[Bioc-devel] SV4Vectors installation problem

[Hervé Pagès]

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
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

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