On Wed, Jan 25, 2012 at 5:07 AM, Andreas Tille <[email protected]> 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/cabgghblnbary15uoraxt89d3my0imtthhlqtmsdnv079ls6...@mail.gmail.com
