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

Morgan, Martin Martin.Morgan at roswellpark.org
Sun Dec 20 09:29:47 CET 2015

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))
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

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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)

[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



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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