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. 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?
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