[Bioc-devel] SV4Vectors installation problem

Michael Lawrence lawrence.michael at gene.com
Fri Oct 16 13:09:45 CEST 2015


On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès <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
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information.  If you are not the intended recipient(s), or the employee
>>> or
>>> agent responsible for the delivery of this message to the intended
>>> recipient(s), you are hereby notified that any disclosure, copying,
>>> distribution, or use of this email message is prohibited.  If you have
>>> received this message in error, please notify the sender immediately by
>>> e-mail and delete this email message from your computer. Thank you.
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]



More information about the Bioc-devel mailing list