[Bioc-devel] report a minor bug in GenomicRanges

[Hervé Pagès]

On 03/21/2014 11:33 AM, Ou, Jianhong wrote:
> Yes, I am calling reduce on a GRanges object. I just hate any warning or
> error message. That's all.

I'm sympathetic: I hate them too :-)

So in GenomicRanges 1.15.40 (should become available tomorrow), you
should be able to use the new 'with.revmap' arg when reducing your
GRanges object. That will get rid of the warning.

Let me know if you run into any further issue with this.

Thanks,
H.

>
> Yours Sincerely,
>
> Jianhong Ou
>
> LRB 670A
> Program in Gene Function and Expression
> 364 Plantation Street Worcester,
> MA 01605
>
>
>
>
> On 3/21/14 1:26 PM, "Hervé Pagès" <hpages at fhcrc.org> wrote:
>
>> Hi Jianhong,
>>
>> On 03/21/2014 07:01 AM, Ou, Jianhong wrote:
>>> Hi,
>>>
>>> When I run sample code for reduce, I got Warning message:
>>>     The 'with.mapping' argument is deprecated.
>>>     Please use the 'with.revmap' argument instead.
>>
>> Not really a bug, just a warning that the 'with.mapping' arg is being
>> replaced by the 'with.revmap' arg, except that 'with.revmap' is not
>> available yet when reducing a GRanges object... sorry :-/ Will be in
>> the next couple of days.
>>
>> Note that it's already available when reducing an IRanges object,
>> but I suspect in your case you're calling reduce() on a GRanges object
>> right?
>>
>> Thanks,
>> H.
>>
>>>
>>> Yours Sincerely,
>>>
>>> Jianhong Ou
>>>
>>> LRB 670A
>>> Program in Gene Function and Expression
>>> 364 Plantation Street Worcester,
>>> MA 01605
>>>
>>> 	[[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 fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>

-- 
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 fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319