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Re: Relation of 'Depends' and 'Imports' from R/CRAN to 'Depends' in 'debian/control'



On Wed, Jan 25, 2012 at 5:07 AM, Andreas Tille <andreas@an3as.eu> wrote:
> Hi Carlos,
>
> On Tue, Jan 24, 2012 at 05:05:24PM -0500, Carlos Borroto wrote:
>> Hi All,
>>
>> I would like to work on packages from R/CRAN and Bioconductor.
>
> Great.  I checked that you are a member of Debian Med packaging team and
> thus you should have commit permissions to SVN where most of our R
> packages reside (some of them are in Git as your example r-bioc-limma.)
> So I would advise to commit your current state of work to the repository
> of your choice even in a not finished state - just mark this by using
> "UNRELEASED" as target distribution and perhaps add a TODO entry inside
> the changelog.
>
>> I'm
>> using as a guide r-cran-rocr and r-bioc-limma. I was wondering if
>> there is a easy translation from 'Depends' and 'Imports' in the CRAN
>> packages to the 'Depends' fields in 'debian/control'.
>
> I'm not really sure whether there is a 1:1 relation.  What I personally
> do when building R packages is the following:  Use
>
>   pbuilder
>
> to be pretty sure that all Build-Depends are fullfilled.  Once you
> have all Build-Depends set this is usually the set of Depends you need
> as well.
>
>> Initially I though CRAN's 'Depends' meant, the package is needed for
>> building and CRAN's 'Imports' meant, the package is needed when using.
>> Which would translate to a 'Depends' entry on 'Source' and 'Package'
>> respectively. This seems incorrect as for example when building
>> reshape2[1], it only has 'Imports' dependencies, it fails with this
>> error:
>> dh_installdirs                usr/lib/R/site-library
>> if test -f /usr/bin/xvfb-run; then                    \
>>                        xvfb-run -a                    \
>>                               R CMD INSTALL -l
>> /tmp/buildd/r-cran-reshape2-1.2.1/debian/r-cran-reshape2/usr/lib/R/site-library
>> --clean     \
>>                                        . ;    \
>>               else                                                    \
>>                        R CMD INSTALL -l
>> /tmp/buildd/r-cran-reshape2-1.2.1/debian/r-cran-reshape2/usr/lib/R/site-library
>>       \
>>                                       --clean  . ;\
>>               fi
>> ERROR: dependencies 'plyr', 'stringr', 'lattice' are not available for
>> package 'reshape2'
>>
>> So my question is, should I list in 'Source' and 'Package' all the
>> dependencies listed in CRAN's 'Depends' and 'Imports'?
>
> I'm not very competent in R itself but if the build process asks for
> those packages, just add them.  This can not be wrong.
>
> Kind regards and thanks for considering building such packages in Debian
> Med team
>

Thanks Andrea,

I will upload a first draft for all the packages I'm building today.
I'm using pbuilder through git-buildpackage to be sure I'm getting all
dependencies right.

Regarding my question, it was more to see if this was a known issue. I
guess is easy enough to put all 'Depends' and 'Imports' in both
sections of 'debian/control'.

I do have another question, how important is to fill a WNPP for each
package I'm working on? My interest is to get cummeRbund[1][2]
packaged, which I found will need another 7 packages not present in
the repository currently. Filling 8 WNPP doesn't sound fun.

[1]http://compbio.mit.edu/cummeRbund/
[2]http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html

Thanks,
Carlos


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