On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> Hi Michael, > > On 10/15/2015 10:08 AM, Michael Lawrence wrote: > >> Tangentially related, it seems like nchar is worth defining in >> BiocGenerics, with a signature of "x". I saw that Biostrings uses "type", >> but I'm not sure why. >> > > The 2 "nchar" methods that dispatch on the 'type' argument are from > the Biostrings 1 era (> 9 years old) and were kept in the > Biostrings/Biostrings1/ folder for legacy only (this code doesn't > get evaluated, not even installed). That reminds me that it's probably > time to get rid of all that stuff. > > But if we're just going to use the signature of 'x', >> I can make nchar dispatch internally, so we don't need an R-level generic. >> Will that work? >> > > If by "make nchar dispatch internally" you mean "turn nchar() into a > primitive in R", like, say, length(), names(), dim(), dimnames(), `[`, > etc... then works for me. > > Essentially, yes. I've modified the methods package to support internal dispatch within .Internal() calls. So no need to make it a primitive. Will move ahead, thanks. > Thanks, > H. > > > >> Michael >> >> On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin < >> martin.mor...@roswellpark.org> wrote: >> >> >>> >>> -----Original Message----- >>>> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of >>>> Marcin Cieslik >>>> Sent: Thursday, October 15, 2015 7:46 AM >>>> To: bioc-devel@r-project.org >>>> Subject: [Bioc-devel] SV4Vectors installation problem >>>> >>>> Dear Bioconductors, >>>> >>>> Somewhere in August S4Vectors stopped installing correctly resulting in >>>> >>> a: >>> >>>> >>>> Creating a generic function for ‘nchar’ from package ‘base’ in package >>>> ‘S4Vectors’ >>>> >>>> message (that cannot be suppressed) each time the package is loaded. The >>>> issue is not fixed by a fresh reinstall of bioconductor. The first hint >>>> >>> of the >>> >>> you're right that this is a message and that it cannot be suppressed, but >>> the package still functions correctly, right? >>> >>> The problem was introduced by a change in R. The above is a work-around. >>> The permanent solution is now to use the current version of R (3.2.2) and >>> Bioc (3.2). The specific commit was >>> >>> ------------------------------------------------------------------------ >>> r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul >>> 2015) | 5 lines >>> >>> define nchar,Rle-method in .onLoad >>> >>> - work-around consequences of changed base::nchar signature for >>> 3.2.1 binary builds used in 3.2.0 >>> >>> ------------------------------------------------------------------------ >>> >>> some related / belated discussion is at >>> >>> https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html >>> >>> Martin >>> >>> >>> problem appears during installation >>>> >>>> http://pastebin.com/UpKdeNTH >>>> >>>> It appears I am not the only one affected a search reveals many >>>> >>> instances: >>> >>>> >>>> e.g. >>>> https://rpubs.com/Pazz/advanced_annotation >>>> http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- >>>> LATEST/S4Vectors/petty-install.html >>>> http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html >>>> >>>> Thanks a lot for your work! If needed I can provide a Docker image that >>>> reproduces the problem. >>>> >>>> Yours, >>>> Marcin >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee >>> or >>> agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> [[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