Hej Herv? (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 Ume? Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Ume? University Tel: +46 90 786 5478 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? S-901 87 Sweden ---------------------------------------------------------------
[Bioc-devel] as.table not available for HitsList anymore?
3 messages · Martin Morgan, Nicolas Delhomme
Hi Nico -- Herv? 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 [bioc-devel-bounces at r-project.org] on behalf of Nicolas Delhomme [nicolas.delhomme at umu.se]
Sent: Sunday, December 20, 2015 3:10 AM
To: Bioc-devel at r-project.org
Subject: [Bioc-devel] as.table not available for HitsList anymore?
Sent: Sunday, December 20, 2015 3:10 AM
To: Bioc-devel at r-project.org
Subject: [Bioc-devel] as.table not available for HitsList anymore?
Hej Herv? (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 Ume? Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Ume? University Tel: +46 90 786 5478 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? S-901 87 Sweden --------------------------------------------------------------- _______________________________________________ Bioc-devel at 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.
Hej Martin! Changing the Import from IRanges to S4Vectors fixed it. Thanks again, Nico --------------------------------------------------------------- Nicolas Delhomme, PhD Acting Manager UPSC bioinformatics core facility Ume? Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Ume? University Tel: +46 90 786 5478 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? S-901 87 Sweden ---------------------------------------------------------------
On 20 Dec 2015, at 09:29, Morgan, Martin <Martin.Morgan at roswellpark.org> wrote: Hi Nico -- Herv? 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 [bioc-devel-bounces at r-project.org] on behalf of Nicolas Delhomme [nicolas.delhomme at umu.se] Sent: Sunday, December 20, 2015 3:10 AM To: Bioc-devel at r-project.org Subject: [Bioc-devel] as.table not available for HitsList anymore? Hej Herv? (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 Ume? Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Ume? University Tel: +46 90 786 5478 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? S-901 87 Sweden --------------------------------------------------------------- _______________________________________________ Bioc-devel at 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.