Eelco Dolstra
9d6a55aefd
~/.nixpkgs -> ~/.config/nixpkgs
...
The former is still respected as a fallback for config.nix for
backwards compatibility (but not for overlays because they're a new
feature).
2017-02-01 16:07:55 +01:00
Chris Hodapp
7638578342
RStudio: Optionally allow packages from custom R environment
...
https://nixos.org/nixpkgs/manual/#r-packages contains a method for
setting up an R environment with a specific set of libraries, and it
creates an R wrapper which points R to those libraries.
The package RStudio relies on the standard R package, which then
cannot access any of the libraries specified in a custom R
environment. While one may easily use pkgs.rstudio.override to change
rstudio's R dependency to the custom R environment, this accomplishes
nothing because while RStudio runs the correct R wrapper it clears out
the environment variable R_LIBS_SITE - and so it is still unable to
use any of those packages.
In order to work around this problem, these changes allow the user to
optionally modify rstudio's wrapper to set environment variable
R_PROFILE_USER to an R script which sets R's .libPaths(..) to point to
the same libraries; that script is generated from R_LIBS_SITE in the R
wrapper.
By default, this change has no effect. If R is overridden to
something else, and if useRPackages is changed from its default of
false, then the change described above is made; for instance:
{
packageOverrides = pkgs: let self = pkgs.pkgs; in
rec {
rEnv = pkgs.rWrapper.override {
packages = with self.rPackages; [
dplyr ggplot2 e1071 rpart reshape
];
};
rstudioEnv = pkgs.rstudio.override { R = rEnv; useRPackages = true; };
};
}
2017-01-27 18:54:50 -05:00
mimadrid
8954412fcc
r-modules: fix snpStats package
2017-01-06 21:07:25 +01:00
mimadrid
b5a0925663
r-modules: fix VariantAnnotation package
2017-01-06 21:07:25 +01:00
mimadrid
6540b6507d
r-modules: fix rtracklayer package
2017-01-06 21:07:25 +01:00
mimadrid
baf65d5000
r-modules: fix Rsubread package
2017-01-06 21:07:25 +01:00
mimadrid
9ebab25442
r-modules: fix gmapR package
2017-01-06 21:07:25 +01:00
mimadrid
286e86f3a5
r-modules: fix oligo package
2017-01-06 21:07:25 +01:00
mimadrid
afd1a4c933
r-modules: fix affyio package
2017-01-06 21:07:25 +01:00
mimadrid
4c0c3c7493
r-modules: fix BitSeq package
2017-01-06 21:07:24 +01:00
mimadrid
272b447ea7
r-modules: fix bamsignals package
2017-01-06 21:07:24 +01:00
mimadrid
c5e4754ca7
r-modules: fix affyPLM package
2017-01-06 21:07:24 +01:00
mimadrid
1d7fd8f3c4
r-modules: fix xml2 package
2017-01-06 21:07:24 +01:00
mimadrid
5b813c2ab0
r-modules: fix XBRL package
2017-01-06 21:07:24 +01:00
mimadrid
512be9e14a
r-modules: fix WhopGenome package
2017-01-06 21:07:24 +01:00
mimadrid
f9d84f8b65
r-modules: fix tkrplot package
2017-01-06 21:07:24 +01:00
mimadrid
0b3e62bb12
r-modules: fix tiff package
2017-01-06 21:07:23 +01:00
mimadrid
9420fa23c6
r-modules: fix TAQMNGR package
2017-01-06 21:07:23 +01:00
mimadrid
2303e63116
r-modules: fix spate package
2017-01-06 21:07:23 +01:00
mimadrid
fcbed4b654
r-modules: fix showtext package
2017-01-06 21:07:23 +01:00
mimadrid
8a6b58d51d
r-modules: fix seqminer package
2017-01-06 21:07:23 +01:00
mimadrid
e1a5eeef06
r-modules: fix seqinr package
2017-01-06 21:07:22 +01:00
mimadrid
1ef67b9e78
r-modules: fix RVowpalWabbit package
2017-01-06 21:05:54 +01:00
mimadrid
ae2723a144
r-modules: fix rtiff package
2017-01-06 21:05:54 +01:00
mimadrid
d7ac90dd0c
r-modules: fix rtfbs package
2017-01-06 21:05:53 +01:00
mimadrid
fd175e4084
r-modules: fix Rssa package
2017-01-06 21:05:52 +01:00
mimadrid
bd2aaada6e
r-modules: fix RSclient package
2017-01-06 21:05:52 +01:00
mimadrid
53235dbe14
r-modules: fix rphast package
2017-01-06 21:05:52 +01:00
mimadrid
780fb79e32
r-modules: fix Rmpfr package
2017-01-06 21:05:51 +01:00
mimadrid
a58db75ccb
r-modules: fix rmatio package
2017-01-06 21:05:51 +01:00
mimadrid
674a2077dd
r-modules: fix rJava package
2017-01-06 21:05:51 +01:00
mimadrid
13a582688f
r-modules: fix RJaCGH package
2017-01-06 21:05:51 +01:00
mimadrid
9922867fa8
r-modules: fix Rhtslib package
2017-01-06 21:05:50 +01:00
mimadrid
bb60f939ae
r-modules: fix Rhpc package
2017-01-06 21:05:50 +01:00
mimadrid
e1bc505da9
r-modules: fix rggobi package
2017-01-06 21:05:50 +01:00
mimadrid
9f2b5e0425
r-modules: fix RGtk2 package
2017-01-06 21:05:50 +01:00
mimadrid
3342f8bd59
r-modules: fix RcppOctave package
2017-01-06 21:05:50 +01:00
mimadrid
ba86a39645
r-modules: fix RcppCNPy package
2017-01-06 21:05:49 +01:00
mimadrid
dd159d06b6
r-modules: fix rcdd package
2017-01-06 21:05:49 +01:00
mimadrid
8b229baf33
r-modules: fix rbamtools package
2017-01-06 21:05:49 +01:00
mimadrid
558f67e85f
r-modules: fix R2SWF package
2017-01-06 21:05:48 +01:00
mimadrid
277efe9896
r-modules: fix sysfonts package
2017-01-06 21:05:48 +01:00
mimadrid
062c9037d1
r-modules: fix PopGenome package
2017-01-06 21:05:48 +01:00
mimadrid
c5ef08cc65
r-modules: fix PKI package
2017-01-06 21:05:48 +01:00
mimadrid
1e9071948f
r-modules: fix mwaved package
2017-01-06 21:05:48 +01:00
mimadrid
4e7de52c26
r-module: fix kza package
2017-01-06 21:05:47 +01:00
mimadrid
debb12ce1a
r-module: fix jpeg package
2017-01-06 21:05:47 +01:00
mimadrid
e3a2c97c7b
r-modules: fix gmp package
2017-01-06 21:05:47 +01:00
mimadrid
72eb6a8644
r-modules: fix fftwtools package
2017-01-06 21:05:47 +01:00
mimadrid
427c4d954a
r-modules: fix fftw package
2017-01-06 21:05:47 +01:00
