Dear All, I can confirm that the issue is fixed in the latest BioC / R versions.
Thanks a lot. Yours, Marcin On Fri, Oct 16, 2015 at 7:09 AM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel