Thanks a lot for your help Martin ! I didn't understand clearly the solution with the snapshot, but I can finally use the DEXSeq package and I ran all the pasilla example given in the vignette without crashing ! So I hope it will work on my dataset too. Since I only need this version of R for the DEXSeq package, I can still use the version 2.13 if something is not working on 2.14. I hope so !
Thank you again, Jane 2011/7/25 Martin Morgan <mtmor...@fhcrc.org> > On 07/25/2011 05:13 AM, Martin Morgan wrote: > >> On 07/25/2011 02:28 AM, Jane Merlevede wrote: >> >>> Hello, >>> >>> As you advise me, I installed R version 2.14 but I can't use the DEXSeq >>> library: package "DEXSeq is not available (for R Under >>> development)"... Do you know why? >>> >> >> It's a Bioconductor package, installed the Bioconductor way, >> >> http://bioconductor.org/**install/ <http://bioconductor.org/install/> >> >> that is, >> >> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R> >> ") >> biocLite("DEXSeq") >> library(DEXSeq) >> >> Glad the installation went ok, and I think DEXSeq will install correctly >> for you. >> >> Usually the 'devel' branch of R is quite stable, but actually just at >> the moment there is some instability and you might experience problems >> when trying to install or load some package combinations. One error >> message is >> >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "[", for signature >> "signature" >> Error: loading failed >> >> and unfortunately the only really accessible solution, if you encounter >> this at a crucial stage of your analysis, is to wait a few days and >> update your R. >> > > Actually, a solution is to build R from a snapshot several days ago, before > 2011-07-21 from > > ftp://ftp.stat.math.ethz.ch/**Software/R<ftp://ftp.stat.math.ethz.ch/Software/R> > > Martin > > >> Martin >> >> Thanks, >>> Jane >>> >>> >>> >R.2.14 >>> >>> R Under development (unstable) (2011-07-24 r56492) >>> Copyright (C) 2011 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R est un logiciel libre livré sans AUCUNE GARANTIE. >>> Vous pouvez le redistribuer sous certaines conditions. >>> Tapez 'license()' ou 'licence()' pour plus de détails. >>> >>> R est un projet collaboratif avec de nombreux contributeurs. >>> Tapez 'contributors()' pour plus d'information et >>> 'citation()' pour la façon de le citer dans les publications. >>> >>> Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide >>> en ligne ou 'help.start()' pour obtenir l'aide au format HTML. >>> Tapez 'q()' pour quitter R. >>> >>> > install.packages("DEXSeq") >>> --- SVP sélectionner un miroir CRAN pour cette session --- >>> CRAN mirror >>> >>> 1: Argentina (La Plata) 2: Argentina (Mendoza) >>> 3: Australia (Canberra) 4: Australia (Melbourne) >>> 5: Austria 6: Belgium >>> 7: Brazil (PR) 8: Brazil (RJ) >>> 9: Brazil (SP 1) 10: Brazil (SP 2) >>> 11: Canada (BC) 12: Canada (NS) >>> 13: Canada (ON) 14: Canada (QC 1) >>> 15: Canada (QC 2) 16: Chile >>> 17: China (Beijing 1) 18: China (Beijing 2) >>> 19: China (Hefei) 20: China (Hong Kong) >>> 21: China (Xiamen) 22: Colombia (Bogota) >>> 23: Colombia (Cali) 24: Denmark >>> 25: France (Toulouse) 26: France (Lyon 1) >>> 27: France (Lyon 2) 28: Germany (Berlin) >>> 29: Germany (Goettingen) 30: Germany (Muenchen) >>> 31: Germany (Wiesbaden) 32: Greece >>> 33: Indonesia 34: Iran >>> 35: Ireland 36: Italy (Milano) >>> 37: Italy (Padua) 38: Italy (Palermo) >>> 39: Japan (Hyogo) 40: Japan (Tsukuba) >>> 41: Korea 42: Mexico (Mexico City) >>> 43: Mexico (Texcoco) 44: Netherlands (Amsterdam) >>> 45: Netherlands (Utrecht) 46: New Zealand >>> 47: Norway 48: Philippines >>> 49: Poland (Gdansk) 50: Poland (Oswiecim) >>> 51: Poland (Wroclaw) 52: Russia >>> 53: Singapore 54: Slovakia 1 >>> 55: Slovakia 2 56: South Africa >>> 57: Spain (Madrid) 58: Sweden >>> 59: Switzerland 60: Taiwan (Taichung) >>> 61: Taiwan (Taipei 1) 62: Taiwan (Taipei 2) >>> 63: Thailand 64: UK (Bristol) >>> 65: UK (London) 66: UK (St Andrews) >>> 67: USA (AZ) 68: USA (CA 1) >>> 69: USA (CA 2) 70: USA (IA) >>> 71: USA (MA) 72: USA (MI) >>> 73: USA (MO) 74: USA (OH) >>> 75: USA (OR) 76: USA (PA 1) >>> 77: USA (PA 2) 78: USA (TX 1) >>> 79: USA (TX 2) 80: USA (WA 1) >>> 81: USA (WA 2) >>> >>> Sélection : 26 >>> Message d'avis : >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package DEXSeq is not available (for R Under development) >>> > >>> >>> >>> >>> 2011/7/24 Martin Morgan <mtmor...@fhcrc.org <mailto:mtmor...@fhcrc.org>> >>> >>> >>> On 07/22/2011 07:40 AM, Jane Merlevede wrote: >>> >>> Hello, >>> >>> I have used DESeq for gene differential expression analysis and >>> I would like >>> to use DEXSeq now for exon differential expression analysis. >>> The point is that the library DEXSeq seems to be available only >>> in R version >>> 2.14.0 (unstable). I am working on Linux (CentOS), with R >>> version 2.13.0. I >>> have not found this R version 2.14.0 for Linux... Finally, I >>> cannot use >>> DEXSeq. >>> I would like to know if DEXSeq will be soon available in R >>> version 2.13.0. >>> Or is the only solution to work with Windows? >>> >>> >>> As Sean mentions, this requires R-devel. It is not that difficult to >>> build R from source on Linux, see sections 1 and 2 of >>> >>> http://cran.fhcrc.org/doc/__**manuals/R-admin.html<http://cran.fhcrc.org/doc/__manuals/R-admin.html> >>> <http://cran.fhcrc.org/doc/**manuals/R-admin.html<http://cran.fhcrc.org/doc/manuals/R-admin.html> >>> > >>> >>> The source code is available here >>> >>> http://cran.fhcrc.org/sources.**__html<http://cran.fhcrc.org/sources.__html> >>> <http://cran.fhcrc.org/**sources.html<http://cran.fhcrc.org/sources.html> >>> > >>> >>> you are looking for R-devel.tar.gz >>> >>> Martin >>> >>> >>> Thank you for your help, >>> Jane Merlevède >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> ______________________________**___________________ >>> Bioc-sig-sequencing mailing list >>> Bioc-sig-sequencing@r-project.**__org >>> <mailto:Bioc-sig-sequencing@r-**project.org<Bioc-sig-sequencing@r-project.org> >>> > >>> >>> https://stat.ethz.ch/mailman/_**_listinfo/bioc-sig-sequencing<https://stat.ethz.ch/mailman/__listinfo/bioc-sig-sequencing> >>> <https://stat.ethz.ch/mailman/**listinfo/bioc-sig-sequencing<https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing> >>> > >>> >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> >>> >> >> > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]
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