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Mot-clefs : R2spec

RPM repository for R packages

Pierre-Yves Chibon

A RPM repository for R packages is being built

Un dépôts de RPM pour les bibliothèques R est en cours de création

English version

At the moment I wrote this lines there is a group of people who have joined their effort to create a RPM repository for R packages in a similar way than Dirk's work for APT.

On the technical point, the RPMs will be built using R2rpm which have some consequences regarding the RPM generation (there is no -devel sub-packages and rpmlint is not silent for example).

We are busy at the moment trying to get and set up the architecture since we would like to support 4 versions:

- CentOS/RHEL 5 i386 and x86_64
- The latest version of Fedora i686 and x86_64

For that we will need some "builders" most likely some VM.

In order to discuss the creation of this project we have set up a mailing list available at: http://www.bioinformatics.org/mailman/listinfo/r-repo-dev

Feel free to join the list to get some more information about its development and to help us making the project reality.



French version

Il y a à l'heure actuelle un petit groupe de personnes qui s'est constitué avec pour objectif de construire un dépôt RPM pour les bibliothèques R. Ce projet est très proche du projet de Dirk pour APT.

D'un point de vue technique, les RPMs seront construits avec R2rpm ce qui a quelque conséquences sur les RPMs généré (pas de sous paquet -devel et rpmlint n'est pas silencieux par exemple).

À l'heure actuelle nous sommes en train d'essayer de réunir l'infrastructure. Nous souhaitons supportés 4 versions:

- CentOS/RHEL 5 i386 and x86_64
- La dernière version de Fedora i686 and x86_64

Il nous faut donc pour ça quelques "builder" vraisemblablement des machines virtuelles.

Pour discuter de ce projet nous venons de mettre en place une liste de diffusion, disponible à : http://www.bioinformatics.org/mailman/listinfo/r-repo-dev

N'hésitez pas à nous rejoindre pour suivre le projet ou pour nous aider à en faire une réalité.

R2rpm on cran

Pierre-Yves Chibon

Building cran RPM via R2rpm

Construire des RPMs du cran avec R2rpm

English format

Using the PACKAGES file from the CRAN I was able to generate a list of 670 packages that do not depend on anything else than R.

This morning I ran R2rpm on the first 100, it took around 3h and there are the results:

89 packages built
['ADGofTest', 'AMORE', 'AlgDesign', 'Animal', 'BGSIMD', 'BMN', 'BPHO', 'BayesValidate', 'Bhat', 'BiasedUrn', 'Biodem', 'Bolstad', 'Bolstad2', 'BootCL', 'CAVIAR', 'CCP', 'CDFt', 'CHsharp', 'CORElearn', 'CTT', 'ClinicalRobustPriors', 
'ComPairWise', 'CompetingRiskFrailty', 'ConvCalendar', 'CreditMetrics', 'CvM2SL1Test', 'CvM2SL2Test', 'DEA', 'DEMEtics', 'DEoptim', 'DTDA', 'DTK', 'Davies', 'Defaults', 'DiversitySampler', 'EMJumpDiffusion', 'EbayesThresh', 
'ElectroGraph', 'ExPD2D', 'FBN', 'FITSio', 'FKBL', 'FNN', 'Flury', 'GPArotation', 'GWRM', 'GeneF', 'GillespieSSA', 'HAPim', 'HI', 'HMM', 'HMR', 'ISOcodes', 'Imap', 'Iso', 'JADE', 'JudgeIt', 'Kendall', 'LDtests', 'LIStest', 'LearnBayes', 
'LearnEDA', 'LogitNet', 'LowRankQP', 'MAMSE', 'MCE', 'MKLE', 'MLDA', 'MLEcens', 'MMG', 'MMIX', 'MPV', 'MSVAR', 'MTSKNN', 'ModelGood', 'Multiclasstesting', 'NMFN', 'NORMT3', 'OPE', 'ORIClust', 'ORMDR', 'Oarray', 'OrdMonReg', 
'PBSddesolve', 'PLIS', 'POT', 'PSAgraphics', 'Peaks', 'PearsonICA']

11 packages failed
['BioStatR', 'BoSSA', 'BradleyTerry', 'BradleyTerry2', 'CPE', 'Cairo', 'FracSim', 'GDD', 'KFAS', 'MImix', 'OAIHarvester']

Damn this is good ! :-)

R2spec / R2rpm

Pierre-Yves Chibon

rpm.pngsource.png

New version of R2spec in the pipes

Une nouvelle version de R2spec dans les tuyaux

English version

There is a new version of R2spec in the pipes, this version fixes some bugs and introduces some new features. The main of these features is the presence of R2rpm now.

R2rpm generate the complete rpm directly from a url, the sources or simply the name of the package. It builds the package twice, once to determine the %file section and once to generate the RPM.

I fixed the length of the %description so that it is not bigger than the mandatory 75 characters, the summary is also corrected if it ends with a dot.

Tonight I have been playing with this new version, I was able to generate in the fly a bit more than 70 RPMs for R libraries in just few minutes (ok maybe it tooks a couple of hours :-)).

All the RPMs work, there are not rpmlint compliant so there would need more work if we want to integrate them into the repository but it is a good basis.

Something that I still want to do before to release officially the version 3.0.0 is the possibility to build the dependencies of a given package. Basically, this would allow to build RPM for one package and all the packages of which it depends.

For those who would like to test you can find the source, srpm and rpm in https://fedorahosted.org/releases/r/2/r2spec/ (latest release so far 3.0.0-0.4).

Do not hesitate to test it and report any issue you find in it :-)

Hope you like it !