Great! Just re-installing the packages via biocLite() would have been sufficient. Martin ________________________________________ From: Sonali B Arora [sar...@fredhutch.org] Sent: Monday, December 21, 2015 4:56 PM To: Morgan, Martin; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’
Hi Martin, Thanks for the quick explanation. I got the latest version of the packages mentioned below from svn - and installed them using Herve's HTS core package stack (http://www.bioconductor.org/help/newsletters/2015_October/#hts-core-package-stack) and I don't see the problem any more. > library(AnnotationHub) > ah =AnnotationHub() snapshotDate(): 2015-11-19 > ah = query(ah , c("Homo sapiens", "org", "GRCH37", "FASTA","75")) > hg37_rrna = ah[["AH10879"]] require(“Rsamtools”) downloading from ‘https://annotationhub.bioconductor.org/fetch/10879’ ‘https://annotationhub.bioconductor.org/fetch/14665’ retrieving 2 resources |======================================================================| 100% |======================================================================| 100% There were 50 or more warnings (use warnings() to see the first 50) Val, thanks for adding the stack to the newsletter ! FYI - I dont see it here - http://www.bioconductor.org/packages/devel/bioc/html/S4Vectors.html under the documentation section. Thanks and Regards, Sonali. On 12/21/2015 1:33 PM, Morgan, Martin wrote: > Hi Sonali -- > > relistToClass was originally in IRanges > > Packages such as Biostrings that Depend: or Import: IRanges and then create a > 'relistToClass' method created a methods table on INSTALLATION, noting that > the generic is in IRanges. > > The 'relistToClass' generic was moved from IRanges to S4Vectors, with > appropriate version bumps for these packages. > > Loading the 'old' version of Biostrings (library(Biostrings)) now sees a new > generic in S4Vectors, but has the old methods table that thinks the methods > are being added to the IRanges generic. > > This results in the warning "multiple methods tables found for > ‘relistToClass’". > > The end-user solution is to re-install the Biostrings package > (biocLite("Biostrings")). This will use the correct methods table. > > Any package that defines a method on relistToClass requires updating; there > are similar problems with 'space' and 'unlist'. I believe the 'core' packages > requiring updating (defining methods, but svn revision older than r111605) > include c("GenomicRanges", "rtracklayer", "GenomicAlignments", "Biostrings", > "BSgenome", "VariantAnnotation"). > > Please let me know if the problem continues after re-installing these > packages. > > I have bumped the versions of each of these packages, so that biocLite() > after tomorrow-ish should force these to be re-installed. > > Usually 'multiple methods tables' is a warning; AnnotationHub:::.require > promotes the warning to an error. > > Martin > > ________________________________________ > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Sonali B > Arora [sar...@fredhutch.org] > Sent: Monday, December 21, 2015 3:08 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple > methods tables found for ‘relistToClass’ > > Hi everyone, > > I am trying to get a FaFile from AnnotationHub - It fails with the > following error > > library(AnnotationHub) > ah =AnnotationHub() > ah = query(ah , c("Homo sapiens", "org", "GRCH37", "FASTA","75")) > hg37_rna = ah[["AH10879"]] > > > hg37_rna = ah[["AH10879"]] > require(“Rsamtools”) > Error: failed to load 'AnnotationHub' resource > name: AH10879 > title: Homo_sapiens.GRCh37.75.ncrna.fa > reason: require(“Rsamtools”) failed: multiple methods tables found > for ‘relistToClass’ > > > > sessionInfo() > R Under development (unstable) (2015-10-15 r69519) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 14.04.2 LTS > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GenomeInfoDb_1.7.3 IRanges_2.5.18 S4Vectors_0.9.15 > [4] AnnotationHub_2.3.6 BiocGenerics_0.17.2 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.2 AnnotationDbi_1.33.3 > [3] magrittr_1.5 zlibbioc_1.17.0 > [5] xtable_1.8-0 R6_2.1.1 > [7] stringr_1.0.0 httr_1.0.0 > [9] tools_3.3.0 Biobase_2.31.3 > [11] DBI_0.3.1 htmltools_0.2.6 > [13] digest_0.6.8 interactiveDisplayBase_1.9.0 > [15] shiny_0.12.2 curl_0.9.4 > [17] RSQLite_1.0.0 mime_0.4 > [19] stringi_1.0-1 BiocInstaller_1.21.2 > [21] httpuv_1.3.3 > > > -- > Thanks and Regards, > Sonali > Office: C2-169 > http://tinyurl.com/sonali-hb-calendar > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. 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