Done in SGSeq 1.6.3 (release) and 1.7.4 (devel). Also done in SomaticSignatures 2.8.4 (release) and 2.9.4 (devel).
I scanned the entire Rpacks folder and those are the only 2 packages I found that contain calls to granges() with 2 unnamed arguments. Sorry for the trouble. H. On 06/16/2016 11:55 PM, Hervé Pagès wrote:
Hi Leonard, I really like having 'use.names' before 'use.mcols'. Sorry for breaking SGSeq, I'll fix it. FWIW I think it's good practice to always name this kind of arguments. Not the first argument 'x' or the first 2 arguments 'x' and 'y' of a unary or binary function, but the toggles that follow them like 'use.names', 'use.mcols', 'ignore.strand' etc.. That makes the code a lot more readable. Cheers, H. On 06/16/2016 04:46 PM, Leonard Goldstein wrote:Hi Hervé, I noticed a recent change in the release and development version of GenomicRanges, which introduces a new argument 'use.names' for granges() and other functions. The change breaks the SGSeq package, since it uses granges() relying on positional argument matching (and 'use.names' has been added preceding existing arguments). Should GenomicRanges be changed so that newly arguments occur after existing arguments? Otherwise I can fix the problem in SGSeq. Many thanks, Leonard [[alternative HTML version deleted]] _______________________________________________ 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
