Re: [Bioc-devel] [[- method dispatch and GenomicRanges
Hi Herve, I reinstalled AnnotationDbi 1.25.17, and now things work flawlessly. Thank you for your help! Michael On 09.04.2014 19:25, Hervé Pagès wrote: Hi Michael, Because of a recent change to IRanges, some information about the as.list method table is now out-of-sync in your installed AnnotationDbi (granted it was installed before the new IRanges propagated to you). Re-installing AnnotationDbi should clear this. I bumped AnnotationDbi version yesterday night (even though AnnotationDbi has not changed) to help clear this up for other users. The new version won't become available before tomorrow though. But, again, this new version (1.25.18) is similar to the current version (1.25.17), so you can re-install now with biocLite(AnnotationDbi). No need to wait until tomorrow. HTH, H. On 04/09/2014 12:23 AM, Michael Stadler wrote: Dear Bioc gurus, Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some unit tests, which turns out to be reproducible independent of QuasR and might be related to R getting the wrong method for [[-. The following works fine... library(GenomicRanges) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) ...but this produces an error: library(GenomicRanges) library(GenomicFeatures) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) #Error in as.list(x, use.names = FALSE) : # could not find function .as.list.CompressedList My guess is that loading the GenomicFeatures library in addition to GenomicRanges influences the methods dispatch, but with my limited understanding of R and S4 classes I was not able to narrow it further down. I noticed that I am using a slightly older version of R (r65206) compared to the build system (r65358), however I also see the error with the most recent release candidate (r65385). Michael My session info: R version 3.1.0 alpha (2014-03-17 r65206) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30IRanges_1.21.43 [7] BiocGenerics_0.9.3 RColorBrewer_1.0-5 loaded via a namespace (and not attached): [1] BBmisc_1.5BSgenome_1.31.13 [3] BatchJobs_1.2 BiocParallel_0.5.19 [5] Biostrings_2.31.21DBI_0.2-7 [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1 [9] RSQLite_0.11.4Rcpp_0.11.1 [11] Rsamtools_1.15.41 XML_3.98-1.1 [13] XVector_0.3.7 biomaRt_2.19.3 [15] bitops_1.0-6 brew_1.0-6 [17] codetools_0.2-8 digest_0.6.4 [19] fail_1.2 foreach_1.4.1 [21] iterators_1.0.6 plyr_1.8.1 [23] rtracklayer_1.23.22 sendmailR_1.1-2 [25] stats4_3.1.0 stringr_0.6.2 [27] tools_3.1.0 zlibbioc_1.9.0 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Michael Stadler, PhD Head of Computational Biology Friedrich Miescher Institute Basel (Switzerland) Phone : +41 61 697 6492 Fax : +41 61 697 3976 Mail : michael.stad...@fmi.ch ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] [[- method dispatch and GenomicRanges
i can't confirm this library(GenomicRanges) Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from 'package:stats': xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges Loading required package: GenomeInfoDb library(GenomicFeatures) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation(Biobase)', and for packages 'citation(pkgname)'. grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), +r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) sessionInfo() R version 3.1.0 alpha (2014-03-19 r65222) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C [3] LC_TIME=en_US.iso88591LC_COLLATE=en_US.iso88591 [5] LC_MONETARY=en_US.iso88591LC_MESSAGES=en_US.iso88591 [7] LC_PAPER=en_US.iso88591 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30IRanges_1.21.43 [7] BiocGenerics_0.9.3 weaver_1.29.1 codetools_0.2-8 [10] digest_0.6.4BiocInstaller_1.13.3 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.5 [3] BiocParallel_0.5.19 biomaRt_2.19.3 [5] Biostrings_2.31.21bitops_1.0-6 [7] brew_1.0-6BSgenome_1.31.13 [9] DBI_0.2-7 fail_1.2 [11] foreach_1.4.1 GenomicAlignments_0.99.37 [13] iterators_1.0.6 plyr_1.8.1 [15] Rcpp_0.11.1 RCurl_1.95-4.1 [17] Rsamtools_1.15.41 RSQLite_0.11.4 [19] rtracklayer_1.23.22 sendmailR_1.1-2 [21] stats4_3.1.0 stringr_0.6.2 [23] XML_3.98-1.1 XVector_0.3.7 [25] zlibbioc_1.9.0 On Wed, Apr 9, 2014 at 3:23 AM, Michael Stadler michael.stad...@fmi.chwrote: Dear Bioc gurus, Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some unit tests, which turns out to be reproducible independent of QuasR and might be related to R getting the wrong method for [[-. The following works fine... library(GenomicRanges) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) ...but this produces an error: library(GenomicRanges) library(GenomicFeatures) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) #Error in as.list(x, use.names = FALSE) : # could not find function .as.list.CompressedList My guess is that loading the GenomicFeatures library in addition to GenomicRanges influences the methods dispatch, but with my limited understanding of R and S4 classes I was not able to narrow it further down. I noticed that I am using a slightly older version of R (r65206) compared to the build system (r65358), however I also see the error with the most recent release candidate (r65385). Michael My session info: R version 3.1.0 alpha (2014-03-17 r65206) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30IRanges_1.21.43 [7] BiocGenerics_0.9.3 RColorBrewer_1.0-5 loaded via a namespace (and not attached): [1] BBmisc_1.5BSgenome_1.31.13 [3] BatchJobs_1.2 BiocParallel_0.5.19 [5] Biostrings_2.31.21DBI_0.2-7 [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1 [9] RSQLite_0.11.4Rcpp_0.11.1 [11] Rsamtools_1.15.41 XML_3.98-1.1 [13] XVector_0.3.7 biomaRt_2.19.3 [15] bitops_1.0-6 brew_1.0-6 [17] codetools_0.2-8 digest_0.6.4 [19] fail_1.2 foreach_1.4.1
Re: [Bioc-devel] [[- method dispatch and GenomicRanges
Hi Michael, Because of a recent change to IRanges, some information about the as.list method table is now out-of-sync in your installed AnnotationDbi (granted it was installed before the new IRanges propagated to you). Re-installing AnnotationDbi should clear this. I bumped AnnotationDbi version yesterday night (even though AnnotationDbi has not changed) to help clear this up for other users. The new version won't become available before tomorrow though. But, again, this new version (1.25.18) is similar to the current version (1.25.17), so you can re-install now with biocLite(AnnotationDbi). No need to wait until tomorrow. HTH, H. On 04/09/2014 12:23 AM, Michael Stadler wrote: Dear Bioc gurus, Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some unit tests, which turns out to be reproducible independent of QuasR and might be related to R getting the wrong method for [[-. The following works fine... library(GenomicRanges) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) ...but this produces an error: library(GenomicRanges) library(GenomicFeatures) grl - GRangesList(r1=GRanges(chr1,IRanges(1,2)), r2=GRanges(chr2,IRanges(3,4))) grl[[1]] - GRanges(chr1,IRanges(10,11)) #Error in as.list(x, use.names = FALSE) : # could not find function .as.list.CompressedList My guess is that loading the GenomicFeatures library in addition to GenomicRanges influences the methods dispatch, but with my limited understanding of R and S4 classes I was not able to narrow it further down. I noticed that I am using a slightly older version of R (r65206) compared to the build system (r65358), however I also see the error with the most recent release candidate (r65385). Michael My session info: R version 3.1.0 alpha (2014-03-17 r65206) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30IRanges_1.21.43 [7] BiocGenerics_0.9.3 RColorBrewer_1.0-5 loaded via a namespace (and not attached): [1] BBmisc_1.5BSgenome_1.31.13 [3] BatchJobs_1.2 BiocParallel_0.5.19 [5] Biostrings_2.31.21DBI_0.2-7 [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1 [9] RSQLite_0.11.4Rcpp_0.11.1 [11] Rsamtools_1.15.41 XML_3.98-1.1 [13] XVector_0.3.7 biomaRt_2.19.3 [15] bitops_1.0-6 brew_1.0-6 [17] codetools_0.2-8 digest_0.6.4 [19] fail_1.2 foreach_1.4.1 [21] iterators_1.0.6 plyr_1.8.1 [23] rtracklayer_1.23.22 sendmailR_1.1-2 [25] stats4_3.1.0 stringr_0.6.2 [27] tools_3.1.0 zlibbioc_1.9.0 ___ 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...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
