[Bioc-devel] SV4Vectors installation problem

[Michael Lawrence]

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.Morgan at roswellpark.org> wrote:

>
>
> > -----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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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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