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* bioconductor: 3.4 -> 3.6Justin Bedo2018-02-21
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* rPackages.pbdZMQ: fix package loading on DarwinMitsuhiro Nakamura2018-02-10
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* rPackages.data_table: OpenMP support on DarwinMitsuhiro Nakamura2018-01-19
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* Merge pull request #33010 from LnL7/cacert-hookDaiderd Jordan2018-01-07
|\ | | | | cacert: add hook that sets SSL_CERT_FILE
| * cacert: cleanup exporting SSL_CERT_FILEDaiderd Jordan2017-12-27
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* | mariadb: lib -> connector-cRobin Gloster2017-12-29
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* R: update package setPeter Simons2017-12-01
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* r-openssl: fix buildPeter Simons2017-11-30
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* Merge pull request #31775 from obsidiansystems/stdenv-both-propagated-filesJohn Ericson2017-11-22
|\ | | | | stdenv setup: Always use both propagated files
| * stdenv setup: Always use both propagated filesJohn Ericson2017-11-21
| | | | | | | | | | | | | | | | | | | | | | This continues #23374, which always kept around both attributes, by always including both propagated files: `propgated-native-build-inputs` and `propagated-build-inputs`. `nativePkgs` and `crossPkgs` are still defined as before, however, so this change should only barely observable. This is an incremental step to fully keeping the dependencies separate in all cases.
* | r-modules: fix evalMatthew Justin Bauer2017-11-12
|/ | | Fixes #31508
* nixpkgs manual: add rstudio shell.nix exampleMaciej Kazulak2017-11-04
| | | | | Provide an example of a self-contained shell.nix for rstudio with additional packages.
* r-modules: Fix a number of popular R packagesHamish Mackenzie2017-10-21
| | | | The R V8 package still depends on V8 3.14 so this is also included.
* R: update package setPeter Simons2017-09-29
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* R: update package setPeter Simons2017-08-31
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* r-pbdZMQ: fix Darwin installMitsuhiro Nakamura2017-07-14
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* r-modules: update package setPeter Simons2017-07-02
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* rstudio: Fix recompilation issue with custom package setChris Hodapp2017-05-01
| | | | | | | | | | | | 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 Simons2017-04-24
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* R: update CRAN and BIOC package setsPeter Simons2017-04-24
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* imager (r-modules): add pkgs.x11 to fix build, unmark imager/ForestTools as ↵Chris Hodapp2017-04-20
| | | | broken
* r-modules: update CRAN package setPeter Simons2017-03-07
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* r-modules: drop broken irkernel package setPeter Simons2017-03-07
| | | | | We can no longer update that package set since, apparently, it has moved to a different packaging scheme.
* r-modules: remove weird version assertionPeter Simons2017-03-07
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* rPackages: remove old cuda-related patchesNikolay Amiantov2017-02-28
| | | | gputools doesn't build but because of unrelated linking issues.
* rPackages: try to unbreak reverse dependencies of cudatoolkitNikolay Amiantov2017-02-28
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* Merge pull request #23104 from dtzWill/fix/generate-shellDomen Kožar2017-02-27
|\ | | | | 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 Dietz2017-02-23
| | | | | | | | | | | | | | 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-readmeDomen Kožar2017-02-27
|\ \ | | | | | | r-modules/README.md: mention generate-shell.nix
| * | r-modules/README.md: mention generate-shell.nixLuke Gorrie2017-02-22
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* | Merge pull request #22817 from jbedo/rDomen Kožar2017-02-27
|\ \ | | | | | | R: 3.2.4 -> 3.3.2
| * | R: unmark edgeR and limma as brokenJustin Bedo2017-02-24
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| * | R: 3.2.4 -> 3.3.2Justin Bedo2017-02-24
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* / R: fix bio3d buildDomen Kožar2017-02-27
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* ~/.nixpkgs -> ~/.config/nixpkgsEelco Dolstra2017-02-01
| | | | | | 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 environmentChris Hodapp2017-01-27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 packagemimadrid2017-01-06
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* r-modules: fix VariantAnnotation packagemimadrid2017-01-06
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* r-modules: fix rtracklayer packagemimadrid2017-01-06
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* r-modules: fix Rsubread packagemimadrid2017-01-06
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* r-modules: fix gmapR packagemimadrid2017-01-06
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* r-modules: fix oligo packagemimadrid2017-01-06
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* r-modules: fix affyio packagemimadrid2017-01-06
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* r-modules: fix BitSeq packagemimadrid2017-01-06
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* r-modules: fix bamsignals packagemimadrid2017-01-06
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* r-modules: fix affyPLM packagemimadrid2017-01-06
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* r-modules: fix xml2 packagemimadrid2017-01-06
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* r-modules: fix XBRL packagemimadrid2017-01-06
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* r-modules: fix WhopGenome packagemimadrid2017-01-06
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* r-modules: fix tkrplot packagemimadrid2017-01-06
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