r-devel August 2008

r-devel@lists.fedoraproject.org

6 participants
7 discussions

useR! 2008
by José Abílio Matos 05 Jan '09

05 Jan '09

Hi, I am writing this from Dortmund, at the useR! 2008 conference http://www.statistik.uni-dortmund.de/useR-2008/ I will have a talk tomorrow about the interaction between R and Fedora. It is a 15 minutes session so there is not much time to expand. I will present Fedora and it interacts with R. There are several issues that are common to the relation between Fedora and languages like perl, python, latex or R. I will also take the opportunity to hear feedback from several types of users regarding the state of R in Fedora. If there is anything relevant I will report back to this list. I have asked pingou (I hope I can use this) to write to the list with the new releases of his package as it would be nice that package automatically in Fedora using yum. Regards, PS: In case you are wondering why I took so long to send this message to the list, believe that it is a long story that involves time shortage. :-) -- José Abílio

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R2spec new release
by Pierre-Yves Chibon 15 Sep '08

15 Sep '08

Dear all As agreed with José there is the news of the new release of R2spec. Have a nice sunday Best regards, Pierre ====================================================================== There is the latest version of R2spec, I have been working quite a bit on it with the suggestion of faceface from #R on irc.freenode.net to improve this software. Therefore the changelog for this new release is quite long and the list of features added seems also important. The principle is still the same: make R packages as simple as possible. Seems there are mainly two sources of libraries for R (Bioconductor and the CRAN) I added two options (--bioc and --cran) that add the Source0 and the URL in the spec file if it has not been defined by the --url option. From that I aslo considered the case of the noarch packages, it now looks for *.c, *.C, *.cp, *.cpp, *.f and *.F files, if it does not find any it consider the package as noarch and thus adapt the specfile for that. It also offers the possibility to move the source to %_topdir (defined in ~/.rpmmacros) so that you can directly run the rpmbuild -ba once you have made the small correction advised on the spec file. That's the main features added, you can see below the changelog for this new release and you can always test and give feed back, report bugs and suggest enhancement on the trac of the R2spec project [1]. The RPMs and sources are available on the git of the R2spec project [2]. Thanks for your attention :-) [1] https://fedorahosted.org/r2spec [2] https://fedorahosted.org/r2spec/browse

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R 2.7.2
by Tom Callaway 29 Aug '08

29 Aug '08

R 2.7.2 is coming! Builds are going for EL-4, EL-5, F-8, F-9, and devel. I'll need to rebuild rpy and push updates, so this won't happen overnight, but this is your official "heads-up". Thanks, ~spot

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useR! 2008 status report
by José Abílio Matos 22 Aug '08

22 Aug '08

Hi all, after a busy week I am finally starting to get back to some kind of normality (no pun intended :-) ). At useR! 2008 I had Martin Plummer, Marc Schwartz and Peter Dalgaard in the audience. The talk went well and it was a fun to do. The room was small for the attendance and in my (biased) view it seemed that I had people coming on purpose for the talk. :-) After the session ended I had a friendly discussion with Martin and Marc regarding Fedora and R relationship. :-) Some of the topics covered were (in no particular order other than my notes). 1) The redundancy between the two mailing lists devoted to R and Fedora (this and SIG list). Actually at that time I forgot the SIG mailing list (my bad). I always keep forgetting about the different purpose of both lists. 2) Martin and Marc suggested one scenario that involved the removal of all R packages from Fedora where the only remaining installed package would be the R core package. Then using some kind of package, the better analogy that I found was a backend to PackageKit providing automatic installs from CRAN. My opinion (that I have also expressed back then) was that this would be a no go for Fedora for two reasons, first the packages dependency outside of CRAN would be hard to get right (think about packages like R-hdf5 that require linking with an external package). The second and probably the most important issue from our (Fedora) point of view would be the liability issue. We would be connecting to a repository that we have no control about, I tried to express the different reasons why this is not possible. 3) There are discussions at R about the next generation CRAN meta-information (improved DESCRIPTION format) and the opinions of distributions are welcome. 4) Is there a link in fedora bugzilla to connect upstream for R bugs reported to Fedora? I am not sure if this is possible with the new bugzilla but I suppose that there are not so many bugs like that reported at Fedora. 5) One problem usually reported in the R users mailing list is the installation procedure used to install R packages (not in Fedora) using the R interface. This problem has been reported again this weekend FWIW. Instead of providing R-devel in the R package as Martin and Marc have suggested I think that we could create a FAQ for R in Fedora. Something like: *********************** Draft to R - Fedora FAQ ************************** Q: I tried to install the following R package in Fedora but R failed with horrendous error messages, what should I do? A: Look to the content of the R package you are trying to install (link to CRAN). 1) Does it contains C or C++ files (.c or .cpp ending filenames)? If yes then install R-devel if it is not yet installed. [Instructions how to install R-devel using yum or packagekit] 2) Does it contains Fortran files (.f or .F ending filenames)? If yes then install gcc-gfortran if it is not yet installed. [Instructions how to install R-devel using yum or packagekit] 3) If the steps above are not enough and the package depends on an external library you need to guarantee that you have installed the files necessary to compile the package. Do not forget that the -devel subpackages are required to be installed to compile and link with the external libraries. ****************************************************************************** This is my fable attempt to document some of the possible of the problems found by our users. :-) We could then expand the FAQ content to other topics like how to search Fedora R packages. The target of the FAQ would be naturally the users and not just the developers. Comments are welcome to all the points above, -- José Abílio

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R package in Fedora
by Pierre-Yves Chibon 12 Aug '08

12 Aug '08

Dear all, Remi Collet has done a great job the past days to make these pages: http://rpms.famillecollet.com/rpmphp/ I think you will be interested specially in this one: http://rpms.famillecollet.com/rpmphp/rpm.php?type=R However, helping him to set up the parsers, we have been facing some problem with some package. For example: R-lmtest As you can see here: http://pingoured.fr/cgi-bin/R.py?name=R-lmtest The version have a '-', this leads to a "outdated" mark of the package in this page http://rpms.famillecollet.com/rpmphp/rpm.php?type=R . The question is then, what should we do ? There is nothing on the guideline that mention what we should do about the library that have a '-' on their version name (second exemple: R-pls http://pingoured.fr/cgi-bin/R.py?name=R-pls ). We also faced the problem that at least one library is present in both CRAN and bioconductor repository (R-qvalue http://pingoured.fr/cgi-bin/R.py?name=R-qvalue ). But the version are pretty clear, we kept only the Bioconductor. So I think, when we have a library in CRAN and Bioconductor, we should only keep the Bioconductor version. For the version with a '-', we skipped everything that was after the '-' until now, should we continue ? Thanks for your comments, Regards, Pierre

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New CRAN packages in Fedora need reviews
by Tom Callaway 12 Aug '08

12 Aug '08

I built a few CRAN packages today that looked useful. If anyone wants to help review these, I'd appreciate it: https://bugzilla.redhat.com/show_bug.cgi?id=454439 (R-nws) https://bugzilla.redhat.com/show_bug.cgi?id=454440 (R-biglm) https://bugzilla.redhat.com/show_bug.cgi?id=454441 (R-bigmemory) Thanks in advance, ~spot

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R2spec v2.3
by Pierre-Yves Chibon 11 Aug '08

11 Aug '08

Dear all, On the suggestion of José I would like to announce here the new release of my project R2spec. At the end of July I release the version 2 re-designed in OO. I corrected a couple of view bugs or typos up to today where I changed the arguments management. Feed back, tester are more than welcome :) There are the links: * The source http://pingoured.fr/public/R2spec/R2spec-2.3.tar.gz * The spec http://pingoured.fr/public/R2spec/R2spec.spec * The SRPM http://pingoured.fr/public/R2spec/R2spec-2.3-1.fc9.src.rpm * The RPM http://pingoured.fr/public/R2spec/R2spec-2.3-1.fc9.noarch.rpm For more information about the different releases of the version 2 see my blog at: http://pingoured.fr/blog/index.php?post/2008/08/10/R2spec-23 http://pingoured.fr/blog/index.php?post/2008/07/31/R2spec_22 http://pingoured.fr/blog/index.php?post/2008/07/30/R2spec-tester-wanted Best regards, Pierre

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r-devel August 2008