[Bioc-devel] SV4Vectors installation problem

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.

Thanks,
H.

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

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