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

[Nicolas Delhomme]

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
---------------------------------------------------------------