[R] Can one get a list of recommended packages?

Dr. David Kirkby david.kirkby at onetel.net
Sun Jun 13 01:09:51 CEST 2010

On 06/12/10 05:27 PM, Douglas Bates wrote:
> On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby
> <david.kirkby at onetel.net>  wrote:
>> R 2.10.1 is used in the Sage maths project. Several recommended packages
>> (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to
>> build on Solaris 10 (SPARC).
> Have you checked the dependencies for those packages?  Some require GNU make.

We used GNU make.

>> We would like to be able to get a list of the recommended packages for R
>> 2.10.1, but ideally via a call to R, so it is not necessary to update that
>> list every time a new version of R is released. We do not want to access the
>> Internet to get this information.
>> Is there a way in R to list the recommended packages?
> I'm not sure I understand the logic of this.  If you are going to
> build R then presumably you have the tar.gz file which contains the
> sources for the recommended packages in the subdirectory
> src/library/Recommended/. Why not get the list from there?

The reason is when the version of R gets updated in Sage, then someone will have 
to check that list again, and more than likely fail to do so, with the result 
tests will fail since packages do not exist, or worst still we will be unaware 
they have failed to build properly.

Therefore, being able to get them from a command would be useful, but can 
understand if that is not possible.

> $ cd ~/src/R-devel/src/library/Recommended/
> $ ls *.tgz
> boot.tgz     codetools.tgz   lattice.tgz  mgcv.tgz  rpart.tgz
> class.tgz    foreign.tgz     MASS.tgz     nlme.tgz  spatial.tgz
> cluster.tgz  KernSmooth.tgz  Matrix.tgz   nnet.tgz  survival.tgz

OK, thank you for that list.

>> Better still, is there a way to list the recommended packages which have not
>> been installed, so getting a list of any failures?
> Again, this seems to be a rather convoluted approach.  Why not check
> why the packages don't install properly?

R had built, and the failure of the packages to build was not very obvious, 
since it did not cause make to exit with a non-zero exit code. Nobody had 
noticed until very recently that there was a problem.

Therefore I proposed to make a test of the packages that should have been 
installed, and ensure they actually all had.

You need to be aware that R is just one part of Sage. Building the whole of Sage 
takes a long time (>24 hours on some computers) so needless to say, people will 
not view every line of error messages. The fact that 'make' succeeded left us a 
false sense of security, when later it was realsed there were problems when R 
run its self-tests.


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