On Thursday 26 April 2007 9:23:49 pm Tom Moertel wrote: > José, > > Thanks for your help. Now, on to your comments: No problem. :-) > José Matos wrote: > > Tom may I suggest that you join fedora-r-devel-list@xxxxxxxxxx > > Done. > > I'm cc:ing this email to the list, too, mainly because of the discussion > on R packaging work-arounds, which probably ought to be archived. For > the same reason, I'm leaving more context in this email than I normally > would. Thank you, this is important. > Tom Moertel wrote: > >> For my internal use, I have packaged a number of R packages for FC6: > >> > >> * R-arm-1.0-2 > >> * R-car-1.2-1 > >> * R-lme4-0.9975-1 > >> * R-Matrix-0.9975-1 > >> * R-R2WinBUGS-2.0-1 > >> * R-coda-0.10-1 > >> * R-leaps-2.7-1 > >> * R-mlmRev-0.995-1 > >> > >> Corresponding specs: > >> http://community.moertel.com/rpms/fedora/6/SPECS/ > >> > >> For more details: > >> http://blog.moertel.com/articles/2007/04/25/new-fedora-core-rpms-for-cra > >>n-packages > > > > Are you aware of cran2rpmspec? > > http://www.fc.up.pt/pessoas/jamatos/R/cran2rpmspec > > No, I was completely unaware of cran2rpmspec. That would have made my > job a bit easier. ;-) > > Thanks for pointing it out (and for writing it). FWIW there a bugzilla entry https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=215927 to add a spectemplate for R modules to rpmdevtools. I would like to ask people in this list to comment if there is any omission or error in there as they are asking for our opinion. :-) Accordingly to my post there I have updated cran2rpmspec with the suggestions done there. So with this template and with cran2rpmspec it should not ever be necessary to start from scratch anymore. :-) > >> Do you think there would be sufficient benefit to the Fedora community > >> to merit adding these packages to Extras? If so, would you mind helping > >> me get the packages into shape for submission? > > > > Sure on both issues. :-) > > Great! > > I assume that normally my next steps would be to create review requests > for the packages, get sponsored, get a Fedora Account, check in my > packages, and eventually queue up builds for my packages. Does that > seem right? > > Looking ahead to that last step, how does the build system handle weird > build-order requirements? Can the system, for example, infer from > BuildRequires statements that it must build and install the R-Matrix > package before it can try to build R-arm? (I couldn't find out how > Plague deals with dependencies from my search of the wiki.) > > >> In any case, I ran into some difficulties during packaging. Can I ask > >> for your advice? > >> > >> First, how do you deal with circular dependencies among R packages? The > >> lme4 CRAN package, for example, "suggests" mlmRev, but mlmRev "depends" > >> on lme4. Thus the %check stage's "R CMD check" for each of the packages > >> tries to require the other package, which prevents either from building. > >> I worked around this problem by disabling the %check stage of > >> R-mlmRev, building that package first, installing it, and then building > >> R-lme4, whose %check I left intact. (Since mlmRev is mainly data files, > >> I felt its check was more expendable.) > >> > >> Can you suggest a better way of dealing with circular dependencies? > > > > The real solution would be for rpm to support these concepts. I think > > that this will come, but for the moment a bootstrap solution like the one > > you have used is necessary. > > What's the preferred method to automate the bootstrap solution? Should > I write a script that builds the collection of packages? No, as I think a bit more on this subject this would fail everytime that we update to a new R version, because the other library is not there. So I advise you to choose which to let only the more important dependency. This is a really an rpm issue and until it is fixed upstream our fixes are only band-aids. :-( > >> Second, R2WinBUGS depends on BRugs, which doesn't build on Linux (yet). > >> As a result, the "R CMD check" for R-R2WinBUGS fails during the > >> RPM-building process. Again, I disabled the %check stage to work around > >> this problem. The result is a partially broken R-R2WinBUGS package, but > >> the packages that depend upon it tangentially (e.g., R-arm) can still be > >> built and installed. > > > > If this was a Fedora review I would suggest placing this comment near > > the referred section. > > I already have the following in > http://community.moertel.com/rpms/fedora/6/SPECS/R-mlmRev.spec: > > %check > # disable check to avoid circular dependency w/ R-lme4. > # since this package is just data files, we disable this package's > # check instead of R-lme4's to break the dependency > # > # cd ..;%{_bindir}/R CMD check %{packname} > > Is that what you meant? Or should I do something else? This is perfect, it explains the reason why the check is commented. > >> Can you suggest a better way of dealing with missing dependencies like > >> BRugs? > > > > http://cran.r-project.org/src/contrib/checkSummary.html > > says that it works. What problems are you getting? > > CheckSummary.html does not claim that the package actually installs. > And, in fact, during the install stage it aborts: > > + R CMD INSTALL BRugs -l \ > /var/tmp/R-BRugs-0.3-1-root-thor/usr/lib64/R/library > > * Installing *source* package 'BRugs' ... > Package 'BRugs' currently only works under Windows. > It is supposed to work under Linux in future releases. > > ERROR: configuration failed for package 'BRugs' > > It might be difficult to work around that problem in the RPM spec. ;-) I agree. :-) Again this is an upstream issue. > Thanks again for your help. > > >> P.S. I have also packaged Emacs Speaks Statistics: > >> http://community.moertel.com/rpms/fedora/5/SPECS/emacs-ess.spec > > > > That would be super. :-) > > My wife asked me for this package but I never got the necessary time to > > do it. > > Coincidentally, ESS 5.3.4 was just released today. This together with the news coming from emacs 22 and 23 fronts are indeed great news. :-) > Cheers, > Tom PS: Usually I do trim the content of replies but in this case it was not obvious where to do it so I left. I am sorry for the redundant info. :-) -- José Abílio
