[Bioc-devel] SV4Vectors installation problem

wrote:

On Thu, Oct 15, 2015 at 11:04 PM, Herv? Pag?s <hpages at fredhutch.org>
wrote:

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.

Essentially, yes. I've modified the methods package to support internal
dispatch within .Internal() calls. So no need to make it a primitive. Will
move ahead, thanks.

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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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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