> -----Original Message----- > From: Bioc-devel [mailto:[email protected]] On Behalf Of > Marcin Cieslik > Sent: Thursday, October 15, 2015 7:46 AM > To: [email protected] > 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 | [email protected] | 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]] > > _______________________________________________ > [email protected] 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. _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
