Commit message (Collapse) | Author | Age | ||
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* | r-modules: Fix a number of popular R packages | Hamish Mackenzie | 2017-10-21 | |
| | | | | The R V8 package still depends on V8 3.14 so this is also included. | |||
* | R: update package set | Peter Simons | 2017-09-29 | |
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* | R: update package set | Peter Simons | 2017-08-31 | |
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* | r-pbdZMQ: fix Darwin install | Mitsuhiro Nakamura | 2017-07-14 | |
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* | r-modules: update package set | Peter Simons | 2017-07-02 | |
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* | rstudio: Fix recompilation issue with custom package set | Chris Hodapp | 2017-05-01 | |
| | | | | | | | | | | | | This attempts to fix the issue described at https://github.com/NixOS/nixpkgs/pull/22219#issuecomment-291801133. Any change to the custom packages passed to RStudio causes this to completely rebuild RStudio, which is completely unnecessary and also a bit of a hindrance as it's a fairly slow build. This rolls back most of that old PR, and instead implements something more like rWrapper. Existing configurations with the old useRPackages will break. | |||
* | R: update list of broken packages (and some cosmetic) | Peter Simons | 2017-04-24 | |
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* | R: update CRAN and BIOC package sets | Peter Simons | 2017-04-24 | |
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* | imager (r-modules): add pkgs.x11 to fix build, unmark imager/ForestTools as ↵ | Chris Hodapp | 2017-04-20 | |
| | | | | broken | |||
* | r-modules: update CRAN package set | Peter Simons | 2017-03-07 | |
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* | r-modules: drop broken irkernel package set | Peter Simons | 2017-03-07 | |
| | | | | | We can no longer update that package set since, apparently, it has moved to a different packaging scheme. | |||
* | r-modules: remove weird version assertion | Peter Simons | 2017-03-07 | |
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* | rPackages: remove old cuda-related patches | Nikolay Amiantov | 2017-02-28 | |
| | | | | gputools doesn't build but because of unrelated linking issues. | |||
* | rPackages: try to unbreak reverse dependencies of cudatoolkit | Nikolay Amiantov | 2017-02-28 | |
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* | Merge pull request #23104 from dtzWill/fix/generate-shell | Domen Kožar | 2017-02-27 | |
|\ | | | | | R/generate-shell: Use R from current tree, fix missing wget dep. | |||
| * | R/generate-shell: Use R from current tree, fix missing wget dep. | Will Dietz | 2017-02-23 | |
| | | | | | | | | | | | | | | Without this change, the 'R' version used might be the wrong one which changes the package lists used. Fixes #19530. | |||
* | | Merge pull request #23069 from lukego/R-packages-readme | Domen Kožar | 2017-02-27 | |
|\ \ | | | | | | | r-modules/README.md: mention generate-shell.nix | |||
| * | | r-modules/README.md: mention generate-shell.nix | Luke Gorrie | 2017-02-22 | |
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* | | Merge pull request #22817 from jbedo/r | Domen Kožar | 2017-02-27 | |
|\ \ | | | | | | | R: 3.2.4 -> 3.3.2 | |||
| * | | R: unmark edgeR and limma as broken | Justin Bedo | 2017-02-24 | |
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| * | | R: 3.2.4 -> 3.3.2 | Justin Bedo | 2017-02-24 | |
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* / | R: fix bio3d build | Domen Kožar | 2017-02-27 | |
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* | ~/.nixpkgs -> ~/.config/nixpkgs | Eelco Dolstra | 2017-02-01 | |
| | | | | | | The former is still respected as a fallback for config.nix for backwards compatibility (but not for overlays because they're a new feature). | |||
* | RStudio: Optionally allow packages from custom R environment | Chris Hodapp | 2017-01-27 | |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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; }; }; } | |||
* | r-modules: fix snpStats package | mimadrid | 2017-01-06 | |
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* | r-modules: fix VariantAnnotation package | mimadrid | 2017-01-06 | |
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* | r-modules: fix rtracklayer package | mimadrid | 2017-01-06 | |
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* | r-modules: fix Rsubread package | mimadrid | 2017-01-06 | |
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* | r-modules: fix gmapR package | mimadrid | 2017-01-06 | |
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* | r-modules: fix oligo package | mimadrid | 2017-01-06 | |
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* | r-modules: fix affyio package | mimadrid | 2017-01-06 | |
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* | r-modules: fix BitSeq package | mimadrid | 2017-01-06 | |
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* | r-modules: fix bamsignals package | mimadrid | 2017-01-06 | |
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* | r-modules: fix affyPLM package | mimadrid | 2017-01-06 | |
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* | r-modules: fix xml2 package | mimadrid | 2017-01-06 | |
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* | r-modules: fix XBRL package | mimadrid | 2017-01-06 | |
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* | r-modules: fix WhopGenome package | mimadrid | 2017-01-06 | |
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* | r-modules: fix tkrplot package | mimadrid | 2017-01-06 | |
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* | r-modules: fix tiff package | mimadrid | 2017-01-06 | |
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* | r-modules: fix TAQMNGR package | mimadrid | 2017-01-06 | |
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* | r-modules: fix spate package | mimadrid | 2017-01-06 | |
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* | r-modules: fix showtext package | mimadrid | 2017-01-06 | |
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* | r-modules: fix seqminer package | mimadrid | 2017-01-06 | |
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* | r-modules: fix seqinr package | mimadrid | 2017-01-06 | |
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* | r-modules: fix RVowpalWabbit package | mimadrid | 2017-01-06 | |
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* | r-modules: fix rtiff package | mimadrid | 2017-01-06 | |
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* | r-modules: fix rtfbs package | mimadrid | 2017-01-06 | |
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* | r-modules: fix Rssa package | mimadrid | 2017-01-06 | |
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* | r-modules: fix RSclient package | mimadrid | 2017-01-06 | |
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* | r-modules: fix rphast package | mimadrid | 2017-01-06 | |
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