1720 lines
67 KiB
Nix
1720 lines
67 KiB
Nix
/* This file defines the composition for CRAN (R) packages. */
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{ R, pkgs, overrides }:
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let
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inherit (pkgs) fetchurl stdenv lib;
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buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
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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}: 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 { 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 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: "http://cran.r-project.org/web/packages/${name}/";
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mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveCran = mkDerive {
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mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
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mkUrls = {name, version}: [
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"mirror://cran/src/contrib/${name}_${version}.tar.gz"
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"mirror://cran/src/contrib/00Archive/${name}/${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.overrideDerivation (attrs: {
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# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
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# });
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# }
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overrideNativeBuildInputs = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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nativeBuildInputs = attrs.nativeBuildInputs ++ value;
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})
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) overrides;
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# Overrides package definitions with buildInputs.
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# For example,
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#
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# overrideBuildInputs {
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# foo = [ pkgs.bar ]
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# } old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideDerivation (attrs: {
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# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
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# });
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# }
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overrideBuildInputs = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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buildInputs = attrs.buildInputs ++ value;
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})
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) overrides;
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# Overrides package definitions with new R dependencies.
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# For example,
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#
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# overrideRDepends {
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# foo = [ self.bar ]
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# } old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideDerivation (attrs: {
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# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
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# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
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# });
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# }
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overrideRDepends = overrides: old:
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lib.mapAttrs (name: value:
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(builtins.getAttr name old).overrideDerivation (attrs: {
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nativeBuildInputs = attrs.nativeBuildInputs ++ value;
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propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
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})
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) overrides;
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# Overrides package definition requiring X running to install.
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# For example,
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#
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# overrideRequireX [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# requireX = true;
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# };
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# }
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overrideRequireX = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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requireX = true;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition to skip check.
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# For example,
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#
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# overrideSkipCheck [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# doCheck = false;
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# };
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# }
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overrideSkipCheck = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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doCheck = false;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition to mark it broken.
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# For example,
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#
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# overrideBroken [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.override {
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# broken = true;
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# };
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# }
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overrideBroken = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).override {
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broken = true;
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};
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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defaultOverrides = old: new:
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let old0 = old; in
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let
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old1 = old0 // (overrideRequireX packagesRequireingX old0);
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old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
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old3 = old2 // (overrideRDepends packagesWithRDepends old2);
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old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
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old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
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old6 = old5 // (overrideBroken brokenPackages old5);
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old = old6;
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in old // (otherOverrides old new);
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# Recursive override pattern.
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# `_self` is a collection of packages;
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# `self` is `_self` with overridden packages;
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# packages in `_self` may depends on overridden packages.
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self = (defaultOverrides _self self) // overrides;
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_self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
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import ./cran-packages.nix { inherit self; derive = deriveCran; };
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# tweaks for the individual packages and "in self" follow
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packagesWithRDepends = {
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FactoMineR = [ self.car ];
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pander = [ self.codetools ];
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};
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packagesWithNativeBuildInputs = {
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abn = [ pkgs.gsl ];
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adimpro = [ pkgs.imagemagick ];
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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 = [ pkgs.readline pkgs.ncurses ];
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bigGP = [ pkgs.openmpi ];
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BiocCheck = [ pkgs.which ];
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Biostrings = [ pkgs.zlib ];
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bnpmr = [ pkgs.gsl ];
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BNSP = [ pkgs.gsl ];
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cairoDevice = [ pkgs.gtk2 ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
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Cardinal = [ pkgs.which ];
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CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
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chebpol = [ pkgs.fftw ];
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ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
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cit = [ pkgs.gsl ];
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curl = [ pkgs.curl ];
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devEMF = [ pkgs.xorg.libXft ];
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diversitree = [ pkgs.gsl pkgs.fftw ];
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EMCluster = [ pkgs.liblapack ];
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fftw = [ pkgs.fftw ];
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fftwtools = [ pkgs.fftw ];
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Formula = [ pkgs.gmp ];
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geoCount = [ pkgs.gsl ];
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git2r = [ pkgs.zlib pkgs.openssl ];
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GLAD = [ pkgs.gsl ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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gmp = [ pkgs.gmp ];
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graphscan = [ pkgs.gsl ];
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gsl = [ pkgs.gsl ];
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HiCseg = [ pkgs.gsl ];
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iBMQ = [ pkgs.gsl ];
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igraph = [ pkgs.gmp ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg ];
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KFKSDS = [ pkgs.gsl ];
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kza = [ pkgs.fftw ];
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libamtrack = [ pkgs.gsl ];
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mixcat = [ pkgs.gsl ];
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mvabund = [ pkgs.gsl ];
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mwaved = [ pkgs.fftw ];
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ncdf4 = [ pkgs.netcdf ];
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ncdf = [ pkgs.netcdf ];
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nloptr = [ pkgs.nlopt ];
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openssl = [ pkgs.openssl ];
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outbreaker = [ pkgs.gsl ];
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pander = [ pkgs.pandoc pkgs.which ];
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pbdMPI = [ pkgs.openmpi ];
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pbdNCDF4 = [ pkgs.netcdf ];
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pbdPROF = [ pkgs.openmpi ];
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PKI = [ pkgs.openssl ];
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png = [ pkgs.libpng ];
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PopGenome = [ pkgs.zlib ];
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proj4 = [ pkgs.proj ];
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qtbase = [ pkgs.qt4 ];
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qtpaint = [ pkgs.qt4 ];
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R2GUESS = [ pkgs.gsl ];
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R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
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RAppArmor = [ pkgs.libapparmor ];
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rapportools = [ pkgs.which ];
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rapport = [ pkgs.which ];
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rbamtools = [ pkgs.zlib ];
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RCA = [ pkgs.gmp ];
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rcdd = [ pkgs.gmp ];
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RcppCNPy = [ pkgs.zlib ];
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RcppGSL = [ pkgs.gsl ];
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RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
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RcppZiggurat = [ pkgs.gsl ];
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rgdal = [ pkgs.proj pkgs.gdal ];
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rgeos = [ pkgs.geos ];
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rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
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rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
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Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2 ];
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Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
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Rhtslib = [ pkgs.zlib ];
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ridge = [ pkgs.gsl ];
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RJaCGH = [ pkgs.zlib ];
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rjags = [ pkgs.jags ];
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rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
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Rlibeemd = [ pkgs.gsl ];
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rmatio = [ pkgs.zlib ];
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Rmpfr = [ pkgs.gmp pkgs.mpfr ];
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Rmpi = [ pkgs.openmpi ];
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RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
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RNetCDF = [ pkgs.netcdf pkgs.udunits ];
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RODBCext = [ pkgs.libiodbc ];
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RODBC = [ pkgs.libiodbc ];
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rpg = [ pkgs.postgresql ];
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rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
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Rpoppler = [ pkgs.poppler ];
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RPostgreSQL = [ pkgs.postgresql ];
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RProtoBuf = [ pkgs.protobuf ];
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rpud = [ pkgs.linuxPackages.nvidia_x11 ];
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rPython = [ pkgs.python ];
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RSclient = [ pkgs.openssl ];
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Rserve = [ pkgs.openssl ];
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Rssa = [ pkgs.fftw ];
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rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
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rtiff = [ pkgs.libtiff ];
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runjags = [ pkgs.jags ];
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RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
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rzmq = [ pkgs.zeromq3 ];
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SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
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sdcTable = [ pkgs.gmp pkgs.glpk ];
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seewave = [ pkgs.fftw pkgs.libsndfile ];
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SemiCompRisks = [ pkgs.gsl ];
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seqinr = [ pkgs.zlib ];
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seqminer = [ pkgs.zlib pkgs.bzip2 ];
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showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
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simplexreg = [ pkgs.gsl ];
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SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
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spate = [ pkgs.fftw ];
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sprint = [ pkgs.openmpi ];
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ssanv = [ pkgs.proj ];
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stsm = [ pkgs.gsl ];
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stringi = [ pkgs.icu ];
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survSNP = [ pkgs.gsl ];
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sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
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TAQMNGR = [ pkgs.zlib ];
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tiff = [ pkgs.libtiff ];
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TKF = [ pkgs.gsl ];
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tkrplot = [ pkgs.xorg.libX11 ];
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topicmodels = [ pkgs.gsl ];
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udunits2 = [ pkgs.udunits pkgs.expat ];
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V8 = [ pkgs.v8 ];
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VBLPCM = [ pkgs.gsl ];
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VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
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WhopGenome = [ pkgs.zlib ];
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XBRL = [ pkgs.zlib pkgs.libxml2 ];
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xml2 = [ pkgs.libxml2 ];
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XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
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};
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packagesWithBuildInputs = {
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# sort -t '=' -k 2
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svKomodo = [ pkgs.which ];
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nat = [ pkgs.which ];
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nat_nblast = [ pkgs.which ];
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nat_templatebrains = [ pkgs.which ];
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RMark = [ pkgs.which ];
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RPushbullet = [ pkgs.which ];
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qtpaint = [ pkgs.cmake ];
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qtbase = [ pkgs.cmake pkgs.perl ];
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gmatrix = [ pkgs.cudatoolkit ];
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WideLM = [ pkgs.cudatoolkit ];
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RCurl = [ pkgs.curl ];
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R2SWF = [ pkgs.pkgconfig ];
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rggobi = [ pkgs.pkgconfig ];
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RGtk2 = [ pkgs.pkgconfig ];
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RProtoBuf = [ pkgs.pkgconfig ];
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Rpoppler = [ pkgs.pkgconfig ];
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VBmix = [ pkgs.pkgconfig ];
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XML = [ pkgs.pkgconfig ];
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cairoDevice = [ pkgs.pkgconfig ];
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chebpol = [ pkgs.pkgconfig ];
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fftw = [ pkgs.pkgconfig ];
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geoCount = [ pkgs.pkgconfig ];
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kza = [ pkgs.pkgconfig ];
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mwaved = [ pkgs.pkgconfig ];
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showtext = [ pkgs.pkgconfig ];
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spate = [ pkgs.pkgconfig ];
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stringi = [ pkgs.pkgconfig ];
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sysfonts = [ pkgs.pkgconfig ];
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Cairo = [ pkgs.pkgconfig ];
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Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
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qtutils = [ pkgs.qt4 ];
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ecoretriever = [ pkgs.which ];
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tcltk2 = [ pkgs.tcl pkgs.tk ];
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tikzDevice = [ pkgs.which pkgs.texLive ];
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rPython = [ pkgs.which ];
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CARramps = [ pkgs.which pkgs.cudatoolkit ];
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gridGraphics = [ pkgs.which ];
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gputools = [ pkgs.which pkgs.cudatoolkit ];
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rpud = [ pkgs.which pkgs.cudatoolkit ];
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adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
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PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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};
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packagesRequireingX = [
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"accrual"
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"ade4TkGUI"
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"adehabitat"
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"analogue"
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"analogueExtra"
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|
"AnalyzeFMRI"
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|
"AnnotLists"
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"AnthropMMD"
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|
"aplpack"
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|
"aqfig"
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|
"arf3DS4"
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|
"asbio"
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"AtelieR"
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|
"BAT"
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"bayesDem"
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"BCA"
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"BEQI2"
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"betapart"
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"betaper"
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"BiodiversityR"
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"BioGeoBEARS"
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"bio_infer"
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"bipartite"
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"biplotbootGUI"
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|
"blender"
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|
"cairoDevice"
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|
"CCTpack"
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|
"cncaGUI"
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|
"cocorresp"
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"CommunityCorrelogram"
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"confidence"
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|
"constrainedKriging"
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|
"ConvergenceConcepts"
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|
"cpa"
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|
"DALY"
|
|
"dave"
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|
"debug"
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|
"Deducer"
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|
"DeducerExtras"
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|
"DeducerPlugInExample"
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"DeducerPlugInScaling"
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"DeducerSpatial"
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"DeducerSurvival"
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"DeducerText"
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"Demerelate"
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"DescTools"
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"detrendeR"
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"dgmb"
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"DivMelt"
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"dpa"
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"DSpat"
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"dynamicGraph"
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|
"dynBiplotGUI"
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|
"EasyqpcR"
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"EcoVirtual"
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"ENiRG"
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"EnQuireR"
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|
"eVenn"
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|
"exactLoglinTest"
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|
"FAiR"
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|
"fat2Lpoly"
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|
"fbati"
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|
"FD"
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|
"feature"
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|
"FeedbackTS"
|
|
"FFD"
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|
"fgui"
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|
"fisheyeR"
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|
"fit4NM"
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"forams"
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|
"forensim"
|
|
"FreeSortR"
|
|
"fscaret"
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|
"fSRM"
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|
"gcmr"
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|
"Geneland"
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|
"GeoGenetix"
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|
"geomorph"
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|
"geoR"
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|
"geoRglm"
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|
"georob"
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|
"GeoXp"
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|
"GGEBiplotGUI"
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|
"gnm"
|
|
"GPCSIV"
|
|
"GrammR"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"gsubfn"
|
|
"GUniFrac"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"HH"
|
|
"HiveR"
|
|
"HomoPolymer"
|
|
"iBUGS"
|
|
"ic50"
|
|
"iDynoR"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"likeLTD"
|
|
"loe"
|
|
"logmult"
|
|
"LS2Wstat"
|
|
"MAR1"
|
|
"MareyMap"
|
|
"memgene"
|
|
"MergeGUI"
|
|
"metacom"
|
|
"Meth27QC"
|
|
"MetSizeR"
|
|
"MicroStrategyR"
|
|
"migui"
|
|
"miniGUI"
|
|
"MissingDataGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"MplusAutomation"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"MTurkR"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"OligoSpecificitySystem"
|
|
"onemap"
|
|
"OpenRepGrid"
|
|
"palaeoSig"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"PKgraph"
|
|
"playwith"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"pmg"
|
|
"PopGenReport"
|
|
"poppr"
|
|
"powerpkg"
|
|
"PredictABEL"
|
|
"prefmod"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"QCAGUI"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"qtutils"
|
|
"R2STATS"
|
|
"r4ss"
|
|
"RandomFields"
|
|
"rareNMtests"
|
|
"rAverage"
|
|
"Rcmdr"
|
|
"RcmdrPlugin_BCA"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_depthTools"
|
|
"RcmdrPlugin_DoE"
|
|
"RcmdrPlugin_doex"
|
|
"RcmdrPlugin_EACSPIR"
|
|
"RcmdrPlugin_EBM"
|
|
"RcmdrPlugin_EcoVirtual"
|
|
"RcmdrPlugin_epack"
|
|
"RcmdrPlugin_EZR"
|
|
"RcmdrPlugin_FactoMineR"
|
|
"RcmdrPlugin_HH"
|
|
"RcmdrPlugin_IPSUR"
|
|
"RcmdrPlugin_KMggplot2"
|
|
"RcmdrPlugin_lfstat"
|
|
"RcmdrPlugin_MA"
|
|
"RcmdrPlugin_mosaic"
|
|
"RcmdrPlugin_MPAStats"
|
|
"RcmdrPlugin_orloca"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_qual"
|
|
"RcmdrPlugin_ROC"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_SM"
|
|
"RcmdrPlugin_sos"
|
|
"RcmdrPlugin_StatisticalURV"
|
|
"RcmdrPlugin_steepness"
|
|
"RcmdrPlugin_survival"
|
|
"RcmdrPlugin_TeachingDemos"
|
|
"RcmdrPlugin_temis"
|
|
"RcmdrPlugin_UCA"
|
|
"recluster"
|
|
"relax"
|
|
"relimp"
|
|
"RenextGUI"
|
|
"reportRx"
|
|
"reshapeGUI"
|
|
"rgl"
|
|
"RHRV"
|
|
"rich"
|
|
"rioja"
|
|
"ripa"
|
|
"rite"
|
|
"rnbn"
|
|
"RNCEP"
|
|
"RQDA"
|
|
"RSDA"
|
|
"rsgcc"
|
|
"RSurvey"
|
|
"RunuranGUI"
|
|
"sdcMicroGUI"
|
|
"sharpshootR"
|
|
"simba"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"SOLOMON"
|
|
"soundecology"
|
|
"SPACECAP"
|
|
"spacodiR"
|
|
"spatsurv"
|
|
"sqldf"
|
|
"SRRS"
|
|
"SSDforR"
|
|
"statcheck"
|
|
"StatDA"
|
|
"STEPCAM"
|
|
"stosim"
|
|
"strvalidator"
|
|
"stylo"
|
|
"svDialogstcltk"
|
|
"svIDE"
|
|
"svSocket"
|
|
"svWidgets"
|
|
"SYNCSA"
|
|
"SyNet"
|
|
"tcltk2"
|
|
"TDMR"
|
|
"TED"
|
|
"TestScorer"
|
|
"TIMP"
|
|
"titan"
|
|
"tkrgl"
|
|
"tkrplot"
|
|
"tmap"
|
|
"tspmeta"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"twiddler"
|
|
"vcdExtra"
|
|
"VecStatGraphs3D"
|
|
"vegan"
|
|
"vegan3d"
|
|
"vegclust"
|
|
"VIMGUI"
|
|
"WMCapacity"
|
|
"x12GUI"
|
|
"xergm"
|
|
];
|
|
|
|
packagesToSkipCheck = [
|
|
"Rmpi" # tries to run MPI processes
|
|
"gmatrix" # requires CUDA runtime
|
|
"sprint" # tries to run MPI processes
|
|
"pbdMPI" # tries to run MPI processes
|
|
];
|
|
|
|
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
|
brokenPackages = [
|
|
"a4Base" # depends on broken package annaffy-1.41.1
|
|
"a4" # depends on broken package annaffy-1.41.1
|
|
"a4Reporting" # depends on broken package annaffy-1.41.1
|
|
"abd" # depends on broken package nlopt-2.4.2
|
|
"Actigraphy" # Build Is Broken
|
|
"adabag" # depends on broken package nlopt-2.4.2
|
|
"ADaCGH2" # depends on broken package tilingArray-1.47.0
|
|
"adSplit" # build is broken
|
|
"AER" # depends on broken package nlopt-2.4.2
|
|
"afex" # depends on broken package nlopt-2.4.2
|
|
"affyContam" # depends on broken package affyio-1.37.0
|
|
"affycoretools" # depends on broken package affyio-1.37.0
|
|
"affy" # depends on broken package affyio-1.37.0
|
|
"AffyExpress" # depends on broken package affyio-1.37.0
|
|
"affyILM" # depends on broken package affyio-1.37.0
|
|
"affyio" # build is broken
|
|
"affylmGUI" # depends on broken package affyio-1.37.0
|
|
"affyPara" # depends on broken package affyio-1.37.0
|
|
"affypdnn" # depends on broken package affyio-1.37.0
|
|
"affyPLM" # depends on broken package affyio-1.37.0
|
|
"affyQCReport" # depends on broken package affyio-1.37.0
|
|
"AffyRNADegradation" # depends on broken package affyio-1.37.0
|
|
"AffyTiling" # depends on broken package affyio-1.37.0
|
|
"AgiMicroRna" # depends on broken package affyio-1.37.0
|
|
"agRee" # depends on broken package nlopt-2.4.2
|
|
"aLFQ" # depends on broken package nlopt-2.4.2
|
|
"AllelicImbalance" # depends on broken package Rsamtools-1.21.8
|
|
"alr3" # depends on broken package nlopt-2.4.2
|
|
"alr4" # depends on broken package nlopt-2.4.2
|
|
"alsace" # depends on broken nloptr-1.0.4
|
|
"altcdfenvs" # depends on broken package affyio-1.37.0
|
|
"ampliQueso" # depends on broken package Rsamtools-1.21.8
|
|
"anacor" # depends on broken package nlopt-2.4.2
|
|
"annaffy" # build is broken
|
|
"annmap" # depends on broken package Rsamtools-1.21.8
|
|
"AnnotationForge" # Build Is Broken
|
|
"AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
|
|
"aods3" # depends on broken package nlopt-2.4.2
|
|
"apComplex" # build is broken
|
|
"apt" # depends on broken package nlopt-2.4.2
|
|
"ArfimaMLM" # depends on broken package nlopt-2.4.2
|
|
"arm" # depends on broken package nlopt-2.4.2
|
|
"ArrayExpress" # depends on broken package affyio-1.37.0
|
|
"ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8
|
|
"arrayMvout" # depends on broken package affyio-1.37.0
|
|
"arrayQualityMetrics" # depends on broken package affyio-1.37.0
|
|
"ArrayTools" # depends on broken package affyio-1.37.0
|
|
"ArrayTV" # depends on broken package affyio-1.37.0
|
|
"ARRmNormalization" # Build Is Broken
|
|
"ARTool" # depends on broken package nlopt-2.4.2
|
|
"attract" # depends on broken package AnnotationForge-1.11.3
|
|
"BACA" # depends on broken package Category-2.35.1
|
|
"BAGS" # build is broken
|
|
"ballgown" # depends on broken package Rsamtools-1.21.8
|
|
"bamsignals" # build is broken
|
|
"bartMachine" # depends on broken package nlopt-2.4.2
|
|
"Basic4Cseq" # depends on broken package Rsamtools-1.21.8
|
|
"bayesDem" # depends on broken package nlopt-2.4.2
|
|
"bayesLife" # depends on broken package nlopt-2.4.2
|
|
"bayesPop" # depends on broken package nlopt-2.4.2
|
|
"Bayesthresh" # depends on broken package nlopt-2.4.2
|
|
"BBRecapture" # depends on broken package nlopt-2.4.2
|
|
"BCA" # depends on broken package nlopt-2.4.2
|
|
"BEAT" # depends on broken package Rsamtools-1.21.8
|
|
"bgmm" # depends on broken package nlopt-2.4.2
|
|
"bgx" # depends on broken package affyio-1.37.0
|
|
"BIFIEsurvey" # depends on broken package nlopt-2.4.2
|
|
"bigGP" # build is broken
|
|
"BiGGR" # depends on broken package rsbml-2.27.0
|
|
"BiodiversityR" # depends on broken package nlopt-2.4.2
|
|
"biomvRCNS" # depends on broken package Rsamtools-1.21.8
|
|
"biotools" # depends on broken package rpanel-1.1-3
|
|
"biovizBase" # depends on broken package Rsamtools-1.21.8
|
|
"birte" # build is broken
|
|
"BiSEp" # depends on broken package GOSemSim-1.27.3
|
|
"BiSeq" # depends on broken package Rsamtools-1.21.8
|
|
"BitSeq" # depends on broken package Rsamtools-1.21.8
|
|
"BLCOP" # depends on broken package Rsymphony-0.1-20
|
|
"blmeco" # depends on broken package nlopt-2.4.2
|
|
"blme" # depends on broken package nlopt-2.4.2
|
|
"bmd" # depends on broken package nlopt-2.4.2
|
|
"bmem" # depends on broken package nlopt-2.4.2
|
|
"bootnet" # depends on broken package nlopt-2.4.2
|
|
"boss" # depends on broken package nlopt-2.4.2
|
|
"BradleyTerry2" # depends on broken package nlopt-2.4.2
|
|
"BRugs" # build is broken
|
|
"BSgenome" # depends on broken package Rsamtools-1.21.8
|
|
"bumphunter" # depends on broken package Rsamtools-1.21.8
|
|
"CADFtest" # depends on broken package nlopt-2.4.2
|
|
"CAFE" # depends on broken package affyio-1.37.0
|
|
"CAGEr" # depends on broken package Rsamtools-1.21.8
|
|
"cAIC4" # depends on broken package nlopt-2.4.2
|
|
"CAMERA" # depends on broken package mzR-2.3.1
|
|
"canceR" # depends on broken package Category-2.35.1
|
|
"candisc" # depends on broken package nlopt-2.4.2
|
|
"carcass" # depends on broken package nlopt-2.4.2
|
|
"car" # depends on broken package nlopt-2.4.2
|
|
"caret" # depends on broken package nlopt-2.4.2
|
|
"caretEnsemble" # depends on broken package nlopt-2.4.2
|
|
"CARrampsOcl" # depends on broken package OpenCL-0.1-3
|
|
"casper" # depends on broken package Rsamtools-1.21.8
|
|
"Category" # Build Is Broken
|
|
"categoryCompare" # depends on broken package Category-2.35.1
|
|
"CCpop" # depends on broken package nlopt-2.4.2
|
|
"cellHTS2" # depends on broken package Category-2.35.1
|
|
"CexoR" # depends on broken package Rsamtools-1.21.8
|
|
"ChainLadder" # depends on broken package nlopt-2.4.2
|
|
"ChAMP" # depends on broken package affyio-1.37.0
|
|
"charm" # depends on broken package affyio-1.37.0
|
|
"ChemmineR" # Build Is Broken
|
|
"chimera" # depends on broken package Rsamtools-1.21.8
|
|
"chipenrich" # build is broken
|
|
"chipPCR" # depends on broken nloptr-1.0.4
|
|
"ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPQC" # depends on broken package AnnotationForge-1.11.3
|
|
"ChIPseeker" # depends on broken package Rsamtools-1.21.8
|
|
"chipseq" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPseqR" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPsim" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPXpress" # depends on broken package affyio-1.37.0
|
|
"ChromHeatMap" # depends on broken package Rsamtools-1.21.8
|
|
"cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8
|
|
"climwin" # depends on broken package nlopt-2.4.2
|
|
"clipper" # depends on broken package Rsamtools-1.21.8
|
|
"CLME" # depends on broken package nlopt-2.4.2
|
|
"clpAPI" # build is broken
|
|
"clusterPower" # depends on broken package nlopt-2.4.2
|
|
"clusterProfiler" # depends on broken package GOSemSim-1.27.3
|
|
"clusterSEs" # depends on broken AER-1.2-4
|
|
"ClustGeo" # depends on broken FactoMineR-1.31.3
|
|
"CNEr" # depends on broken package Rsamtools-1.21.8
|
|
"cn_farms" # depends on broken package affyio-1.37.0
|
|
"cn_mops" # depends on broken package Rsamtools-1.21.8
|
|
"CNORfuzzy" # depends on broken package nlopt-2.4.2
|
|
"CNVPanelizer" # depends on broken cn.mops-1.15.1
|
|
"CNVrd2" # depends on broken package Rsamtools-1.21.8
|
|
"cobindR" # depends on broken package Rsamtools-1.21.8
|
|
"CoCiteStats" # Build Is Broken
|
|
"CODEX" # depends on broken package Rsamtools-1.21.8
|
|
"COHCAP" # build is broken
|
|
"colorscience"
|
|
"coMET" # depends on broken package Rsamtools-1.21.8
|
|
"compEpiTools" # depends on broken package topGO-2.21.0
|
|
"CompGO" # depends on broken package Category-2.35.1
|
|
"conformal" # depends on broken package nlopt-2.4.2
|
|
"ConsensusClusterPlus" # Build Is Broken
|
|
"conumee" # depends on broken package Rsamtools-1.21.8
|
|
"CopyNumber450k" # depends on broken package Rsamtools-1.21.8
|
|
"CopywriteR" # depends on broken package Rsamtools-1.21.8
|
|
"corHMM" # depends on broken package nlopt-2.4.2
|
|
"Cormotif" # depends on broken package affyio-1.37.0
|
|
"coRNAi" # depends on broken package Category-2.35.1
|
|
"cosmiq" # depends on broken package mzR-2.3.1
|
|
"CosmoPhotoz" # depends on broken package nlopt-2.4.2
|
|
"CoverageView" # depends on broken package Rsamtools-1.21.8
|
|
"cplexAPI" # build is broken
|
|
"cpvSNP" # depends on broken package Rsamtools-1.21.8
|
|
"CRISPRseek" # depends on broken package Rsamtools-1.21.8
|
|
"crlmm" # depends on broken package affyio-1.37.0
|
|
"Crossover" # Build Is Broken
|
|
"CrypticIBDcheck" # depends on broken package nlopt-2.4.2
|
|
"csaw" # depends on broken package Rsamtools-1.21.8
|
|
"cudaBayesreg" # build is broken
|
|
"cummeRbund" # depends on broken package Rsamtools-1.21.8
|
|
"customProDB" # depends on broken package Rsamtools-1.21.8
|
|
"daff" # depends on broken package V8-0.6
|
|
"dagbag" # build is broken
|
|
"dagLogo" # depends on broken package Rsamtools-1.21.8
|
|
"DAMisc" # depends on broken package nlopt-2.4.2
|
|
"DBKGrad" # depends on broken package rpanel-1.1-3
|
|
"Deducer" # depends on broken package nlopt-2.4.2
|
|
"DeducerExtras" # depends on broken package nlopt-2.4.2
|
|
"DeducerPlugInExample" # depends on broken package nlopt-2.4.2
|
|
"DeducerPlugInScaling" # depends on broken package nlopt-2.4.2
|
|
"DeducerSpatial" # depends on broken package nlopt-2.4.2
|
|
"DeducerSurvival" # depends on broken package nlopt-2.4.2
|
|
"DeducerText" # depends on broken package nlopt-2.4.2
|
|
"deepSNV" # depends on broken package Rsamtools-1.21.8
|
|
"DEGraph" # depends on broken package RCytoscape-1.19.0
|
|
"demi" # depends on broken package affyio-1.37.0
|
|
"derfinder" # depends on broken package Rsamtools-1.21.8
|
|
"derfinderPlot" # depends on broken package Rsamtools-1.21.8
|
|
"destiny" # depends on broken package VIM-4.3.0
|
|
"DEXSeq" # depends on broken package Rsamtools-1.21.8
|
|
"DiagTest3Grp" # depends on broken package nlopt-2.4.2
|
|
"DiffBind" # depends on broken package AnnotationForge-1.11.3
|
|
"diffHic" # depends on broken package rhdf5-2.13.1
|
|
"difR" # depends on broken package nlopt-2.4.2
|
|
"DirichletMultinomial" # Build Is Broken
|
|
"discSurv" # depends on broken package nlopt-2.4.2
|
|
"DistatisR" # depends on broken package nlopt-2.4.2
|
|
"diveRsity" # depends on broken package nlopt-2.4.2
|
|
"DMRcate" # depends on broken package Rsamtools-1.21.8
|
|
"DMRforPairs" # depends on broken package Rsamtools-1.21.8
|
|
"domainsignatures" # build is broken
|
|
"doMPI" # build is broken
|
|
"DOQTL" # depends on broken package Rsamtools-1.21.8
|
|
"DOSE" # depends on broken package GOSemSim-1.27.3
|
|
"dpa" # depends on broken package nlopt-2.4.2
|
|
"dpcR" # depends on broken nloptr-1.0.4
|
|
"drc" # depends on broken package nlopt-2.4.2
|
|
"drfit" # depends on broken package nlopt-2.4.2
|
|
"drsmooth" # depends on broken package nlopt-2.4.2
|
|
"DrugVsDisease" # depends on broken package affyio-1.37.0
|
|
"dualKS" # depends on broken package affyio-1.37.0
|
|
"dynlm" # depends on broken package nlopt-2.4.2
|
|
"easyanova" # depends on broken package nlopt-2.4.2
|
|
"easyRNASeq" # depends on broken package Rsamtools-1.21.8
|
|
"EDASeq" # depends on broken package Rsamtools-1.21.8
|
|
"edge" # depends on broken package nlopt-2.4.2
|
|
"eeptools" # depends on broken package nlopt-2.4.2
|
|
"EffectLiteR" # depends on broken package nlopt-2.4.2
|
|
"effects" # depends on broken package nlopt-2.4.2
|
|
"eiR" # depends on broken package ChemmineR-2.21.7
|
|
"eisa" # depends on broken package Category-2.35.1
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"ELMER" # depends on broken package Rsamtools-1.21.8
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"EMA" # depends on broken package nlopt-2.4.2
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"ENmix" # depends on broken package affyio-1.37.0
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"EnQuireR" # depends on broken package nlopt-2.4.2
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"EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2
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"ensembldb" # depends on broken package interactiveDisplayBase-1.7.0
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"ensemblVEP" # depends on broken package Rsamtools-1.21.8
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"epigenomix" # depends on broken package Rsamtools-1.21.8
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"episplineDensity" # depends on broken package nlopt-2.4.2
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"epivizr" # depends on broken package Rsamtools-1.21.8
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"epr" # depends on broken package nlopt-2.4.2
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"erer" # depends on broken package nlopt-2.4.2
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"erma" # depends on broken GenomicFiles-1.5.4
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"erpR" # depends on broken package rpanel-1.1-3
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"ExiMiR" # depends on broken package affyio-1.37.0
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"exomeCopy" # depends on broken package Rsamtools-1.21.8
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"ExomeDepth" # depends on broken package Rsamtools-1.21.8
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"exomePeak" # depends on broken package Rsamtools-1.21.8
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"ExpressionView" # depends on broken package Category-2.35.1
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"extRemes" # depends on broken package nlopt-2.4.2
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"ez" # depends on broken package nlopt-2.4.2
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"facopy" # depends on broken package nlopt-2.4.2
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"FactoMineR" # depends on broken package nlopt-2.4.2
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"Factoshiny" # depends on broken package nlopt-2.4.2
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"faoutlier" # depends on broken package nlopt-2.4.2
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"farms" # depends on broken package affyio-1.37.0
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"fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0
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"fastR" # depends on broken package nlopt-2.4.2
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"FDRreg" # depends on broken package nlopt-2.4.2
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"FEM" # build is broken
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"ffpe" # depends on broken package affyio-1.37.0
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"flagme" # depends on broken package mzR-2.3.1
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"flowDensity" # depends on broken package nlopt-2.4.2
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"flowPeaks" # build is broken
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"flowQ" # build is broken
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"FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0
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"flowStats" # depends on broken package ncdfFlow-2.15.2
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"flowVS" # depends on broken package ncdfFlow-2.15.2
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"flowWorkspace" # depends on broken package ncdfFlow-2.15.2
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"fmcsR" # depends on broken package ChemmineR-2.21.7
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"FourCSeq" # depends on broken package Rsamtools-1.21.8
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"fPortfolio" # depends on broken package Rsymphony-0.1-20
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"freqweights" # depends on broken package nlopt-2.4.2
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"frma" # depends on broken package affyio-1.37.0
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"frmaTools" # depends on broken package affyio-1.37.0
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"fscaret" # depends on broken package nlopt-2.4.2
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"FunciSNP" # depends on broken package snpStats-1.19.0
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"FunctionalNetworks" # Build Is Broken
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"fxregime" # depends on broken package nlopt-2.4.2
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"gamclass" # depends on broken package nlopt-2.4.2
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"gamlss_demo" # depends on broken package rpanel-1.1-3
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"gamm4" # depends on broken package nlopt-2.4.2
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"gCMAP" # depends on broken package Category-2.35.1
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"gCMAPWeb" # depends on broken package Category-2.35.1
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"gcmr" # depends on broken package nlopt-2.4.2
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"gcrma" # depends on broken package affyio-1.37.0
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"GDAtools" # depends on broken package nlopt-2.4.2
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"GENE_E" # depends on broken package rhdf5-2.13.1
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"GeneExpressionSignature" # depends on broken package annaffy-1.41.1
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"GeneticTools" # depends on broken package snpStats-1.19.0
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"genomation" # depends on broken package Rsamtools-1.21.8
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"GenomicAlignments" # depends on broken package Rsamtools-1.21.8
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"GenomicFeatures" # depends on broken package Rsamtools-1.21.8
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"GenomicFiles" # depends on broken package Rsamtools-1.21.8
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"GenomicInteractions" # depends on broken package Rsamtools-1.21.8
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"genotypeeval" # depends on broken package r-rtracklayer-1.29.12
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"GenoView" # depends on broken package Rsamtools-1.21.8
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"genridge" # depends on broken package nlopt-2.4.2
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"geojsonio" # depends on broken package V8-0.6
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"GEOsubmission" # depends on broken package affyio-1.37.0
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"gespeR" # depends on broken package Category-2.35.1
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"GEWIST" # depends on broken package nlopt-2.4.2
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"GGBase" # depends on broken package snpStats-1.19.0
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"ggbio" # depends on broken package Rsamtools-1.21.8
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"GGtools" # depends on broken package snpStats-1.19.0
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"gimme" # depends on broken package nlopt-2.4.2
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"girafe" # depends on broken package Rsamtools-1.21.8
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"gmapR" # depends on broken package Rsamtools-1.21.8
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"gmatrix" # depends on broken package cudatoolkit-5.5.22
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"gMCP" # build is broken
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"GOFunction" # build is broken
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"GOGANPA" # depends on broken package WGCNA-1.47
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"GoogleGenomics" # depends on broken package Rsamtools-1.21.8
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"goProfiles" # build is broken
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"GOSemSim" # Build Is Broken
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"goseq" # build is broken
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"GOSim" # depends on broken package topGO-2.21.0
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"GOstats" # depends on broken package AnnotationForge-1.11.3
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"GOTHiC" # depends on broken package Rsamtools-1.21.8
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"goTools" # build is broken
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"gplm" # depends on broken package nlopt-2.4.2
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"gputools" # depends on broken package cudatoolkit-5.5.22
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"gQTLstats" # depends on broken package snpStats-1.19.0
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"granova" # depends on broken package nlopt-2.4.2
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"graphicalVAR" # depends on broken package nlopt-2.4.2
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"GraphPCA" # depends on broken package nlopt-2.4.2
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"GreyListChIP" # depends on broken package Rsamtools-1.21.8
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"groHMM" # depends on broken package Rsamtools-1.21.8
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"GSCA" # depends on broken package rhdf5-2.13.1
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"GUIDE" # depends on broken package rpanel-1.1-3
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"Gviz" # depends on broken package Rsamtools-1.21.8
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"GWAF" # depends on broken package nlopt-2.4.2
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"gwascat" # depends on broken package interactiveDisplayBase-1.7.0
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"h2o" # build is broken
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"h5" # build is broken
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"h5vc" # depends on broken package rhdf5-2.13.1
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"Harshlight" # depends on broken package affyio-1.37.0
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"hbsae" # depends on broken package nlopt-2.4.2
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"heplots" # depends on broken package nlopt-2.4.2
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"hiAnnotator" # depends on broken package Rsamtools-1.21.8
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"hierGWAS"
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"HierO" # Build Is Broken
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"highriskzone"
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"HilbertVisGUI" # Build Is Broken
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"HiPLARM" # Build Is Broken
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"hiReadsProcessor" # depends on broken package Rsamtools-1.21.8
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"HistDAWass" # depends on broken package nlopt-2.4.2
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"HiTC" # depends on broken package Rsamtools-1.21.8
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"HLMdiag" # depends on broken package nlopt-2.4.2
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"HTqPCR" # depends on broken package affyio-1.37.0
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"HTSanalyzeR" # depends on broken package Category-2.35.1
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"HTSeqGenie" # depends on broken package Rsamtools-1.21.8
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"htSeqTools" # depends on broken package Rsamtools-1.21.8
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"hysteresis" # depends on broken package nlopt-2.4.2
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"IATscores" # depends on broken package nlopt-2.4.2
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"ibd" # depends on broken package nlopt-2.4.2
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"ibh" # build is broken
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"iccbeta" # depends on broken package nlopt-2.4.2
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"IdeoViz" # depends on broken package Rsamtools-1.21.8
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"ifaTools" # depends on broken package r-OpenMx-2.2.6
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"iFes" # depends on broken package cudatoolkit-5.5.22
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"imageHTS" # depends on broken package Category-2.35.1
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"immunoClust" # build is broken
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"imputeR" # depends on broken package nlopt-2.4.2
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"in2extRemes" # depends on broken package nlopt-2.4.2
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"inferference" # depends on broken package nlopt-2.4.2
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"influence_ME" # depends on broken package nlopt-2.4.2
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"InPAS" # depends on broken package Rsamtools-1.21.8
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"inSilicoMerging" # build is broken
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"INSPEcT" # depends on broken GenomicFeatures-1.21.13
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"intansv" # depends on broken package Rsamtools-1.21.8
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"interactiveDisplayBase" # build is broken
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"interactiveDisplay" # depends on broken package Category-2.35.1
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"interplot" # depends on broken arm-1.8-5
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"IONiseR" # depends on broken rhdf5-2.13.4
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"iptools"
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"IsingFit" # depends on broken package nlopt-2.4.2
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"IsoGene" # depends on broken package affyio-1.37.0
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"IsoGeneGUI" # depends on broken package affyio-1.37.0
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"ITALICS" # depends on broken package oligo-1.33.0
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"IVAS" # depends on broken package nlopt-2.4.2
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"ivpack" # depends on broken package nlopt-2.4.2
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"JAGUAR" # depends on broken package nlopt-2.4.2
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"jetset"
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"joda" # depends on broken package nlopt-2.4.2
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"jomo" # build is broken
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"js" # depends on broken package V8-0.6
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"KANT" # depends on broken package affyio-1.37.0
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"keggorthology" # build is broken
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"KEGGprofile" # Build Is Broken
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"lawn" # depends on broken package V8-0.6
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"learnstats" # depends on broken package nlopt-2.4.2
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"lefse" # build is broken
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"lessR" # depends on broken package nlopt-2.4.2
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"lfe" # build is broken
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"lgcp" # depends on broken package rpanel-1.1-3
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"limmaGUI" # depends on broken package affyio-1.37.0
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"LinRegInteractive" # depends on broken package rpanel-1.1-3
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"LiquidAssociation" # build is broken
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"lmdme" # build is broken
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"lme4" # depends on broken package nlopt-2.4.2
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"LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
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"lmerTest" # depends on broken package nlopt-2.4.2
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"LMGene" # depends on broken package affyio-1.37.0
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"lmSupport" # depends on broken package nlopt-2.4.2
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"LogisticDx" # depends on broken package nlopt-2.4.2
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"logitT" # depends on broken package affyio-1.37.0
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"longpower" # depends on broken package nlopt-2.4.2
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"LowMACA" # depends on broken package Rsamtools-1.21.8
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"lumi" # depends on broken package affyio-1.37.0
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"LVSmiRNA" # depends on broken package affyio-1.37.0
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"M3D" # depends on broken package Rsamtools-1.21.8
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"MAIT" # depends on broken package nlopt-2.4.2
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"makecdfenv" # depends on broken package affyio-1.37.0
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"mAPKL" # build is broken
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"maPredictDSC" # depends on broken package nlopt-2.4.2
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"marked" # depends on broken package nlopt-2.4.2
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"maskBAD" # depends on broken package affyio-1.37.0
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"MatrixRider" # depends on broken package DirichletMultinomial-1.11.1
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"MaxPro" # depends on broken package nlopt-2.4.2
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"mbest" # depends on broken package nlopt-2.4.2
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"MBmca" # depends on broken nloptr-1.0.4
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"mBPCR" # depends on broken package affyio-1.37.0
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"mcaGUI" # depends on broken package Rsamtools-1.21.8
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"MCRestimate" # build is broken
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"mdgsa" # build is broken
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"meboot" # depends on broken package nlopt-2.4.2
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"mediation" # depends on broken package r-lme4-1.1-8
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"MEDIPS" # depends on broken package Rsamtools-1.21.8
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"MEDME" # depends on broken package nlopt-2.4.2
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"MEMSS" # depends on broken package nlopt-2.4.2
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"meshr" # depends on broken package Category-2.35.1
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"Metab" # depends on broken package mzR-2.3.1
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"metagear" # build is broken
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"metagene" # depends on broken package Rsamtools-1.21.8
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"metaMix" # build is broken
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"metaMS" # depends on broken package mzR-2.3.1
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"metaplus" # depends on broken package nlopt-2.4.2
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"metaSEM" # depends on broken package OpenMx-2.2.4
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"metaseqR" # depends on broken package affyio-1.37.0
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"Metatron" # depends on broken package nlopt-2.4.2
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"methyAnalysis" # depends on broken package affyio-1.37.0
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"MethylAid" # depends on broken package Rsamtools-1.21.8
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"methylPipe" # depends on broken package Rsamtools-1.21.8
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"MethylSeekR" # depends on broken package Rsamtools-1.21.8
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"methylumi" # depends on broken package Rsamtools-1.21.8
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"miceadds" # depends on broken package nlopt-2.4.2
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"micEconAids" # depends on broken package nlopt-2.4.2
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"micEconCES" # depends on broken package nlopt-2.4.2
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"micEconSNQP" # depends on broken package nlopt-2.4.2
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"mi" # depends on broken package nlopt-2.4.2
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"MigClim" # Build Is Broken
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"migui" # depends on broken package nlopt-2.4.2
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"MineICA" # depends on broken package AnnotationForge-1.11.3
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"minfi" # depends on broken package Rsamtools-1.21.8
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"minimist" # depends on broken package V8-0.6
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"MinimumDistance" # depends on broken package affyio-1.37.0
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"mirIntegrator" # build is broken
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"missDeaths"
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"missMDA" # depends on broken package nlopt-2.4.2
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"missMethyl" # depends on broken package Rsamtools-1.21.8
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"mitoODE" # build is broken
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"mixAK" # depends on broken package nlopt-2.4.2
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"mixlm" # depends on broken package nlopt-2.4.2
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"MixMAP" # depends on broken package nlopt-2.4.2
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"mlmRev" # depends on broken package nlopt-2.4.2
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"MLP" # depends on broken package affyio-1.37.0
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"MLSeq" # depends on broken package nlopt-2.4.2
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"mlVAR" # depends on broken package nlopt-2.4.2
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"MMDiff" # depends on broken package AnnotationForge-1.11.3
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"MmPalateMiRNA" # depends on broken package affyio-1.37.0
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"mongolite" # build is broken
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"monocle" # build is broken
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"mosaic" # depends on broken package nlopt-2.4.2
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"MotifDb" # depends on broken package Rsamtools-1.21.8
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"motifRG" # depends on broken package Rsamtools-1.21.8
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"motifStack" # depends on broken package Rsamtools-1.21.8
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"MotIV" # depends on broken package Rsamtools-1.21.8
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"MSeasy" # depends on broken package mzR-2.3.1
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"MSeasyTkGUI" # depends on broken package mzR-2.3.1
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"MSGFgui" # depends on broken package MSGFplus-1.3.0
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"MSGFplus" # Build Is Broken
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"msmsEDA" # depends on broken package affyio-1.37.0
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"msmsTests" # depends on broken package affyio-1.37.0
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"MSnbase" # depends on broken package affyio-1.37.0
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"MSnID" # depends on broken package affyio-1.37.0
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"MSstats" # depends on broken package nlopt-2.4.2
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"multiDimBio" # depends on broken package nlopt-2.4.2
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"MultiRR" # depends on broken package nlopt-2.4.2
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"muma" # depends on broken package nlopt-2.4.2
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"munsellinterpol"
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"mutossGUI" # build is broken
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"mvGST" # depends on broken package AnnotationForge-1.11.3
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"mvinfluence" # depends on broken package nlopt-2.4.2
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"mygene" # depends on broken package Rsamtools-1.21.8
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"mzR" # build is broken
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"NanoStringQCPro" # build is broken
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"nCal" # depends on broken package nlopt-2.4.2
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"ncdfFlow" # build is broken
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"NCIgraph" # depends on broken package RCytoscape-1.19.0
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"netbenchmark" # build is broken
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"nettools" # depends on broken package WGCNA-1.47
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"NGScopy"
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"NHPoisson" # depends on broken package nlopt-2.4.2
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"nloptr" # depends on broken package nlopt-2.4.2
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"nondetects" # depends on broken package affyio-1.37.0
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"nonrandom" # depends on broken package nlopt-2.4.2
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"NormqPCR" # depends on broken package affyio-1.37.0
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"NORRRM" # build is broken
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"npIntFactRep" # depends on broken package nlopt-2.4.2
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"nucleR" # depends on broken package Rsamtools-1.21.8
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"oligoClasses" # depends on broken package affyio-1.37.0
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"oligo" # depends on broken package affyio-1.37.0
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"OmicsMarkeR" # depends on broken package nlopt-2.4.2
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"oneChannelGUI" # depends on broken package affyio-1.37.0
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"OpenCL" # build is broken
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"openCyto" # depends on broken package ncdfFlow-2.15.2
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"OpenMx" # build is broken
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"OperaMate" # depends on broken package Category-2.35.1
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"optBiomarker" # depends on broken package rpanel-1.1-3
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"ora" # depends on broken package ROracle-1.1-12
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"ordBTL" # depends on broken package nlopt-2.4.2
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"OrganismDbi" # depends on broken package Rsamtools-1.21.8
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"OTUbase" # depends on broken package Rsamtools-1.21.8
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"OUwie" # depends on broken package nlopt-2.4.2
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"PADOG" # build is broken
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"pamm" # depends on broken package nlopt-2.4.2
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"PANDA" # build is broken
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"panelAR" # depends on broken package nlopt-2.4.2
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"panp" # depends on broken package affyio-1.37.0
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"papeR" # depends on broken package nlopt-2.4.2
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"parboost" # depends on broken package nlopt-2.4.2
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"parma" # depends on broken package nlopt-2.4.2
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"Pasha" # depends on broken package GenomicAlignments-1.5.12
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"pathClass" # depends on broken package affyio-1.37.0
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"pathRender" # build is broken
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"pathview" # build is broken
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"PatternClass" # build is broken
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"Pbase" # depends on broken package affyio-1.37.0
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"pbdBASE" # depends on broken package pbdSLAP-0.2-0
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"pbdDEMO" # depends on broken package pbdSLAP-0.2-0
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"pbdDMAT" # depends on broken package pbdSLAP-0.2-0
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"pbdSLAP" # build is broken
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"PBImisc" # depends on broken package nlopt-2.4.2
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"pbkrtest" # depends on broken package nlopt-2.4.2
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"PBSddesolve" # build is broken
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"PBSmapping" # build is broken
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"pcaBootPlot" # depends on broken FactoMineR-1.31.3
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"pcaL1" # build is broken
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"PCpheno" # depends on broken package Category-2.35.1
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"pdInfoBuilder" # depends on broken package affyio-1.37.0
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"pdmclass" # build is broken
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"PECA" # depends on broken package affyio-1.37.0
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"pedigreemm" # depends on broken package nlopt-2.4.2
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"pedometrics" # depends on broken package nlopt-2.4.2
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"pequod" # depends on broken package nlopt-2.4.2
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"permGPU" # build is broken
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"PGA" # depends on broken package Rsamtools-1.21.8
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"PGSEA" # depends on broken package annaffy-1.41.1
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"PharmacoGx"
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"phenoDist" # depends on broken package Category-2.35.1
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"phenoTest" # depends on broken package Category-2.35.1
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"PhenStat" # depends on broken package nlopt-2.4.2
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"phia" # depends on broken package nlopt-2.4.2
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"phylocurve" # depends on broken package nlopt-2.4.2
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"phyloTop" # depends on broken package nlopt-2.4.2
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"PICS" # depends on broken package Rsamtools-1.21.8
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"PING" # depends on broken package Rsamtools-1.21.8
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"plateCore" # depends on broken package ncdfFlow-2.15.2
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"plier" # depends on broken package affyio-1.37.0
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"plsRbeta" # depends on broken package nlopt-2.4.2
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"plsRcox" # depends on broken package nlopt-2.4.2
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"plsRglm" # depends on broken package nlopt-2.4.2
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"plw" # depends on broken package affyio-1.37.0
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"pmclust" # build is broken
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"pmm" # depends on broken package nlopt-2.4.2
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"podkat" # depends on broken package Rsamtools-1.21.8
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"polytomous" # depends on broken package nlopt-2.4.2
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"pomp" # depends on broken package nlopt-2.4.2
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"ppiPre" # depends on broken package GOSemSim-1.27.3
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"ppiStats" # depends on broken package Category-2.35.1
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"prebs" # depends on broken package affyio-1.37.0
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"predictmeans" # depends on broken package nlopt-2.4.2
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"prLogistic" # depends on broken package nlopt-2.4.2
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"proBAMr" # depends on broken package Rsamtools-1.21.8
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"ProCoNA" # depends on broken package AnnotationForge-1.11.3
|
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"pRoloc" # depends on broken package nlopt-2.4.2
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"pRolocGUI" # depends on broken package nlopt-2.4.2
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"proteoQC" # depends on broken package affyio-1.37.0
|
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"PSAboot" # depends on broken package nlopt-2.4.2
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"ptw" # depends on broken nloptr-1.0.4
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"puma" # depends on broken package affyio-1.37.0
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"pvac" # depends on broken package affyio-1.37.0
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"pvca" # depends on broken package nlopt-2.4.2
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"Pviz" # depends on broken package Rsamtools-1.21.8
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"pwOmics" # depends on broken package interactiveDisplayBase-1.7.0
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"PythonInR"
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"qcmetrics" # build is broken
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"QDNAseq" # depends on broken package Rsamtools-1.21.8
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"QFRM"
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"qgraph" # depends on broken package nlopt-2.4.2
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"qpcrNorm" # depends on broken package affyio-1.37.0
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"qpgraph" # depends on broken package Rsamtools-1.21.8
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"qrqc" # depends on broken package Rsamtools-1.21.8
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"qtbase" # build is broken
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"qtlnet" # depends on broken package nlopt-2.4.2
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"qtpaint" # depends on broken package qtbase-1.0.9
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"qtutils" # depends on broken package qtbase-1.0.9
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"QUALIFIER" # depends on broken package ncdfFlow-2.15.2
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"quantification" # depends on broken package nlopt-2.4.2
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"quantro" # depends on broken package Rsamtools-1.21.8
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"QuasR" # depends on broken package Rsamtools-1.21.8
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"R2STATS" # depends on broken package nlopt-2.4.2
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"R3CPET" # depends on broken package Rsamtools-1.21.8
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"r3Cseq" # depends on broken package Rsamtools-1.21.8
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"R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8
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"radiant" # depends on broken package nlopt-2.4.2
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"raincpc" # build is broken
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"rainfreq" # build is broken
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"RamiGO" # depends on broken package RCytoscape-1.19.0
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"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
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"RAPIDR" # depends on broken package Rsamtools-1.21.8
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"RareVariantVis" # depends on broken VariantAnnotation-1.15.19
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"Rariant" # depends on broken package Rsamtools-1.21.8
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"rasclass" # depends on broken package nlopt-2.4.2
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"RBerkeley"
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"RbioRXN" # depends on broken package ChemmineR-2.21.7
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"Rcade" # depends on broken package Rsamtools-1.21.8
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"rCGH" # depends on broken package r-affy-1.47.1
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"Rchemcpp" # depends on broken package ChemmineR-2.21.7
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"Rcmdr" # depends on broken package nlopt-2.4.2
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"RcmdrMisc" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_StatisticalURV" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2
|
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"RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2
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"RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2
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"Rcpi" # depends on broken package ChemmineR-2.21.7
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"Rcplex" # Build Is Broken
|
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"RcppAPT" # Build Is Broken
|
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"RcppOctave" # build is broken
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"RcppRedis" # build is broken
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"RCytoscape" # Build Is Broken
|
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"RDAVIDWebService" # depends on broken package Category-2.35.1
|
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"rdd" # depends on broken package nlopt-2.4.2
|
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"rddtools" # depends on broken package r-AER-1.2-4
|
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"rDEA" # build is broken
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"RDieHarder" # build is broken
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"ReactomePA" # depends on broken package GOSemSim-1.27.3
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"ReadqPCR" # depends on broken package affyio-1.37.0
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"REBayes" # depends on broken package Rmosek-1.2.5.1
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"REDseq" # depends on broken package Rsamtools-1.21.8
|
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"referenceIntervals" # depends on broken package nlopt-2.4.2
|
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"RefNet" # depends on broken package interactiveDisplayBase-1.7.0
|
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"RefPlus" # depends on broken package affyio-1.37.0
|
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"refund" # depends on broken package nlopt-2.4.2
|
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"regioneR" # depends on broken package Rsamtools-1.21.8
|
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"regionReport" # depends on broken package Rsamtools-1.21.8
|
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"repijson" # depends on broken package V8-0.6
|
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"Repitools" # depends on broken package affyio-1.37.0
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"ReportingTools" # depends on broken package Category-2.35.1
|
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"ReQON" # depends on broken package Rsamtools-1.21.8
|
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"REST" # depends on broken package nlopt-2.4.2
|
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"rfPred" # depends on broken package Rsamtools-1.21.8
|
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"rGADEM" # depends on broken package Rsamtools-1.21.8
|
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"rgbif" # depends on broken package V8-0.6
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"Rgnuplot"
|
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"rgp" # build is broken
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"rgpui" # depends on broken package rgp-0.4-1
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"rgsepd" # depends on broken package goseq-1.21.1
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"rhdf5" # build is broken
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"rHVDM" # depends on broken package affyio-1.37.0
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"Ringo" # depends on broken package affyio-1.37.0
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"RIPSeeker" # depends on broken package Rsamtools-1.21.8
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"Risa" # depends on broken package affyio-1.37.0
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"rjade" # depends on broken package V8-0.6
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"rJPSGCS" # build is broken
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"rLindo" # build is broken
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"RMassBank" # depends on broken package mzR-2.3.1
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"rMAT" # build is broken
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"rmgarch" # depends on broken package nlopt-2.4.2
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"rminer" # depends on broken package nlopt-2.4.2
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"RmiR" # Build Is Broken
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"Rmosek" # build is broken
|
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"RNAinteract" # depends on broken package Category-2.35.1
|
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"RNAither" # depends on broken package nlopt-2.4.2
|
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"RNAprobR" # depends on broken package Rsamtools-1.21.8
|
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"rnaSeqMap" # depends on broken package Rsamtools-1.21.8
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"RnaSeqSampleSize" # Build Is Broken
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"RnavGraph" # build is broken
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"RnBeads" # depends on broken package Rsamtools-1.21.8
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"Rnits" # depends on broken package affyio-1.37.0
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"roar" # depends on broken package Rsamtools-1.21.8
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"RobLoxBioC" # depends on broken package affyio-1.37.0
|
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"robustlmm" # depends on broken package nlopt-2.4.2
|
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"rockchalk" # depends on broken package nlopt-2.4.2
|
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"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20
|
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"Rolexa" # depends on broken package Rsamtools-1.21.8
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"rols" # build is broken
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"ROracle" # Build Is Broken
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"RPA" # depends on broken package affyio-1.37.0
|
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"rpanel" # build is broken
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"rpubchem" # depends on broken package nlopt-2.4.2
|
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"Rqc" # depends on broken package Rsamtools-1.21.8
|
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"RQuantLib" # build is broken
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"rr" # depends on broken package nlopt-2.4.2
|
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"Rsamtools" # Build Is Broken
|
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"RSAP" # build is broken
|
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"rsbml" # build is broken
|
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"rscala" # build is broken
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"RSDA" # depends on broken package nlopt-2.4.2
|
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"rSFFreader" # depends on broken package Rsamtools-1.21.8
|
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"Rsubread" # Build Is Broken
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"RSVSim" # depends on broken package Rsamtools-1.21.8
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"Rsymphony" # build is broken
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"rTANDEM" # build is broken
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"RTN" # depends on broken package nlopt-2.4.2
|
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"rtracklayer" # depends on broken package Rsamtools-1.21.8
|
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"rTRMui" # depends on broken package Rsamtools-1.21.8
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"rugarch" # depends on broken package nlopt-2.4.2
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"RUVcorr" # build is broken
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"RUVnormalize" # Build Is Broken
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"RUVSeq" # depends on broken package Rsamtools-1.21.8
|
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"RVAideMemoire" # depends on broken package nlopt-2.4.2
|
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"RVFam" # depends on broken package nlopt-2.4.2
|
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"RVideoPoker" # depends on broken package rpanel-1.1-3
|
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"ryouready" # depends on broken package nlopt-2.4.2
|
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"sampleSelection" # depends on broken package nlopt-2.4.2
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"sapFinder" # depends on broken package rTANDEM-1.9.0
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"SCAN_UPC" # depends on broken package affyio-1.37.0
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"ScISI" # depends on broken package apComplex-2.35.0
|
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"sdcMicro" # depends on broken package nlopt-2.4.2
|
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"sdcMicroGUI" # depends on broken package nlopt-2.4.2
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"SDD" # depends on broken package rpanel-1.1-3
|
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"seeg" # depends on broken package nlopt-2.4.2
|
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"segmentSeq" # depends on broken package Rsamtools-1.21.8
|
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"sem" # depends on broken package nlopt-2.4.2
|
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"semdiag" # depends on broken package nlopt-2.4.2
|
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"SemDist" # Build Is Broken
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"semGOF" # depends on broken package nlopt-2.4.2
|
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"semPlot" # depends on broken package nlopt-2.4.2
|
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"SensoMineR" # depends on broken package nlopt-2.4.2
|
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"SEPA" # depends on broken package topGO-2.21.0
|
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"seq2pathway" # depends on broken package WGCNA-1.47
|
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"SeqArray" # depends on broken package Rsamtools-1.21.8
|
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"seqbias" # depends on broken package Rsamtools-1.21.8
|
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"seqCNA" # build is broken
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"SeqGrapheR" # Build Is Broken
|
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"seqplots" # depends on broken package Rsamtools-1.21.8
|
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"seqTools" # build is broken
|
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"SeqVarTools" # depends on broken package Rsamtools-1.21.8
|
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"SGSeq" # depends on broken package Rsamtools-1.21.8
|
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"shinyMethyl" # depends on broken package Rsamtools-1.21.8
|
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"shinyTANDEM" # depends on broken package rTANDEM-1.9.0
|
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"ShortRead" # depends on broken package Rsamtools-1.21.8
|
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"SIMAT" # depends on broken package mzR-2.3.1
|
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"SimBindProfiles" # depends on broken package affyio-1.37.0
|
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"similaRpeak" # depends on broken package Rsamtools-1.21.8
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"simpleaffy" # depends on broken package affyio-1.37.0
|
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"SimRAD" # depends on broken package Rsamtools-1.21.8
|
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"sirt" # depends on broken package nlopt-2.4.2
|
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"sjPlot" # depends on broken package nlopt-2.4.2
|
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"skewr" # depends on broken package affyio-1.37.0
|
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"SLGI" # depends on broken package apComplex-2.35.0
|
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"SNAGEE" # build is broken
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"snapCGH" # depends on broken package tilingArray-1.47.0
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"snm" # depends on broken package nlopt-2.4.2
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"SNPchip" # depends on broken package affyio-1.37.0
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"snpEnrichment" # depends on broken package snpStats-1.19.0
|
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"snpStats" # build is broken
|
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"snpStatsWriter" # depends on broken package snpStats-1.19.0
|
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"SNPtools" # depends on broken package Rsamtools-1.21.8
|
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"SOD" # depends on broken package cudatoolkit-5.5.22
|
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"soGGi" # depends on broken package Rsamtools-1.21.8
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"soilphysics" # depends on broken package rpanel-1.1-3
|
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"SomaticSignatures" # depends on broken package Rsamtools-1.21.8
|
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"SoyNAM" # depends on broken package r-lme4-1.1-8
|
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"spacom" # depends on broken package nlopt-2.4.2
|
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"specificity" # depends on broken package nlopt-2.4.2
|
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"spliceR" # depends on broken package Rsamtools-1.21.8
|
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"SplicingGraphs" # depends on broken package Rsamtools-1.21.8
|
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"spocc" # depends on broken package V8-0.6
|
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"spoccutils" # depends on broken spocc-0.3.0
|
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"spsann" # depends on broken package r-pedometrics-0.6-2
|
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"sscore" # depends on broken package affyio-1.37.0
|
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"ssmrob" # depends on broken package nlopt-2.4.2
|
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"ssviz" # depends on broken package Rsamtools-1.21.8
|
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"stagePop" # depends on broken package PBSddesolve-1.11.29
|
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"staRank" # depends on broken package Category-2.35.1
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"Starr" # depends on broken package affyio-1.37.0
|
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"STATegRa" # depends on broken package affyio-1.37.0
|
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"stcm" # depends on broken package nlopt-2.4.2
|
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"stepp" # depends on broken package nlopt-2.4.2
|
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"stringgaussnet" # build is broken
|
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"Surrogate" # depends on broken package nlopt-2.4.2
|
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"SVM2CRM" # depends on broken package Rsamtools-1.21.8
|
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"sybilSBML" # build is broken
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"synapter" # depends on broken package affyio-1.37.0
|
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"systemfit" # depends on broken package nlopt-2.4.2
|
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"systemPipeR" # depends on broken package AnnotationForge-1.11.3
|
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"TargetSearch" # depends on broken package mzR-2.3.1
|
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"TcGSA" # depends on broken package nlopt-2.4.2
|
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"TDMR" # depends on broken package nlopt-2.4.2
|
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"TEQC" # depends on broken package Rsamtools-1.21.8
|
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"TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
|
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"tigerstats" # depends on broken package nlopt-2.4.2
|
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"tilingArray" # depends on broken package affyio-1.37.0
|
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"TIN" # depends on broken package WGCNA-1.47
|
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"TitanCNA" # depends on broken package Rsamtools-1.21.8
|
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"ToPASeq" # depends on broken package Rsamtools-1.21.8
|
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"topGO" # build is broken
|
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"topologyGSA" # depends on broken package Rsamtools-1.21.8
|
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"tracktables" # depends on broken package Rsamtools-1.21.8
|
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"trackViewer" # depends on broken package Rsamtools-1.21.8
|
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"translateSPSS2R" # depends on broken car-2.0-25
|
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"tRanslatome" # depends on broken package GOSemSim-1.27.3
|
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"TransView" # depends on broken package Rsamtools-1.21.8
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"traseR"
|
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"TriMatch" # depends on broken package nlopt-2.4.2
|
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"TROM" # depends on broken package topGO-2.21.0
|
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"TurboNorm" # depends on broken package affyio-1.37.0
|
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"unifiedWMWqPCR" # depends on broken package affyio-1.37.0
|
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"userfriendlyscience" # depends on broken package nlopt-2.4.2
|
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"V8" # build is broken
|
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"VanillaICE" # depends on broken package affyio-1.37.0
|
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"variancePartition" # depends on broken package lme4-1.1-8
|
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"VariantAnnotation" # depends on broken package Rsamtools-1.21.8
|
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"VariantFiltering" # depends on broken package Rsamtools-1.21.8
|
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"VariantTools" # depends on broken package Rsamtools-1.21.8
|
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"VIM" # depends on broken package nlopt-2.4.2
|
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"VIMGUI" # depends on broken package nlopt-2.4.2
|
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"vmsbase" # depends on broken package PBSmapping-2.69.76
|
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"vows" # depends on broken package nlopt-2.4.2
|
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"vsn" # depends on broken package affyio-1.37.0
|
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"vtpnet" # depends on broken package interactiveDisplayBase-1.7.0
|
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"wateRmelon" # depends on broken package affyio-1.37.0
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"wavClusteR" # depends on broken package Rsamtools-1.21.8
|
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"waveTiling" # depends on broken package affyio-1.37.0
|
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"webbioc" # depends on broken package affyio-1.37.0
|
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"wfe" # depends on broken package nlopt-2.4.2
|
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"WGCNA" # build is broken
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"wgsea" # depends on broken package snpStats-1.19.0
|
|
"WideLM" # depends on broken package cudatoolkit-5.5.22
|
|
"xcms" # depends on broken package mzR-2.3.1
|
|
"xergm" # depends on broken package nlopt-2.4.2
|
|
"xps" # build is broken
|
|
"yaqcaffy" # depends on broken package affyio-1.37.0
|
|
"ZeligMultilevel" # depends on broken package nlopt-2.4.2
|
|
"zetadiv" # depends on broken package nlopt-2.4.2
|
|
];
|
|
|
|
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";
|
|
});
|
|
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "export CURL_INCLUDES=${pkgs.curl.dev}/include";
|
|
});
|
|
|
|
iFes = old.iFes.overrideDerivation (attrs: {
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
rpf = old.rpf.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesXsrc.patch ];
|
|
});
|
|
|
|
rJava = old.rJava.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
JavaGD = old.JavaGD.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
Mposterior = old.Mposterior.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr}/include"
|
|
];
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
|
|
];
|
|
});
|
|
|
|
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RAppArmor.patch ];
|
|
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
|
|
});
|
|
|
|
RMySQL = old.RMySQL.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RMySQL.patch ];
|
|
MYSQL_DIR="${pkgs.mysql.lib}";
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft}/lib -lXft";
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
gputools = old.gputools.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gputools.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/CARramps.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
gmatrix = old.gmatrix.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gmatrix.patch ];
|
|
CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
|
|
R_INC_PATH = "${pkgs.R}/lib/R/include";
|
|
CUDA_INC_PATH = "${pkgs.cudatoolkit}/include";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/rpud.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
WideLM = old.WideLM.overrideDerivation (attrs: {
|
|
patches = [ ./patches/WideLM.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
OPENSSL_INCLUDES = "${pkgs.openssl}/include";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
nloptr = old.nloptr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
|
|
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
|
|
];
|
|
});
|
|
|
|
V8 = old.V8.overrideDerivation (attrs: {
|
|
preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
|
|
});
|
|
|
|
};
|
|
in
|
|
self
|