Thanks Hervé. Leonard
On Fri, Jun 17, 2016 at 2:11 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > 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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
