I will commit my fix to coMET and cross fingers that the error doesn't appear in the build system
Tiphaine ________________________________________ From: Hervé Pagès <hpa...@fredhutch.org> Sent: 10 April 2015 20:30 To: Michael Lawrence; Martin, Tiphaine Cc: bioc-devel Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’ On 04/10/2015 11:45 AM, Michael Lawrence wrote: > The score generic was removed from IRanges in version 2.1.41. So your > IRanges is up to date. My guess is that something is cached and you need > to reinstall one or more of the other Bioc infrastructure packages... That's a good point. In any case, this should not prevent you from committing your fix to coMET. The issue is specific to the state of your current installation and it won't show up on the build system (where all dependencies are re-installed every day at the beginning of the builds). Also, for you, the issue will automatically go away when all package versions get bumped the day of the release. Cheers, H. > > On Fri, Apr 10, 2015 at 11:35 AM, Martin, Tiphaine > <tiphaine.mar...@kcl.ac.uk <mailto:tiphaine.mar...@kcl.ac.uk>> wrote: > > Hi Herve, > > When I tried to update IRanges, I have only the version 2.1.43 and > not 2.1.44. > How to force BiocLite to have the lastest version of IRanges. did I > miss something? > > source("http://bioconductor.org/biocLite.R";) > Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help > biocLite("IRanges") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0. > Installing package(s) ‘IRanges’ > trying URL > > 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.43.tar.gz' > > > Tiphaine > > ________________________________________ > From: Hervé Pagès <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> > Sent: 10 April 2015 19:20 > To: Martin, Tiphaine; bioc-devel > Subject: Re: [Bioc-devel] Warning message: multiple methods tables > found for ‘score’ > > Hi Martin, > > On 04/10/2015 11:12 AM, Martin, Tiphaine wrote: > > Dear Everybody, > > > > > > I updated my package because I have an error message. Before > submitting my package on svn, I run > > > > R CMD check coMET > > > > I receive a new error message: > > > > > > Warning message: > > multiple methods tables found for �score� > > > > > > If I am looking at the reference manual of IRanges, I see that > there is the function "score" and before updating, when I run > ?score, the function "score" belonged to the package IRanges > > > > But now when I run ?score, the function "score" belongs to the > package:BiocGenerics. > > > > > > I am wondering if there is an conflict between two packages. How > can I manage it? > > AFAIK there is no conflict. Your IRanges version is probably lagging > behind. Remember to keep your installation up-to-date by running > biocLite() (with no arguments) on a regular basis. > > > > > How can I know which packages have the function "score"? > > Only the BiocGenerics package now defines the score() generic. There is > no score() generic in the latest IRanges (2.1.44). > > Thanks for taking care of coMET. > > H. > > > > > > > Thanks, > > > > Tiphaine > > > > > > ---------------------------- > > Tiphaine Martin > > PhD Research Student | King's College > > The Department of Twin Research & Genetic Epidemiology | Genetics > & Molecular Medicine Division > > St Thomas' Hospital > > 4th Floor, Block D, South Wing > > SE1 7EH, London > > United Kingdom > > > > email : tiphaine.mar...@kcl.ac.uk <mailto:tiphaine.mar...@kcl.ac.uk> > > Fax: +44 (0) 207 188 6761 <tel:%2B44%20%280%29%20207%20188%206761> > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> > Phone: (206) 667-5791 <tel:%28206%29%20667-5791> > Fax: (206) 667-1319 <tel:%28206%29%20667-1319> > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
