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List:       bioc-devel
Subject:    Re: [Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps
From:       Nicolas Delhomme <nicolas.delhomme () umu ! se>
Date:       2015-12-26 10:13:40
Message-ID: 642BF66A-ED22-4085-8C08-4DA81AFE5723 () umu ! se
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Hej Hervé!

This is now working for me and it also builds fine on Bioc.

I tend to use biocValid(fix=TRUE) and if I've understood the output correctly, it \
seems to me that the function will fetch the most recent version available, building \
it from source if necessary.

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@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

> On 26 Dec 2015, at 07:46, Hervé Pagès <hpages@fredhutch.org> wrote:
> 
> 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@umu.se
> > SLU - Umeå universitet
> > Umeå S-901 87 Sweden
> > ---------------------------------------------------------------
> > 
> > _______________________________________________
> > Bioc-devel@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@fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

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