commit 92d53362d4da7e19b6a7a6b1b936a0a34a17c0c9 · pyrox.dev/nixpkgs

+20 -20

doc/default.nix

···

       45
       45
        
           cp -s '${sources-langs}'/* ./languages-frameworks

     

       46
       46
        
         ''

     

       47
       47
        
         + toDocbook {

     

       48
       48
       -
             inputFile = ./introduction.md;

     

       49
       49
       -
             outputFile = "introduction.xml";

     

       48
       48
       +
             inputFile = ./introduction.chapter.md;

     

       49
       49
       +
             outputFile = "introduction.chapter.xml";

     

       50
       50
        
             useChapters = true;

     

       51
       51
        
           }

     

       52
       52
        
         + toDocbook {

     

       53
       53
       -
             inputFile = ./shell.md;

     

       54
       54
       -
             outputFile = "shell.xml";

     

       53
       53
       +
             inputFile = ./shell.section.md;

     

       54
       54
       +
             outputFile = "shell.section.xml";

     

       55
       55
        
           }

     

       56
       56
        
         + toDocbook {

     

       57
       57
       -
             inputFile = ./languages-frameworks/python.md;

     

       58
       58
       -
             outputFile = "./languages-frameworks/python.xml";

     

       57
       57
       +
             inputFile = ./languages-frameworks/python.section.md;

     

       58
       58
       +
             outputFile = "./languages-frameworks/python.section.xml";

     

       59
       59
        
           }

     

       60
       60
        
         + toDocbook {

     

       61
       61
       -
             inputFile = ./languages-frameworks/haskell.md;

     

       62
       62
       -
             outputFile = "./languages-frameworks/haskell.xml";

     

       61
       61
       +
             inputFile = ./languages-frameworks/haskell.section.md;

     

       62
       62
       +
             outputFile = "./languages-frameworks/haskell.section.xml";

     

       63
       63
        
           }

     

       64
       64
        
         + toDocbook {

     

       65
       65
       -
             inputFile = ../pkgs/development/idris-modules/README.md;

     

       66
       66
       -
             outputFile = "languages-frameworks/idris.xml";

     

       65
       65
       +
             inputFile = ./languages-frameworks/idris.section.md;

     

       66
       66
       +
             outputFile = "languages-frameworks/idris.section.xml";

     

       67
       67
        
           }

     

       68
       68
        
         + toDocbook {

     

       69
       69
       -
             inputFile = ../pkgs/development/node-packages/README.md;

     

       70
       70
       -
             outputFile = "languages-frameworks/node.xml";

     

       69
       69
       +
             inputFile = ./languages-frameworks/node.section.md;

     

       70
       70
       +
             outputFile = "languages-frameworks/node.section.xml";

     

       71
       71
        
           }

     

       72
       72
        
         + toDocbook {

     

       73
       73
       -
             inputFile = ../pkgs/development/r-modules/README.md;

     

       74
       74
       -
             outputFile = "languages-frameworks/r.xml";

     

       73
       73
       +
             inputFile = ./languages-frameworks/r.section.md;

     

       74
       74
       +
             outputFile = "languages-frameworks/r.section.xml";

     

       75
       75
        
           }

     

       76
       76
        
         + toDocbook {

     

       77
       77
       -
             inputFile = ./languages-frameworks/rust.md;

     

       78
       78
       -
             outputFile = "./languages-frameworks/rust.xml";

     

       77
       77
       +
             inputFile = ./languages-frameworks/rust.section.md;

     

       78
       78
       +
             outputFile = "./languages-frameworks/rust.section.xml";

     

       79
       79
        
           }

     

       80
       80
        
         + toDocbook {

     

       81
       81
       -
             inputFile = ./languages-frameworks/vim.md;

     

       82
       82
       -
             outputFile = "./languages-frameworks/vim.xml";

     

       81
       81
       +
             inputFile = ./languages-frameworks/vim.section.md;

     

       82
       82
       +
             outputFile = "./languages-frameworks/vim.section.xml";

     

       83
       83
        
           }

     

       84
       84
        
         + toDocbook {

     

       85
       85
       -
             inputFile = ./languages-frameworks/emscripten.md;

     

       86
       86
       -
             outputFile = "./languages-frameworks/emscripten.xml";

     

       85
       85
       +
             inputFile = ./languages-frameworks/emscripten.section.md;

     

       86
       86
       +
             outputFile = "./languages-frameworks/emscripten.section.xml";

     

       87
       87
        
           }

     

       88
       88
        
         + ''

     

       89
       89
        
           echo ${lib.nixpkgsVersion} > .version

doc/introduction.md doc/introduction.chapter.md

doc/languages-frameworks/emscripten.md doc/languages-frameworks/emscripten.section.md

doc/languages-frameworks/haskell.md doc/languages-frameworks/haskell.section.md

+39

doc/languages-frameworks/idris.section.md

···

       1
       1
       +
       Idris packages

     

       2
       2
       +
       ==============

     

       3
       3
       +
       

     

       4
       4
       +
       This directory contains build rules for idris packages. In addition,

     

       5
       5
       +
       it contains several functions to build and compose those packages.

     

       6
       6
       +
       Everything is exposed to the user via the `idrisPackages` attribute.

     

       7
       7
       +
       

     

       8
       8
       +
       callPackage

     

       9
       9
       +
       ------------

     

       10
       10
       +
       

     

       11
       11
       +
       This is like the normal nixpkgs callPackage function, specialized to

     

       12
       12
       +
       idris packages.

     

       13
       13
       +
       

     

       14
       14
       +
       builtins

     

       15
       15
       +
       ---------

     

       16
       16
       +
       

     

       17
       17
       +
       This is a list of all of the libraries that come packaged with Idris

     

       18
       18
       +
       itself.

     

       19
       19
       +
       

     

       20
       20
       +
       build-idris-package

     

       21
       21
       +
       --------------------

     

       22
       22
       +
       

     

       23
       23
       +
       A function to build an idris package. Its sole argument is a set like

     

       24
       24
       +
       you might pass to `stdenv.mkDerivation`, except `build-idris-package`

     

       25
       25
       +
       sets several attributes for you. See `build-idris-package.nix` for

     

       26
       26
       +
       details.

     

       27
       27
       +
       

     

       28
       28
       +
       build-builtin-package

     

       29
       29
       +
       ----------------------

     

       30
       30
       +
       

     

       31
       31
       +
       A version of `build-idris-package` specialized to builtin libraries.

     

       32
       32
       +
       Mostly for internal use.

     

       33
       33
       +
       

     

       34
       34
       +
       with-packages

     

       35
       35
       +
       -------------

     

       36
       36
       +
       

     

       37
       37
       +
       Bundle idris together with a list of packages. Because idris currently

     

       38
       38
       +
       only supports a single directory in its library path, you must include

     

       39
       39
       +
       all desired libraries here, including `prelude` and `base`.

+8 -8

doc/languages-frameworks/index.xml

···

       17
       17
        
       <xi:include href="bower.xml" />

     

       18
       18
        
       <xi:include href="coq.xml" />

     

       19
       19
        
       <xi:include href="go.xml" />

     

       20
       20
       -
       <xi:include href="haskell.xml" />

     

       21
       21
       -
       <xi:include href="idris.xml" /> <!-- generated from ../../pkgs/development/idris-modules/README.md  -->

     

       20
       20
       +
       <xi:include href="haskell.section.xml" />

     

       21
       21
       +
       <xi:include href="idris.section.xml" />

     

       22
       22
        
       <xi:include href="java.xml" />

     

       23
       23
        
       <xi:include href="lua.xml" />

     

       24
       24
       -
       <xi:include href="node.xml" /> <!-- generated from ../../pkgs/development/node-packages/README.md  -->

     

       24
       24
       +
       <xi:include href="node.section.xml" />

     

       25
       25
        
       <xi:include href="perl.xml" />

     

       26
       26
       -
       <xi:include href="python.xml" />

     

       26
       26
       +
       <xi:include href="python.section.xml" />

     

       27
       27
        
       <xi:include href="qt.xml" />

     

       28
       28
       -
       <xi:include href="r.xml" /> <!-- generated from ../../pkgs/development/r-modules/README.md  -->

     

       28
       28
       +
       <xi:include href="r.section.xml" />

     

       29
       29
        
       <xi:include href="ruby.xml" />

     

       30
       30
       -
       <xi:include href="rust.xml" />

     

       30
       30
       +
       <xi:include href="rust.section.xml" />

     

       31
       31
        
       <xi:include href="texlive.xml" />

     

       32
       32
       -
       <xi:include href="vim.xml" />

     

       33
       33
       -
       <xi:include href="emscripten.xml" />

     

       32
       32
       +
       <xi:include href="vim.section.xml" />

     

       33
       33
       +
       <xi:include href="emscripten.section.xml" />

     

       34
       34
        
       

     

       35
       35
        
       

     

       36
       36
        
       </chapter>

+51

doc/languages-frameworks/node.section.md

···

       1
       1
       +
       Node.js packages

     

       2
       2
       +
       ================

     

       3
       3
       +
       The `pkgs/development/node-packages` folder contains a generated collection of

     

       4
       4
       +
       [NPM packages](https://npmjs.com/) that can be installed with the Nix package

     

       5
       5
       +
       manager.

     

       6
       6
       +
       

     

       7
       7
       +
       As a rule of thumb, the package set should only provide *end user* software

     

       8
       8
       +
       packages, such as command-line utilities. Libraries should only be added to the

     

       9
       9
       +
       package set if there is a non-NPM package that requires it.

     

       10
       10
       +
       

     

       11
       11
       +
       When it is desired to use NPM libraries in a development project, use the

     

       12
       12
       +
       `node2nix` generator directly on the `package.json` configuration file of the

     

       13
       13
       +
       project.

     

       14
       14
       +
       

     

       15
       15
       +
       The package set also provides support for multiple Node.js versions. The policy

     

       16
       16
       +
       is that a new package should be added to the collection for the latest stable LTS

     

       17
       17
       +
       release (which is currently 6.x), unless there is an explicit reason to support

     

       18
       18
       +
       a different release.

     

       19
       19
       +
       

     

       20
       20
       +
       If your package uses native addons, you need to examine what kind of native

     

       21
       21
       +
       build system it uses. Here are some examples:

     

       22
       22
       +
       

     

       23
       23
       +
       * `node-gyp`

     

       24
       24
       +
       * `node-gyp-builder`

     

       25
       25
       +
       * `node-pre-gyp`

     

       26
       26
       +
       

     

       27
       27
       +
       After you have identified the correct system, you need to override your package

     

       28
       28
       +
       expression while adding in build system as a build input. For example, `dat`

     

       29
       29
       +
       requires `node-gyp-build`, so we override its expression in `default-v6.nix`:

     

       30
       30
       +
       

     

       31
       31
       +
       ```nix

     

       32
       32
       +
       dat = nodePackages.dat.override (oldAttrs: {

     

       33
       33
       +
         buildInputs = oldAttrs.buildInputs ++ [ nodePackages.node-gyp-build ];

     

       34
       34
       +
       });

     

       35
       35
       +
       ```

     

       36
       36
       +
       

     

       37
       37
       +
       To add a package from NPM to nixpkgs:

     

       38
       38
       +
       

     

       39
       39
       +
        1. Modify `pkgs/development/node-packages/node-packages-v6.json` to add, update

     

       40
       40
       +
           or remove package entries. (Or `pkgs/development/node-packages/node-packages-v4.json`

     

       41
       41
       +
           for packages depending on Node.js 4.x)

     

       42
       42
       +
        2. Run the script: `(cd pkgs/development/node-packages && ./generate.sh)`.

     

       43
       43
       +
        3. Build your new package to test your changes:

     

       44
       44
       +
           `cd /path/to/nixpkgs && nix-build -A nodePackages.<new-or-updated-package>`.

     

       45
       45
       +
           To build against a specific Node.js version (e.g. 4.x):

     

       46
       46
       +
           `nix-build -A nodePackages_4_x.<new-or-updated-package>`

     

       47
       47
       +
        4. Add and commit all modified and generated files.

     

       48
       48
       +
       

     

       49
       49
       +
       For more information about the generation process, consult the

     

       50
       50
       +
       [README.md](https://github.com/svanderburg/node2nix) file of the `node2nix`

     

       51
       51
       +
       tool.

doc/languages-frameworks/python.md doc/languages-frameworks/python.section.md

+120

doc/languages-frameworks/r.section.md

···

       1
       1
       +
       R packages

     

       2
       2
       +
       ==========

     

       3
       3
       +
       

     

       4
       4
       +
       ## Installation

     

       5
       5
       +
       

     

       6
       6
       +
       Define an environment for R that contains all the libraries that you'd like to

     

       7
       7
       +
       use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:

     

       8
       8
       +
       

     

       9
       9
       +
       ```nix

     

       10
       10
       +
       {

     

       11
       11
       +
           packageOverrides = super: let self = super.pkgs; in

     

       12
       12
       +
           {

     

       13
       13
       +
       

     

       14
       14
       +
               rEnv = super.rWrapper.override {

     

       15
       15
       +
                   packages = with self.rPackages; [

     

       16
       16
       +
                       devtools

     

       17
       17
       +
                       ggplot2

     

       18
       18
       +
                       reshape2

     

       19
       19
       +
                       yaml

     

       20
       20
       +
                       optparse

     

       21
       21
       +
                       ];

     

       22
       22
       +
               };

     

       23
       23
       +
           };

     

       24
       24
       +
       }

     

       25
       25
       +
       ```

     

       26
       26
       +
       

     

       27
       27
       +
       Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user

     

       28
       28
       +
       profile. The set of available libraries can be discovered by running the

     

       29
       29
       +
       command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that

     

       30
       30
       +
       output is the name that has to be passed to rWrapper in the code snipped above.

     

       31
       31
       +
       

     

       32
       32
       +
       However, if you'd like to add a file to your project source to make the

     

       33
       33
       +
       environment available for other contributors, you can create a `default.nix`

     

       34
       34
       +
       file like so:

     

       35
       35
       +
       ```nix

     

       36
       36
       +
       let

     

       37
       37
       +
         pkgs = import <nixpkgs> {};

     

       38
       38
       +
         stdenv = pkgs.stdenv;

     

       39
       39
       +
       in with pkgs; {

     

       40
       40
       +
         myProject = stdenv.mkDerivation {

     

       41
       41
       +
           name = "myProject";

     

       42
       42
       +
           version = "1";

     

       43
       43
       +
           src = if pkgs.lib.inNixShell then null else nix;

     

       44
       44
       +
       

     

       45
       45
       +
           buildInputs = with rPackages; [

     

       46
       46
       +
             R

     

       47
       47
       +
             ggplot2

     

       48
       48
       +
             knitr

     

       49
       49
       +
           ];

     

       50
       50
       +
         };

     

       51
       51
       +
       }

     

       52
       52
       +
       ```

     

       53
       53
       +
       and then run `nix-shell .` to be dropped into a shell with those packages

     

       54
       54
       +
       available.

     

       55
       55
       +
       

     

       56
       56
       +
       ## RStudio

     

       57
       57
       +
       

     

       58
       58
       +
       RStudio uses a standard set of packages and ignores any custom R

     

       59
       59
       +
       environments or installed packages you may have.  To create a custom

     

       60
       60
       +
       environment, see `rstudioWrapper`, which functions similarly to

     

       61
       61
       +
       `rWrapper`:

     

       62
       62
       +
       

     

       63
       63
       +
       ```nix

     

       64
       64
       +
       {

     

       65
       65
       +
           packageOverrides = super: let self = super.pkgs; in

     

       66
       66
       +
           {

     

       67
       67
       +
       

     

       68
       68
       +
               rstudioEnv = super.rstudioWrapper.override {

     

       69
       69
       +
                   packages = with self.rPackages; [

     

       70
       70
       +
                       dplyr

     

       71
       71
       +
                       ggplot2

     

       72
       72
       +
                       reshape2

     

       73
       73
       +
                       ];

     

       74
       74
       +
               };

     

       75
       75
       +
           };

     

       76
       76
       +
       }

     

       77
       77
       +
       ```

     

       78
       78
       +
       

     

       79
       79
       +
       Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install

     

       80
       80
       +
       this into your user profile.

     

       81
       81
       +
       

     

       82
       82
       +
       Alternatively, you can create a self-contained `shell.nix` without the need to

     

       83
       83
       +
       modify any configuration files:

     

       84
       84
       +
       

     

       85
       85
       +
       ```nix

     

       86
       86
       +
       { pkgs ? import <nixpkgs> {}

     

       87
       87
       +
       }:

     

       88
       88
       +
       

     

       89
       89
       +
       pkgs.rstudioWrapper.override {

     

       90
       90
       +
         packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];

     

       91
       91
       +
       }

     

       92
       92
       +
       

     

       93
       93
       +
       ```

     

       94
       94
       +
       

     

       95
       95
       +
       Executing `nix-shell` will then drop you into an environment equivalent to the

     

       96
       96
       +
       one above. If you need additional packages just add them to the list and

     

       97
       97
       +
       re-enter the shell.

     

       98
       98
       +
       

     

       99
       99
       +
       ## Updating the package set

     

       100
       100
       +
       

     

       101
       101
       +
       ```bash

     

       102
       102
       +
       nix-shell generate-shell.nix

     

       103
       103
       +
       

     

       104
       104
       +
       Rscript generate-r-packages.R cran  > cran-packages.nix.new

     

       105
       105
       +
       mv cran-packages.nix.new cran-packages.nix

     

       106
       106
       +
       

     

       107
       107
       +
       Rscript generate-r-packages.R bioc  > bioc-packages.nix.new

     

       108
       108
       +
       mv bioc-packages.nix.new bioc-packages.nix

     

       109
       109
       +
       ```

     

       110
       110
       +
       

     

       111
       111
       +
       `generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.

     

       112
       112
       +
       

     

       113
       113
       +
       

     

       114
       114
       +
       ## Testing if the Nix-expression could be evaluated

     

       115
       115
       +
       

     

       116
       116
       +
       ```bash

     

       117
       117
       +
       nix-build test-evaluation.nix --dry-run

     

       118
       118
       +
       ```

     

       119
       119
       +
       

     

       120
       120
       +
       If this exits fine, the expression is ok. If not, you have to edit `default.nix`

doc/languages-frameworks/rust.md doc/languages-frameworks/rust.section.md

doc/languages-frameworks/vim.md doc/languages-frameworks/vim.section.md

+1 -1

doc/manual.xml

···

       9
       9
        
       

     

       10
       10
        
         </info>

     

       11
       11
        
       

     

       12
       12
       -
         <xi:include href="introduction.xml" />

     

       12
       12
       +
         <xi:include href="introduction.chapter.xml" />

     

       13
       13
        
         <xi:include href="quick-start.xml" />

     

       14
       14
        
         <xi:include href="stdenv.xml" />

     

       15
       15
        
         <xi:include href="multiple-output.xml" />

doc/shell.md doc/shell.section.md

+1 -39

pkgs/development/idris-modules/README.md

···

       1
       1
       -
       Idris packages

     

       2
       2
       -
       ==============

     

       3
       3
       -
       

     

       4
       4
       -
       This directory contains build rules for idris packages. In addition,

     

       5
       5
       -
       it contains several functions to build and compose those packages.

     

       6
       6
       -
       Everything is exposed to the user via the `idrisPackages` attribute.

     

       7
       7
       -
       

     

       8
       8
       -
       callPackage

     

       9
       9
       -
       ------------

     

       10
       10
       -
       

     

       11
       11
       -
       This is like the normal nixpkgs callPackage function, specialized to

     

       12
       12
       -
       idris packages.

     

       13
       13
       -
       

     

       14
       14
       -
       builtins

     

       15
       15
       -
       ---------

     

       16
       16
       -
       

     

       17
       17
       -
       This is a list of all of the libraries that come packaged with Idris

     

       18
       18
       -
       itself.

     

       19
       19
       -
       

     

       20
       20
       -
       build-idris-package

     

       21
       21
       -
       --------------------

     

       22
       22
       -
       

     

       23
       23
       -
       A function to build an idris package. Its sole argument is a set like

     

       24
       24
       -
       you might pass to `stdenv.mkDerivation`, except `build-idris-package`

     

       25
       25
       -
       sets several attributes for you. See `build-idris-package.nix` for

     

       26
       26
       -
       details.

     

       27
       27
       -
       

     

       28
       28
       -
       build-builtin-package

     

       29
       29
       -
       ----------------------

     

       30
       30
       -
       

     

       31
       31
       -
       A version of `build-idris-package` specialized to builtin libraries.

     

       32
       32
       -
       Mostly for internal use.

     

       33
       33
       -
       

     

       34
       34
       -
       with-packages

     

       35
       35
       -
       -------------

     

       36
       36
       -
       

     

       37
       37
       -
       Bundle idris together with a list of packages. Because idris currently

     

       38
       38
       -
       only supports a single directory in its library path, you must include

     

       39
       39
       -
       all desired libraries here, including `prelude` and `base`.
     

       1
       1
       +
       Moved to [/doc/languages-frameworks/idris.section.md](/doc/languages-frameworks/idris.section.md)

+1 -51

pkgs/development/node-packages/README.md

···

       1
       1
       -
       Node.js packages

     

       2
       2
       -
       ================

     

       3
       3
       -
       The `pkgs/development/node-packages` folder contains a generated collection of

     

       4
       4
       -
       [NPM packages](https://npmjs.com/) that can be installed with the Nix package

     

       5
       5
       -
       manager.

     

       6
       6
       -
       

     

       7
       7
       -
       As a rule of thumb, the package set should only provide *end user* software

     

       8
       8
       -
       packages, such as command-line utilities. Libraries should only be added to the

     

       9
       9
       -
       package set if there is a non-NPM package that requires it.

     

       10
       10
       -
       

     

       11
       11
       -
       When it is desired to use NPM libraries in a development project, use the

     

       12
       12
       -
       `node2nix` generator directly on the `package.json` configuration file of the

     

       13
       13
       -
       project.

     

       14
       14
       -
       

     

       15
       15
       -
       The package set also provides support for multiple Node.js versions. The policy

     

       16
       16
       -
       is that a new package should be added to the collection for the latest stable LTS

     

       17
       17
       -
       release (which is currently 6.x), unless there is an explicit reason to support

     

       18
       18
       -
       a different release.

     

       19
       19
       -
       

     

       20
       20
       -
       If your package uses native addons, you need to examine what kind of native

     

       21
       21
       -
       build system it uses. Here are some examples:

     

       22
       22
       -
       

     

       23
       23
       -
       * `node-gyp`

     

       24
       24
       -
       * `node-gyp-builder`

     

       25
       25
       -
       * `node-pre-gyp`

     

       26
       26
       -
       

     

       27
       27
       -
       After you have identified the correct system, you need to override your package

     

       28
       28
       -
       expression while adding in build system as a build input. For example, `dat`

     

       29
       29
       -
       requires `node-gyp-build`, so we override its expression in `default-v6.nix`:

     

       30
       30
       -
       

     

       31
       31
       -
       ```nix

     

       32
       32
       -
       dat = nodePackages.dat.override (oldAttrs: {

     

       33
       33
       -
         buildInputs = oldAttrs.buildInputs ++ [ nodePackages.node-gyp-build ];

     

       34
       34
       -
       });

     

       35
       35
       -
       ```

     

       36
       36
       -
       

     

       37
       37
       -
       To add a package from NPM to nixpkgs:

     

       38
       38
       -
       

     

       39
       39
       -
        1. Modify `pkgs/development/node-packages/node-packages-v6.json` to add, update

     

       40
       40
       -
           or remove package entries. (Or `pkgs/development/node-packages/node-packages-v4.json`

     

       41
       41
       -
           for packages depending on Node.js 4.x)

     

       42
       42
       -
        2. Run the script: `(cd pkgs/development/node-packages && ./generate.sh)`.

     

       43
       43
       -
        3. Build your new package to test your changes:

     

       44
       44
       -
           `cd /path/to/nixpkgs && nix-build -A nodePackages.<new-or-updated-package>`.

     

       45
       45
       -
           To build against a specific Node.js version (e.g. 4.x):

     

       46
       46
       -
           `nix-build -A nodePackages_4_x.<new-or-updated-package>`

     

       47
       47
       -
        4. Add and commit all modified and generated files.

     

       48
       48
       -
       

     

       49
       49
       -
       For more information about the generation process, consult the

     

       50
       50
       -
       [README.md](https://github.com/svanderburg/node2nix) file of the `node2nix`

     

       51
       51
       -
       tool.

     

       1
       1
       +
       Moved to [/doc/languages-frameworks/node.section.md](/doc/languages-frameworks/node.section.md)

+1 -120

pkgs/development/r-modules/README.md

···

       1
       1
       -
       R packages

     

       2
       2
       -
       ==========

     

       3
       3
       -
       

     

       4
       4
       -
       ## Installation

     

       5
       5
       -
       

     

       6
       6
       -
       Define an environment for R that contains all the libraries that you'd like to

     

       7
       7
       -
       use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:

     

       8
       8
       -
       

     

       9
       9
       -
       ```nix

     

       10
       10
       -
       {

     

       11
       11
       -
           packageOverrides = super: let self = super.pkgs; in

     

       12
       12
       -
           {

     

       13
       13
       -
       

     

       14
       14
       -
               rEnv = super.rWrapper.override {

     

       15
       15
       -
                   packages = with self.rPackages; [

     

       16
       16
       -
                       devtools

     

       17
       17
       -
                       ggplot2

     

       18
       18
       -
                       reshape2

     

       19
       19
       -
                       yaml

     

       20
       20
       -
                       optparse

     

       21
       21
       -
                       ];

     

       22
       22
       -
               };

     

       23
       23
       -
           };

     

       24
       24
       -
       }

     

       25
       25
       -
       ```

     

       26
       26
       -
       

     

       27
       27
       -
       Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user

     

       28
       28
       -
       profile. The set of available libraries can be discovered by running the

     

       29
       29
       -
       command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that

     

       30
       30
       -
       output is the name that has to be passed to rWrapper in the code snipped above.

     

       31
       31
       -
       

     

       32
       32
       -
       However, if you'd like to add a file to your project source to make the

     

       33
       33
       -
       environment available for other contributors, you can create a `default.nix`

     

       34
       34
       -
       file like so:

     

       35
       35
       -
       ```nix

     

       36
       36
       -
       let

     

       37
       37
       -
         pkgs = import <nixpkgs> {};

     

       38
       38
       -
         stdenv = pkgs.stdenv;

     

       39
       39
       -
       in with pkgs; {

     

       40
       40
       -
         myProject = stdenv.mkDerivation {

     

       41
       41
       -
           name = "myProject";

     

       42
       42
       -
           version = "1";

     

       43
       43
       -
           src = if pkgs.lib.inNixShell then null else nix;

     

       44
       44
       -
       

     

       45
       45
       -
           buildInputs = with rPackages; [

     

       46
       46
       -
             R

     

       47
       47
       -
             ggplot2

     

       48
       48
       -
             knitr

     

       49
       49
       -
           ];

     

       50
       50
       -
         };

     

       51
       51
       -
       }

     

       52
       52
       -
       ```

     

       53
       53
       -
       and then run `nix-shell .` to be dropped into a shell with those packages

     

       54
       54
       -
       available.

     

       55
       55
       -
       

     

       56
       56
       -
       ## RStudio

     

       57
       57
       -
       

     

       58
       58
       -
       RStudio uses a standard set of packages and ignores any custom R

     

       59
       59
       -
       environments or installed packages you may have.  To create a custom

     

       60
       60
       -
       environment, see `rstudioWrapper`, which functions similarly to

     

       61
       61
       -
       `rWrapper`:

     

       62
       62
       -
       

     

       63
       63
       -
       ```nix

     

       64
       64
       -
       {

     

       65
       65
       -
           packageOverrides = super: let self = super.pkgs; in

     

       66
       66
       -
           {

     

       67
       67
       -
       

     

       68
       68
       -
               rstudioEnv = super.rstudioWrapper.override {

     

       69
       69
       -
                   packages = with self.rPackages; [

     

       70
       70
       -
                       dplyr

     

       71
       71
       -
                       ggplot2

     

       72
       72
       -
                       reshape2

     

       73
       73
       -
                       ];

     

       74
       74
       -
               };

     

       75
       75
       -
           };

     

       76
       76
       -
       }

     

       77
       77
       -
       ```

     

       78
       78
       -
       

     

       79
       79
       -
       Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install

     

       80
       80
       -
       this into your user profile.

     

       81
       81
       -
       

     

       82
       82
       -
       Alternatively, you can create a self-contained `shell.nix` without the need to

     

       83
       83
       -
       modify any configuration files:

     

       84
       84
       -
       

     

       85
       85
       -
       ```nix

     

       86
       86
       -
       { pkgs ? import <nixpkgs> {}

     

       87
       87
       -
       }:

     

       88
       88
       -
       

     

       89
       89
       -
       pkgs.rstudioWrapper.override {

     

       90
       90
       -
         packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];

     

       91
       91
       -
       }

     

       92
       92
       -
       

     

       93
       93
       -
       ```

     

       94
       94
       -
       

     

       95
       95
       -
       Executing `nix-shell` will then drop you into an environment equivalent to the

     

       96
       96
       -
       one above. If you need additional packages just add them to the list and

     

       97
       97
       -
       re-enter the shell.

     

       98
       98
       -
       

     

       99
       99
       -
       ## Updating the package set

     

       100
       100
       -
       

     

       101
       101
       -
       ```bash

     

       102
       102
       -
       nix-shell generate-shell.nix

     

       103
       103
       -
       

     

       104
       104
       -
       Rscript generate-r-packages.R cran  > cran-packages.nix.new

     

       105
       105
       -
       mv cran-packages.nix.new cran-packages.nix

     

       106
       106
       -
       

     

       107
       107
       -
       Rscript generate-r-packages.R bioc  > bioc-packages.nix.new

     

       108
       108
       -
       mv bioc-packages.nix.new bioc-packages.nix

     

       109
       109
       -
       ```

     

       110
       110
       -
       

     

       111
       111
       -
       `generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.

     

       112
       112
       -
       

     

       113
       113
       -
       

     

       114
       114
       -
       ## Testing if the Nix-expression could be evaluated

     

       115
       115
       -
       

     

       116
       116
       -
       ```bash

     

       117
       117
       -
       nix-build test-evaluation.nix --dry-run

     

       118
       118
       -
       ```

     

       119
       119
       -
       

     

       120
       120
       -
       If this exits fine, the expression is ok. If not, you have to edit `default.nix`

     

       1
       1
       +
       Moved to [/doc/languages-frameworks/r.section.md](/doc/languages-frameworks/r.section.md)