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

Uwe Ligges ligges at statistik.tu-dortmund.de
Sun Jun 13 15:28:48 CEST 2010

On 13.06.2010 01:09, Dr. David Kirkby wrote:
> 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.
> Dave

But if you really want to sense some security, you should really run
make check-all
after the installation, particularly since you are on a platform that is 
not really mainstream any more.

Uwe Ligges

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