Merge pull request #25390 from Hodapp87/rstudio_fix

rstudio: Fix recompilation issue with custom package set
This commit is contained in:
Peter Simons 2017-05-02 16:43:41 +02:00 committed by GitHub
commit 287e670462
5 changed files with 52 additions and 47 deletions

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@ -1,13 +1,5 @@
{ stdenv, fetchurl, makeDesktopItem, cmake, boost163, zlib, openssl,
R, qt5, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc,
# If you have set up an R wrapper with other packages by following
# something like https://nixos.org/nixpkgs/manual/#r-packages, RStudio
# by default not be able to access any of those R packages. In order
# to do this, override the argument "R" here with your respective R
# wrapper, and set "useRPackages" to true. This will add the
# environment variable R_PROFILE_USER to the RStudio wrapper, pointing
# to an R script which will allow R to use these packages.
useRPackages ? false
R, qt5, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc
}:
let
@ -111,14 +103,8 @@ stdenv.mkDerivation rec {
mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
};
postInstall = let rProfile =
# RStudio seems to bypass the environment variables that the R
# wrapper already applies, and so this sets R_PROFILE_USER to
# again make those R packages accessible:
if useRPackages
then "--set R_PROFILE_USER ${R}/${R.passthru.fixLibsR}" else "";
in ''
wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin ${rProfile}
postInstall = ''
wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin
mkdir $out/share
cp -r ${desktopItem}/share/applications $out/share
mkdir $out/share/icons

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@ -55,28 +55,23 @@ available.
## RStudio
RStudio by default will not use the libraries installed like above.
You must override its R version with your custom R environment, and
set `useRPackages` to `true`, like below:
RStudio uses a standard set of packages and ignores any custom R
environments or installed packages you may have. To create a custom
environment, see `rstudioWrapper`, which functions similarly to
`rWrapper`:
```nix
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
rstudioEnv = super.rstudioWrapper.override {
packages = with self.rPackages; [
devtools
dplyr
ggplot2
reshape2
yaml
optparse
];
};
rstudioEnv = super.rstudio.override {
R = rEnv;
useRPackages = true;
};
};
}
```

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@ -0,0 +1,33 @@
{ stdenv, R, rstudio, makeWrapper, recommendedPackages, packages }:
stdenv.mkDerivation rec {
name = rstudio.name + "-wrapper";
buildInputs = [makeWrapper R rstudio] ++ recommendedPackages ++ packages;
unpackPhase = ":";
# rWrapper points R to a specific set of packages by using a wrapper
# (as in https://nixos.org/nixpkgs/manual/#r-packages) which sets
# R_LIBS_SITE. Ordinarily, it would be possible to make RStudio use
# this same set of packages by simply overriding its version of R
# with the wrapped one, however, RStudio internally overrides
# R_LIBS_SITE. The below works around this by turning R_LIBS_SITE
# into an R file (fixLibsR) which achieves the same effect, then
# uses R_PROFILE_USER to load this code at startup in RStudio.
fixLibsR = "fix_libs.R";
installPhase = ''
mkdir $out
echo "# Autogenerated by wrapper-rstudio.nix from R_LIBS_SITE" > $out/${fixLibsR}
echo -n ".libPaths(c(.libPaths(), \"" >> $out/${fixLibsR}
echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/${fixLibsR}
echo -n "\"))" >> $out/${fixLibsR}
echo >> $out/${fixLibsR}
makeWrapper ${rstudio}/bin/rstudio $out/bin/rstudio --set R_PROFILE_USER $out/${fixLibsR}
'';
meta = {
platforms = stdenv.lib.platforms.unix;
};
}

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@ -1,19 +1,12 @@
{ stdenv, R, makeWrapper, recommendedPackages, packages }:
stdenv.mkDerivation rec {
stdenv.mkDerivation {
name = R.name + "-wrapper";
buildInputs = [makeWrapper R] ++ recommendedPackages ++ packages;
unpackPhase = ":";
# This filename is used in 'installPhase', but needs to be
# referenced elsewhere. This will be relative to this package's
# path.
passthru = {
fixLibsR = "fix_libs.R";
};
installPhase = ''
mkdir -p $out/bin
cd ${R}/bin
@ -21,17 +14,6 @@ stdenv.mkDerivation rec {
makeWrapper ${R}/bin/$exe $out/bin/$exe \
--prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
done
# RStudio (and perhaps other packages) overrides the R_LIBS_SITE
# which the wrapper above applies, and as a result packages
# installed in the wrapper (as in the method described in
# https://nixos.org/nixpkgs/manual/#r-packages) aren't visible.
# The below turns R_LIBS_SITE into some R startup code which can
# correct this.
echo "# Autogenerated by wrapper.nix from R_LIBS_SITE" > $out/${passthru.fixLibsR}
echo -n ".libPaths(c(.libPaths(), \"" >> $out/${passthru.fixLibsR}
echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/${passthru.fixLibsR}
echo -n "\"))" >> $out/${passthru.fixLibsR}
echo >> $out/${passthru.fixLibsR}
'';
meta = {

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@ -10610,6 +10610,15 @@ with pkgs;
packages = [];
};
rstudioWrapper = callPackage ../development/r-modules/wrapper-rstudio.nix {
recommendedPackages = with rPackages; [
boot class cluster codetools foreign KernSmooth lattice MASS
Matrix mgcv nlme nnet rpart spatial survival
];
# Override this attribute to register additional libraries.
packages = [];
};
rPackages = callPackage ../development/r-modules {
overrides = (config.rPackageOverrides or (p: {})) pkgs;
};