On 26 Dec 2015, at 07:46, Herv? Pag?s <hpages at 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
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
---------------------------------------------------------------