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. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel