From alexl at users.sourceforge.net Sun Dec 2 23:21:14 2007 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sun, 02 Dec 2007 16:21:14 -0700 Subject: [Fedora-r-devel-list] Bioconductor in Fedora Message-ID: This is just a heads-up about packaging of Bioconductor. Currently Pierre-Yves is spearheading the packaging of Bioconductor, and I'm helping out with reviews. Initially Pierre started with the unstable (will be 2.2): http://www.bioconductor.org/packages/2.2/bioc/ but that's a moving target and won't be officially released until 2008 and is targeting R 3.0 (?) so we dropped back to the stable (2.1) release: http://www.bioconductor.org/packages/2.1/bioc/ Unfortunately a couple of packages (R-tkWidgets and some others) from 2.2 have already made their way into Fedora, but they are only at most 1 or 2 minor releases away from 2.1, so in discussion with Tom Callaway and Pierre-Yves on #fedora-devel, we decided to stick with those packages but use only 2.1 releases for everything else. Once 2.2 is released we can update all packages to that then. I'm currently working on the review of R-Biobase, the core package: https://bugzilla.redhat.com/show_bug.cgi?id=240500 We could perhaps also create a tracker bug and make all Bioconductor module package reviews block the tracker bug. If anybody would like to help, let us know! Cheers, Alex From escobarebio at yahoo.com Thu Dec 6 03:47:25 2007 From: escobarebio at yahoo.com (D.Enrique ESCOBAR ESPINOZA) Date: Wed, 5 Dec 2007 19:47:25 -0800 (PST) Subject: [Fedora-r-devel-list] R-BioC rpm package Message-ID: <352371.63519.qm@web30514.mail.mud.yahoo.com> hi, In an effort to help the biolinux community www.biolinux.org , I put at your disposition R-BioC for R 2.5.x for fedora core 6. Comments for improvement will be welcome. It is not an official fedora rpm because fedora plans to support only R. Unfortunatly is the only fc6 rpm for now but they are more for previous fc It works well, and it contains 102 very usefull sources: abind adSplit affxparser affy affycomp affydata affyio affylmGUI affypdnn affyPLM annaffy annotate arrayMagic Biobase bioDist Biostrings Bolstad BufferedMatrix BufferedMatrixMethods Category cMAP cyp450cdf DBI DynDoc ellipse gcrma genefilter GeneMeta geneplotter GeneR GGtools globaltest GO GOstats goTools gp53cdf gpls graph hgfocus hgfocuscdf hgfocusprobe hgu133a hgu133acdf hgu133aprobe hgu95av2 hgu95av2cdf hgu95av2probe Icens IDPmisc impute KEGG limma limmaGUI maanova makecdfenv marray matchprobes Matrix mgu74av2 mgu74av2cdf mgu74av2probe multtest pamr PFAM pvclust R2HTML RankProd RBGL R-BioC.sh R.cache RColorBrewer RCurl Rdbi RdbiPgSQL reposTools Rgraphviz R.huge RMySQL ROC R.oo RSPerl RSPython RSQLite RSvgDevice RSVGTipsDevice RUnit R.utils samr scatterplot3d siggenes sma som SparseM statmod tkrplot tkWidgets VR vsn widgetTools XML xtable YEAST Best regards and good work. ____________________________________________________________________________________ Looking for last minute shopping deals? 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Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From tcallawa at redhat.com Thu Dec 6 04:48:25 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 06 Dec 2007 10:18:25 +0530 Subject: [Fedora-r-devel-list] R-BioC rpm package In-Reply-To: <352371.63519.qm@web30514.mail.mud.yahoo.com> References: <352371.63519.qm@web30514.mail.mud.yahoo.com> Message-ID: <1196916505.3360.1.camel@localhost.localdomain> On Wed, 2007-12-05 at 19:47 -0800, D.Enrique ESCOBAR ESPINOZA wrote: > hi, > > In an effort to help the biolinux community > www.biolinux.org , > I put at your disposition > R-BioC for R 2.5.x for fedora core 6. > Comments for improvement will be welcome. > It is not an official fedora rpm because fedora plans to support only > R. > Unfortunatly is the only fc6 rpm for now but they are more for > previous fc > It works well, and it contains 102 very usefull sources: Instead of doing it like you've done, which is a massive overload on the package, it would be much better to package all of these items individually. For example, Fedora already has R-abind. I know that we have some active efforts in progress to package up all of the BioConductor RPMS, anyone want to chime in with a status report? ~spot From pingoufc4 at yahoo.fr Thu Dec 6 07:24:21 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 06 Dec 2007 08:24:21 +0100 Subject: [Fedora-r-devel-list] R-BioC rpm package In-Reply-To: <1196916505.3360.1.camel@localhost.localdomain> References: <352371.63519.qm@web30514.mail.mud.yahoo.com> <1196916505.3360.1.camel@localhost.localdomain> Message-ID: <4757A3A5.9080101@yahoo.fr> Tom "spot" Callaway wrote: > On Wed, 2007-12-05 at 19:47 -0800, D.Enrique ESCOBAR ESPINOZA wrote: >> hi, >> >> In an effort to help the biolinux community >> www.biolinux.org , >> I put at your disposition >> R-BioC for R 2.5.x for fedora core 6. >> Comments for improvement will be welcome. >> It is not an official fedora rpm because fedora plans to support only >> R. >> Unfortunatly is the only fc6 rpm for now but they are more for >> previous fc > For example, Fedora already has R-abind. > > I know that we have some active efforts in progress to package up all of > the BioConductor RPMS, anyone want to chime in with a status report? > Hi Fedora supports only R ? Below is an output of my yum list R-\* They are not all on the fedora repo yet, but there is several review in progress and more to come. You can see them all there http://pingoured.fr/public/fedora/SPECS/ available for Fedora 7 and Fedora 8 in i386 and x86_64. Would you like to be involved in this project (getting bioconductor on Fedora) ? Regards, Pierre ~pingou Installed Packages R.x86_64 2.6.1-1.fc8 installed R-ACME.x86_64 1.5.0-1.fc8 installed R-ALL.noarch 1.4.3-1.fc8 installed R-AnnotationDbi.noarch 1.1.6-1.fc8 installed R-BSgenome.noarch 1.7.0-1.fc8 installed R-BSgenome.Celegans.UCSC.ce2.noarch 1.2.0-3.fc8 installed R-BSgenome.Dmelanogaster.FlyBase.r51.noa 1.2.0-2.fc8 installed R-Biobase.x86_64 1.17.3-1.fc8 installed R-Biostrings.x86_64 2.7.2-1.fc8 installed R-BufferedMatrix.x86_64 1.3.0-1.fc8 installed R-BufferedMatrix-devel.x86_64 1.3.0-1.fc8 installed R-DBI.noarch 0.2-1.fc8 installed R-DynDoc.noarch 1.17.0-1.fc8 installed R-GO.noarch 2.0.1-1.fc8 installed R-KEGG.noarch 2.0.1-1.fc8 installed R-R2HTML.noarch 1.58-1.fc8 installed R-RColorBrewer.noarch 1.0-1.fc8 installed R-RSQLite.x86_64 0.5-1.fc8 installed R-RScaLAPACK.x86_64 0.5.1-10.fc8.1 installed R-RUnit.noarch 0.4.17-1.fc8 installed R-Rgraphviz.x86_64 1.17.7-1.fc8 installed R-SparseM.x86_64 0.74-1.fc8 installed R-XML.x86_64 1.9-1.fc8 installed R-abind.noarch 1.1-1.fc8 installed R-acepack.x86_64 1.3-2.fc8.1 installed R-affy.x86_64 1.17.2-2.fc8 installed R-affyPLM.x86_64 1.15.0-1.fc8 installed R-affyQCReport.noarch 1.17.0-1.fc8 installed R-affydata.noarch 1.11.2-1.fc8 installed R-affyio.x86_64 1.7.2-1.fc8 installed R-annaffy.noarch 1.11.0-1.fc8 installed R-annotate.noarch 1.17.1-3.fc8 installed R-devel.x86_64 2.6.1-1.fc8 installed R-fibroEset.noarch 1.4.2-1.fc8 installed R-gcrma.x86_64 2.11.0-1.fc8 installed R-genefilter.x86_64 1.17.2-1.fc8 installed R-geneplotter.noarch 1.17.0-1.fc8 installed R-graph.x86_64 1.17.10-1.fc8 installed R-hdf5.x86_64 1.6.6-2.fc8 installed R-hgu133a.noarch 1.16.0-1.fc8 installed R-hgu133acdf.noarch 1.16.0-1.fc8 installed R-hgu95aprobe.noarch 1.16.4-1.fc8 installed R-hgu95av2.noarch 1.16.0-1.fc8 installed R-hgu95av2.db.noarch 2.0.2-1.fc8 installed R-hgu95av2cdf.noarch 1.16.0-1.fc8 installed R-hgu95av2probe.noarch 1.16.3-2.fc8 installed R-hsahomology.noarch 1.16.0-1.fc8 installed R-hu6800.noarch 1.16.0-1.fc8 installed R-hu6800cdf.noarch 1.16.0-1.fc8 installed R-hu6800probe.noarch 1.16.2-1.fc8 installed R-limma.noarch 2.13.1-1.fc8 installed R-mAr.x86_64 1.1-11.fc8 installed R-maanova.x86_64 1.4.0-3.fc8 installed R-matchprobes.x86_64 1.11.0-1.fc8 installed R-multcomp.noarch 0.992-3.fc8 installed R-multtest.x86_64 1.19.0-1.fc8 installed R-mvtnorm.x86_64 0.8-3.fc8 installed R-pls.noarch 2.0-4.fc8 installed R-preprocessCore.x86_64 1.1.0-2.fc8 installed R-preprocessCore-devel.x86_64 1.1.0-2.fc8 installed R-qvalue.noarch 1.13.0-1.fc8 installed R-rae230a.noarch 1.16.0-2.fc8 installed R-rae230aprobe.noarch 1.16.2-2.fc8 installed R-randomForest.x86_64 4.5-1.fc8 installed R-rlecuyer.x86_64 0.1-3.fc8 installed R-siggenes.noarch 1.13.0-1.fc8 installed R-simpleaffy.x86_64 2.15.02-1.fc8 installed R-simpleaffy-devel.x86_64 2.15.02-1.fc8 installed R-systemfit.noarch 0.8-6.fc8 installed R-tkWidgets.noarch 1.16.0-1.fc8 installed R-vsn.x86_64 3.3.6-1.fc8 installed R-waveslim.x86_64 1.6-4.fc8 installed R-wavethresh.x86_64 2.2-7.fc8 installed R-widgetTools.noarch 1.15.0-1.fc8 installed R-xlahomology.noarch 1.16.0-1.fc8 installed R-xtable.noarch 1.5-1.fc8 installed ___________________________________________________________________________ Yahoo! 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