···

       
96
       
 
       


     

       
97
       
 
       
## Updating the package set {#updating-the-package-set}

     

       
98
       
 
       


     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
99
       
 
       
```bash

     

       
100
       
 
       
nix-shell generate-shell.nix

     

       
101
       
 
       


     
···

       
112
       
 
       
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix

     

       
113
       
 
       
```

     

       
114
       
 
       


     

       
115
       
-
       
`generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

···

       
96
       
 
       


     

       
97
       
 
       
## Updating the package set {#updating-the-package-set}

     

       
98
       
 
       


     

       
99
       
+
       
There is a script and associated environment for regenerating the package

     

       
100
       
+
       
sets and synchronising the rPackages tree to the current CRAN and matching

     

       
101
       
+
       
BIOC release. These scripts are found in the `pkgs/development/r-modules`

     

       
102
       
+
       
directory and executed as follows:

     

       
103
       
+
       


     

       
104
       
 
       
```bash

     

       
105
       
 
       
nix-shell generate-shell.nix

     

       
106
       
 
       


     
···

       
117
       
 
       
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix

     

       
118
       
 
       
```

     

       
119
       
 
       


     

       
120
       
+
       
`generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefore

     

       
121
       
+
       
the renaming.

     

       
122
       
+
       


     

       
123
       
+
       
Some packages require overrides to specify external dependencies or other

     

       
124
       
+
       
patches and special requirements. These overrides are specified in the

     

       
125
       
+
       
`pkgs/development/r-modules/default.nix` file. As the `*-packages.nix`

     

       
126
       
+
       
contents are automatically generated it should not be edited and broken

     

       
127
       
+
       
builds should be addressed using overrides.