[Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps

[Hervé Pagès]

Hi Nico,

The current version of GenomicAlignments is 1.7.8. Unfortunately the
Mavericks binary that is currently available via biocLite() is lagging
behind (1.7.3) so you need to install the latest GenomicAlignments from
source:

   biocLite("GenomicAlignments", type="source")

Hopefully you'll be able to update all your packages from source
with biocLite(type="source") (untested, hope this works for you).

Cheers,
H.

On 12/21/2015 07:22 AM, Nicolas Delhomme wrote:
> Hej!
>
> I'm getting this error when using summarizrOverlaps:
>
>   Error in findOverlaps(features, reads, algorithm = match.arg(algorithm),  :
>    could not find symbol "algorithm" in environment of the generic function
>
> Here is the stack:
>
> 16: summarizeOverlaps(features, chunk, ignore.strand = !stranded, inter.feature
> 17: .local(features, reads, mode, algorithm, ignore.strand, ...)
> 18: .dispatchOverlaps(features, reads, mode, match.arg(algorithm), ignore.stran
> 19: mode(features, reads, algorithm = algorithm, ignore.strand = ignore.strand,
> 20: findOverlaps(features, reads, algorithm = match.arg(algorithm), ignore.stra
>
> As it looks, it seems that summarizeOverlaps through its dispatch provide the argument algorithm to the findOverlaps function, which now does not support that argument anymore.
>
> Here's my sessionInfo:
>
> 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] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>   [1] GenomicAlignments_1.7.3     Rsamtools_1.23.1
>   [3] Biostrings_2.39.3           XVector_0.11.1
>   [5] SummarizedExperiment_1.1.11 Biobase_2.31.3
>   [7] GenomicRanges_1.23.7        GenomeInfoDb_1.7.3
>   [9] IRanges_2.5.18              S4Vectors_0.9.15
> [11] BiocGenerics_0.17.2         BiocInstaller_1.21.2
> [13] RnaSeqTutorial_0.9.0        RUnit_0.4.31
> [15] easyRNASeq_2.7.1
>
> loaded via a namespace (and not attached):
>   [1] RColorBrewer_1.1-2     futile.logger_1.4.1    tools_3.3.0
>   [4] futile.options_1.0.0   bitops_1.0-6           zlibbioc_1.17.0
>   [7] biomaRt_2.27.2         annotate_1.49.0        RSQLite_1.0.0
> [10] lattice_0.20-33        DBI_0.3.1              DESeq_1.23.0
> [13] genefilter_1.53.0      hwriter_1.3.2          locfit_1.5-9.1
> [16] grid_3.3.0             LSD_3.0                AnnotationDbi_1.33.3
> [19] XML_3.98-1.3           survival_2.38-3        BiocParallel_1.5.1
> [22] limma_3.27.6           latticeExtra_0.6-26    geneplotter_1.49.0
> [25] lambda.r_1.1.7         edgeR_3.13.4           intervals_0.15.1
> [28] genomeIntervals_1.27.0 splines_3.3.0          ShortRead_1.29.1
> [31] xtable_1.8-0           RCurl_1.95-4.7
>
>
> Am I overlooking something or is it just that I got slightly out of sync packages?
>
> Cheers,
>
> 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
> ---------------------------------------------------------------
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
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