus.overrideAttrs (_: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
gmailr = old.gmailr.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
heck = old.heck.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
surtvep = old.surtvep.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
purrr = old.purrr.overrideAttrs (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
luajr = old.luajr.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
RcppGetconf = old.RcppGetconf.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
SpliceWiz = old.SpliceWiz.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
zoomerjoin = old.zoomerjoin.overrideAttrs (attrs: {
|
|
nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
b64 = old.b64.overrideAttrs (attrs: {
|
|
nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
ocf = old.ocf.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
data_table = old.data_table.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fopenmp";
|
|
};
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
cisPath = old.cisPath.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
HilbertVis = old.HilbertVis.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
HilbertVisGUI = old.HilbertVisGUI.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
MANOR = old.MANOR.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
rGADEM = old.rGADEM.overrideAttrs (attrs: {
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
rsgeo = old.rsgeo.overrideAttrs (attrs: {
|
|
nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
instantiate = old.instantiate.overrideAttrs (attrs: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
exifr = old.exifr.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
for f in .onLoad .onAttach ; do
|
|
substituteInPlace R/load_hook.R \
|
|
--replace-fail \
|
|
"$f <- function(libname, pkgname) {" \
|
|
"$f <- function(libname, pkgname) {
|
|
options(
|
|
exifr.perlpath = \"${lib.getBin pkgs.perl}/bin/perl\",
|
|
exifr.exiftoolcommand = \"${lib.getBin pkgs.exiftool}/bin/exiftool\"
|
|
)"
|
|
done
|
|
'';
|
|
});
|
|
|
|
NGCHM = old.NGCHM.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace "inst/base.config/conf.d/01-server-protocol-scl.R" \
|
|
--replace-fail \
|
|
"/bin/hostname" "${lib.getBin pkgs.hostname}/bin/hostname"
|
|
'';
|
|
});
|
|
|
|
ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp";
|
|
};
|
|
});
|
|
|
|
rawrr = old.rawrr.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace "R/zzz.R" "R/dotNetAssembly.R" --replace-warn \
|
|
"Sys.which('mono')" "'${lib.getBin pkgs.mono}/bin/mono'"
|
|
|
|
substituteInPlace "R/dotNetAssembly.R" --replace-warn \
|
|
"Sys.which(\"xbuild\")" "\"${lib.getBin pkgs.mono}/bin/xbuild\""
|
|
|
|
substituteInPlace "R/dotNetAssembly.R" --replace-warn \
|
|
"cmd <- ifelse(Sys.which(\"msbuild\") != \"\", \"msbuild\", \"xbuild\")" \
|
|
"cmd <- \"${lib.getBin pkgs.mono}/bin/xbuild\""
|
|
|
|
substituteInPlace "R/rawrr.R" --replace-warn \
|
|
"Sys.which(\"mono\")" "\"${lib.getBin pkgs.mono}/bin/mono\""
|
|
'';
|
|
});
|
|
|
|
rpf = old.rpf.overrideAttrs (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
rJava = old.rJava.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
JavaGD = old.JavaGD.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
jqr = old.jqr.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
pathfindR = old.pathfindR.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace "R/zzz.R" \
|
|
--replace-fail " check_java_version()" " Sys.setenv(JAVA_HOME = \"${lib.getBin pkgs.jre_minimal}\"); check_java_version()"
|
|
substituteInPlace "R/active_snw_search.R" \
|
|
--replace-fail "system(paste0(\"java" "system(paste0(\"${lib.getBin pkgs.jre_minimal}/bin/java"
|
|
'';
|
|
});
|
|
|
|
pbdZMQ = old.pbdZMQ.overrideAttrs (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' $file
|
|
done
|
|
'';
|
|
});
|
|
|
|
quarto = old.quarto.overrideAttrs (attrs: {
|
|
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.quarto ];
|
|
postPatch = ''
|
|
substituteInPlace "R/quarto.R" \
|
|
--replace-fail "Sys.getenv(\"QUARTO_PATH\", unset = NA_character_)" "Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')"
|
|
'';
|
|
});
|
|
|
|
Rhisat2 = old.Rhisat2.overrideAttrs (attrs: {
|
|
enableParallelBuilding = false;
|
|
});
|
|
|
|
s2 = old.s2.overrideAttrs (attrs: {
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideAttrs (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideAttrs (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr.dev}/include"
|
|
];
|
|
});
|
|
|
|
covidsymptom = old.covidsymptom.overrideAttrs (attrs: {
|
|
preConfigure = "rm R/covidsymptomdata.R";
|
|
});
|
|
|
|
cubature = old.cubature.overrideAttrs (attrs: {
|
|
enableParallelBuilding = false;
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
|
|
];
|
|
});
|
|
|
|
RAppArmor = old.RAppArmor.overrideAttrs (attrs: {
|
|
patches = [ ./patches/RAppArmor.patch ];
|
|
LIBAPPARMOR_HOME = pkgs.libapparmor;
|
|
});
|
|
|
|
RMySQL = old.RMySQL.overrideAttrs (attrs: {
|
|
MYSQL_DIR = "${pkgs.libmysqlclient}";
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.libmysqlclient.dev}/include/mysql";
|
|
NIX_CFLAGS_LINK = "-L${pkgs.libmysqlclient}/lib/mysql -lmysqlclient";
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideAttrs (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
|
|
NIX_LDFLAGS = "-lX11";
|
|
});
|
|
|
|
hdf5r = old.hdf5r.overrideAttrs (attrs: {
|
|
buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ];
|
|
});
|
|
|
|
slfm = old.slfm.overrideAttrs (attrs: {
|
|
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideAttrs (attrs: {
|
|
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
|
|
});
|
|
|
|
FLAMES = old.FLAMES.overrideAttrs (attrs: {
|
|
patches = [ ./patches/FLAMES.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
|
|
});
|
|
|
|
websocket = old.websocket.overrideAttrs (attrs: {
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideAttrs (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
universalmotif = old.universalmotif.overrideAttrs (attrs: {
|
|
patches = [ ./patches/universalmotif.patch];
|
|
});
|
|
|
|
V8 = old.V8.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace configure \
|
|
--replace-fail " -lv8_libplatform" ""
|
|
# Bypass the test checking if pointer compression is needed
|
|
substituteInPlace configure \
|
|
--replace-fail "./pctest1" "true"
|
|
'';
|
|
|
|
preConfigure = ''
|
|
export INCLUDE_DIR=${pkgs.nodejs.libv8}/include
|
|
export LIB_DIR=${pkgs.nodejs.libv8}/lib
|
|
patchShebangs configure
|
|
'';
|
|
|
|
R_MAKEVARS_SITE = lib.optionalString (pkgs.stdenv.system == "aarch64-linux")
|
|
(pkgs.writeText "Makevars" ''
|
|
CXX14PICFLAGS = -fPIC
|
|
'');
|
|
});
|
|
|
|
acs = old.acs.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
gdtools = old.gdtools.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
NIX_LDFLAGS = "-lfontconfig -lfreetype";
|
|
});
|
|
|
|
magick = old.magick.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
libgeos = old.libgeos.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
protolite = old.protolite.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
rgoslin = old.rgoslin.overrideAttrs (attrs: {
|
|
enableParallelBuilding = false;
|
|
});
|
|
|
|
rpanel = old.rpanel.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
|
|
'';
|
|
TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
|
|
});
|
|
|
|
networkscaleup = old.networkscaleup.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
# needed to avoid "log limit exceeded" on Hydra
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
|
|
};
|
|
|
|
# consumes a lot of resources in parallel
|
|
enableParallelBuilding = false;
|
|
});
|
|
|
|
RPostgres = old.RPostgres.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
export INCLUDE_DIR=${pkgs.postgresql}/include
|
|
export LIB_DIR=${pkgs.postgresql.lib}/lib
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
OpenMx = old.OpenMx.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
# needed to avoid "log limit exceeded" on Hydra
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
|
|
};
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
odbc = old.odbc.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
x13binary = old.x13binary.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
FlexReg = old.FlexReg.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
# needed to avoid "log limit exceeded" on Hydra
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
|
|
};
|
|
|
|
# consumes a lot of resources in parallel
|
|
enableParallelBuilding = false;
|
|
});
|
|
|
|
geojsonio = old.geojsonio.overrideAttrs (attrs: {
|
|
buildInputs = [ cacert ] ++ attrs.buildInputs;
|
|
});
|
|
|
|
|
|
immunotation = let
|
|
MHC41alleleList = fetchurl {
|
|
url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list";
|
|
hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg=";
|
|
};
|
|
|
|
MHCII40alleleList = fetchurl {
|
|
url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list";
|
|
hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40=";
|
|
};
|
|
|
|
# List of valid countries, regions and ethnic groups
|
|
# The original page is changing a bit every day, but the relevant
|
|
# content does not. Use archive.org to get a stable snapshot.
|
|
# It can be updated from time to time, or when the package becomes
|
|
# deficient. This may be difficult to know.
|
|
# Update the snapshot date, and add id_ after it, as described here:
|
|
# https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/
|
|
validGeographics = fetchurl {
|
|
url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp";
|
|
hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak=";
|
|
};
|
|
in old.immunotation.overrideAttrs (attrs: {
|
|
patches = [ ./patches/immunotation.patch ];
|
|
postPatch = ''
|
|
substituteInPlace "R/external_resources_input.R" --replace-fail \
|
|
"nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
|
|
|
|
substituteInPlace "R/external_resources_input.R" --replace-fail \
|
|
"nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
|
|
|
|
substituteInPlace "R/AFND_interface.R" --replace-fail \
|
|
"nix-valid-geographics" ${validGeographics}
|
|
'';
|
|
});
|
|
|
|
nearfar = let
|
|
angrist = fetchurl {
|
|
url = "https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv";
|
|
hash = "sha256-lb+HMHnRGonc26merFGB0B7Vk1Lk+sIJlay+JtQC8m4=";
|
|
};
|
|
in old.nearfar.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace "R/nearfar.R" --replace-fail \
|
|
'url("https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv")' '"${angrist}"'
|
|
'';
|
|
});
|
|
|
|
rstan = old.rstan.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
|
|
};
|
|
});
|
|
|
|
mongolite = old.mongolite.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include";
|
|
PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
|
|
});
|
|
|
|
ChemmineOB = let
|
|
# R package doesn't compile with the latest (unstable) version.
|
|
# Override from nixpkgs-23.11
|
|
openbabel3 = pkgs.openbabel.overrideAttrs (attrs: {
|
|
version = "3.1.1";
|
|
src = pkgs.fetchFromGitHub {
|
|
owner = "openbabel";
|
|
repo = "openbabel";
|
|
rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}";
|
|
sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
|
|
};
|
|
});
|
|
in
|
|
old.ChemmineOB.overrideAttrs (attrs: {
|
|
# pkg-config knows openbabel-3 without the .0
|
|
# Eigen3 is also looked for in the wrong location
|
|
postPatch = ''
|
|
substituteInPlace configure \
|
|
--replace-fail openbabel-3.0 openbabel-3
|
|
substituteInPlace src/Makevars.in \
|
|
--replace-fail "-I/usr/include/eigen3" "-I${pkgs.eigen}/include/eigen3"
|
|
'';
|
|
buildInputs = attrs.buildInputs ++ [openbabel3];
|
|
});
|
|
|
|
ps = old.ps.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
rlang = old.rlang.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
systemfonts = old.systemfonts.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
littler = old.littler.overrideAttrs (attrs: with pkgs; {
|
|
buildInputs = [ pcre xz 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 $out/library/littler/script-tests
|
|
'';
|
|
});
|
|
|
|
lpsymphony = old.lpsymphony.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
sodium = old.sodium.overrideAttrs (attrs: with pkgs; {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
nativeBuildInputs = [ pkg-config ] ++ attrs.nativeBuildInputs;
|
|
buildInputs = [ libsodium.dev ] ++ attrs.buildInputs;
|
|
});
|
|
|
|
keyring = old.keyring.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
Rhtslib = old.Rhtslib.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
|
|
'';
|
|
});
|
|
|
|
h2o = old.h2o.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
# prevent download of jar file during install and postpone to first use
|
|
sed -i '/downloadJar()/d' R/zzz.R
|
|
|
|
# during runtime the package directory is not writable as it's in the
|
|
# nix store, so store the jar in the user's cache directory instead
|
|
substituteInPlace R/connection.R --replace \
|
|
'dest_file <- file.path(dest_folder, "h2o.jar")' \
|
|
'dest_file <- file.path("~/.cache/", "h2o.jar")'
|
|
'';
|
|
});
|
|
|
|
SICtools = old.SICtools.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
substituteInPlace src/Makefile --replace-fail "-lcurses" "-lncurses"
|
|
'';
|
|
hardeningDisable = [ "format" ];
|
|
});
|
|
|
|
Rbwa = old.Rbwa.overrideAttrs (attrs: {
|
|
# Parallel build cleans up *.o before they can be packed in a library
|
|
postPatch = ''
|
|
substituteInPlace src/Makefile --replace-fail \
|
|
"all:\$(PROG) ../inst/bwa clean" \
|
|
"all:\$(PROG) ../inst/bwa" \
|
|
'';
|
|
});
|
|
|
|
ROracle = old.ROracle.overrideAttrs (attrs: {
|
|
configureFlags = [
|
|
"--with-oci-lib=${pkgs.oracle-instantclient.lib}/lib"
|
|
"--with-oci-inc=${pkgs.oracle-instantclient.dev}/include"
|
|
];
|
|
});
|
|
|
|
xslt = old.xslt.overrideAttrs (attrs: {
|
|
env = (attrs.env or { }) // {
|
|
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
|
|
};
|
|
});
|
|
|
|
sparklyr = old.sparklyr.overrideAttrs (attrs: {
|
|
# Pyspark's spark is full featured and better maintained than pkgs.spark
|
|
preConfigure = ''
|
|
substituteInPlace R/zzz.R \
|
|
--replace ".onLoad <- function(...) {" \
|
|
".onLoad <- function(...) {
|
|
Sys.setenv(\"SPARK_HOME\" = Sys.getenv(\"SPARK_HOME\", unset = \"${pkgs.python3Packages.pyspark}/${pkgs.python3Packages.python.sitePackages}/pyspark\"))
|
|
Sys.setenv(\"JAVA_HOME\" = Sys.getenv(\"JAVA_HOME\", unset = \"${pkgs.jdk}\"))"
|
|
'';
|
|
});
|
|
|
|
proj4 = old.proj4.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
substituteInPlace configure \
|
|
--replace "-lsqlite3" "-L${lib.makeLibraryPath [ pkgs.sqlite ]} -lsqlite3"
|
|
'';
|
|
});
|
|
|
|
rrd = old.rrd.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
ChIPXpress = old.ChIPXpress.override { hydraPlatforms = []; };
|
|
|
|
rgl = old.rgl.overrideAttrs (attrs: {
|
|
RGL_USE_NULL = "true";
|
|
});
|
|
|
|
Rrdrand = old.Rrdrand.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
|
|
|
|
symengine = old.symengine.overrideAttrs (_: {
|
|
preConfigure = ''
|
|
rm configure
|
|
cat > src/Makevars << EOF
|
|
PKG_LIBS=-lsymengine
|
|
all: $(SHLIB)
|
|
EOF
|
|
'';
|
|
});
|
|
|
|
RandomFieldsUtils = old.RandomFieldsUtils.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
|
|
|
|
flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
|
|
|
|
RcppCGAL = old.RcppCGAL.overrideAttrs (_: {
|
|
postPatch = "patchShebangs configure";
|
|
});
|
|
|
|
SharedObject = old.SharedObject.overrideAttrs (attrs: {
|
|
# backport PR resolving build issues: https://github.com/Jiefei-Wang/SharedObject/pull/17
|
|
patches = let inherit (pkgs) fetchpatch; in [
|
|
(fetchpatch {
|
|
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/50c4b2964649d7f5a14d843bd7089ab62650fcd3.patch";
|
|
sha256 = "sha256-zn535IeOYRvyQ2yxgoGEq2wccrl9xdu9nREmy7sV+PQ=";
|
|
})
|
|
(fetchpatch {
|
|
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/bf096a39858e9210cbe246d4b136905d4cfbfaf4.patch";
|
|
sha256 = "sha256-Z+BZOkFnLgIBiVuPsAHp7bMXzADcvuHV4hILdmLvd+k=";
|
|
})
|
|
];
|
|
});
|
|
|
|
httr2 = old.httr2.overrideAttrs (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
dbarts = old.dbarts.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
|
|
|
|
geomorph = old.geomorph.overrideAttrs (attrs: {
|
|
RGL_USE_NULL = "true";
|
|
});
|
|
|
|
gpuMagic = old.gpuMagic.overrideAttrs (_: {
|
|
hardeningDisable = ["format"];
|
|
});
|
|
|
|
Rdisop = old.Rdisop.overrideAttrs (_: {
|
|
hardeningDisable = ["format"];
|
|
});
|
|
|
|
opencv = let
|
|
opencvGtk = pkgs.opencv.override (old : { enableGtk2 = true; });
|
|
in old.opencv.overrideAttrs (attrs: {
|
|
buildInputs = attrs.buildInputs ++ [ opencvGtk ];
|
|
});
|
|
|
|
Rhdf5lib = let
|
|
hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ [ "--enable-cxx" ];});
|
|
in old.Rhdf5lib.overrideAttrs (attrs: {
|
|
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ];
|
|
patches = [ ./patches/Rhdf5lib.patch ];
|
|
passthru.hdf5 = hdf5;
|
|
});
|
|
|
|
rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: {
|
|
patches = [ ./patches/rhdf5filters.patch ];
|
|
});
|
|
|
|
rhdf5= old.rhdf5.overrideAttrs (attrs: {
|
|
patches = [ ./patches/rhdf5.patch ];
|
|
});
|
|
|
|
rmarkdown = old.rmarkdown.overrideAttrs (_: {
|
|
preConfigure = ''
|
|
substituteInPlace R/pandoc.R \
|
|
--replace '"~/opt/pandoc"' '"~/opt/pandoc", "${pkgs.pandoc}/bin"'
|
|
'';
|
|
});
|
|
|
|
redland = old.redland.overrideAttrs (_: {
|
|
PKGCONFIG_CFLAGS="-I${pkgs.redland}/include -I${pkgs.librdf_raptor2}/include/raptor2 -I${pkgs.librdf_rasqal}/include/rasqal";
|
|
PKGCONFIG_LIBS="-L${pkgs.redland}/lib -L${pkgs.librdf_raptor2}/lib -L${pkgs.librdf_rasqal}/lib -lrdf -lraptor2 -lrasqal";
|
|
});
|
|
|
|
textshaping = old.textshaping.overrideAttrs (attrs: {
|
|
env.NIX_LDFLAGS = "-lfribidi -lharfbuzz";
|
|
});
|
|
|
|
httpuv = old.httpuv.overrideAttrs (_: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
oligo = old.oligo.overrideAttrs (_: {
|
|
hardeningDisable = ["format"];
|
|
});
|
|
|
|
tesseract = old.tesseract.overrideAttrs (_: {
|
|
preConfigure = ''
|
|
substituteInPlace configure \
|
|
--replace 'PKG_CONFIG_NAME="tesseract"' 'PKG_CONFIG_NAME="tesseract lept"'
|
|
'';
|
|
});
|
|
|
|
ijtiff = old.ijtiff.overrideAttrs (_: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
torch = old.torch.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
|
|
pak = old.pak.overrideAttrs (attrs: {
|
|
preConfigure = ''
|
|
patchShebangs configure
|
|
patchShebangs src/library/curl/configure
|
|
patchShebangs src/library/pkgdepends/configure
|
|
patchShebangs src/library/ps/configure
|
|
'';
|
|
});
|
|
|
|
pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
|
|
postPatch = ''
|
|
patchShebangs configure
|
|
'';
|
|
});
|
|
};
|
|
in
|
|
self
|