[Bioc-devel] SV4Vectors installation problem

[Morgan, Martin]

> -----Original Message-----
> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
> Marcin Cieslik
> Sent: Thursday, October 15, 2015 7:46 AM
> To: bioc-devel at 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 | mtmorgan at 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]]
> 
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