[Bioc-devel] as.table not available for HitsList anymore?

Nicolas Delhomme nicolas.delhomme at umu.se
Sun Dec 20 17:02:35 CET 2015


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: nicolas.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

> On 20 Dec 2015, at 09:29, Morgan, Martin <Martin.Morgan at roswellpark.org> 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 [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 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: nicolas.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
> 
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