Hej Martin! Changing the Import from IRanges to S4Vectors fixed it.
Thanks again, Nico --------------------------------------------------------------- Nicolas Delhomme, PhD Acting Manager UPSC bioinformatics core facility Umeå Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Umeå University Tel: +46 90 786 5478 Email: [email protected] SLU - Umeå universitet Umeå S-901 87 Sweden --------------------------------------------------------------- > On 20 Dec 2015, at 09:29, Morgan, Martin <[email protected]> > wrote: > > Hi Nico -- Hervé is on vacation until early January. My minimal example > 'works', so I wonder if this is a conflict with another package (does > S4Vectors::as.table(ovl) work?) or a unique feature of your HitsList? > traceback() output after the error might help. Martin > >> library(S4Vectors) >> as.table(split(Hits(1:2, 1:2, 2, 2), 1:2)) > range > 1 2 3 4 > 1 0 0 1 >> methods(as.table) > [1] as.table,ANY-method as.table.default as.table.ftable* > [4] as.table,HitsList-method as.table,Hits-method > see '?methods' for accessing help and source code >> sessionInfo() > R Under development (unstable) (2015-12-19 r69790) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 14.04.3 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] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] S4Vectors_0.9.15 BiocGenerics_0.17.2 BiocInstaller_1.21.2 > > loaded via a namespace (and not attached): > [1] IRanges_2.5.18 tools_3.3.0 > > > ________________________________________ > From: Bioc-devel [[email protected]] on behalf of Nicolas > Delhomme [[email protected]] > Sent: Sunday, December 20, 2015 3:10 AM > To: [email protected] > Subject: [Bioc-devel] as.table not available for HitsList anymore? > > Hej Hervé (I guess that ones for you :-)! > > In R dev / Bioc 3.3; calling as.table on an HitsList stopped working: > > Browse[2]> ovl > HitsList of length 6 > names(6): chr2L chr2R chr3L chr3R chr4 chrX > Browse[2]> as.table(ovl) > Error during wrapup: cannot coerce to a table > > I suppose this may have to do with the refactoring of the IRanges/S4Vectors > packages? Will the functionality be re-instated, or should I switch my code > to using as.matrix instead? > > My session info: > > R Under development (unstable) (2015-12-15 r69777) > Platform: x86_64-apple-darwin13.4.0 (64-bit) > Running under: OS X 10.11.2 (El Capitan) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RnaSeqTutorial_0.9.0 easyRNASeq_2.7.2 > > loaded via a namespace (and not attached): > [1] RColorBrewer_1.1-2 futile.logger_1.4.1 > [3] GenomeInfoDb_1.7.3 XVector_0.11.1 > [5] futile.options_1.0.0 bitops_1.0-6 > [7] tools_3.3.0 zlibbioc_1.17.0 > [9] biomaRt_2.27.2 annotate_1.49.0 > [11] RSQLite_1.0.0 lattice_0.20-33 > [13] DBI_0.3.1 parallel_3.3.0 > [15] DESeq_1.23.0 genefilter_1.53.0 > [17] hwriter_1.3.2 Biostrings_2.39.3 > [19] S4Vectors_0.9.15 IRanges_2.5.18 > [21] locfit_1.5-9.1 stats4_3.3.0 > [23] grid_3.3.0 LSD_3.0 > [25] Biobase_2.31.3 AnnotationDbi_1.33.3 > [27] XML_3.98-1.3 survival_2.38-3 > [29] BiocParallel_1.5.1 limma_3.27.6 > [31] latticeExtra_0.6-26 geneplotter_1.49.0 > [33] lambda.r_1.1.7 edgeR_3.13.4 > [35] intervals_0.15.1 Rsamtools_1.23.1 > [37] genomeIntervals_1.27.0 splines_3.3.0 > [39] BiocGenerics_0.17.2 GenomicAlignments_1.7.3 > [41] GenomicRanges_1.23.7 ShortRead_1.29.1 > [43] SummarizedExperiment_1.1.11 xtable_1.8-0 > [45] RCurl_1.95-4.7 > > Thanks! > > Nico > > PS Have a good Christmas time! > > --------------------------------------------------------------- > Nicolas Delhomme, PhD > > Acting Manager > UPSC bioinformatics core facility > Umeå Plant Science Center, > Swedish University for Agricultural > Sciences (SLU) and Umeå University > > Tel: +46 90 786 5478 > Email: [email protected] > SLU - Umeå universitet > Umeå S-901 87 Sweden > --------------------------------------------------------------- > > _______________________________________________ > [email protected] 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. _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
