Message-ID: <297E0900-6E9B-4341-BDF4-A04D54AEA854@umu.se>
Date: 2015-12-20T16:02:35Z
From: Nicolas Delhomme
Subject: [Bioc-devel] as.table not available for HitsList anymore?
In-Reply-To: <DF23DAC5A53912408040FF04D8B780AAE42394@EXMB3RSC.roswellpark.org>
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
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>
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