[Bioc-devel] Bug tracker for Bioconductor?

Sean Davis sdavis2 at mail.nih.gov
Fri May 23 22:41:44 CEST 2014


On Fri, May 23, 2014 at 4:34 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> I like the idea about extracting important environmental information.
> Possibly the function that browses to the bug tracker could print out the
> sessionInfo for copy/paste.
>
> It is tempting to push the automation further, e.g. talking to github via a
> web API to pre-populate, but it's a slippery slope and I'm not sure if we
> want to invest in a full bug tracking abstraction. Not only would you need
> to worry about filing bugs, but also searching them (to avoid duplication),
> and watching/monitoring them.  Would rather leave all that to the trackers
> and assume users are comfortable using a web browser, which we would
> probably use for prompting the user anyway.

You gotta love the R community!  If one restricts things to github,
this is potentially useful.

https://github.com/cscheid/rgithub

And specifically:

https://github.com/cscheid/rgithub/blob/master/R/issues.R

>
>
>
>
>
> On Fri, May 23, 2014 at 1:24 PM, Vincent Carey
> <stvjc at channing.harvard.edu>wrote:
>
>> urls, browsers ... :(
>>
>> how about a variation on utils:: bug.report in biobase?  each package
>> could have a bugReportHandle method that is called when reportBug is called
>> with the package name as argument.  the biobase version would gather key
>> environmental information at the time of the call and could prompt for
>> specifics.  bug data could be centralized and decentralized depending on
>> how these tools are crafted.
>>
>>
>> On Fri, May 23, 2014 at 4:10 PM, Yihui Xie <xie at yihui.name> wrote:
>>
>>> The CRAN page for a package also includes the BugReports field
>>> (besides the URL field), and I believe that is certainly a better link
>>> for bug reporting purposes.
>>>
>>> Regards,
>>> Yihui
>>> --
>>> Yihui Xie <xieyihui at gmail.com>
>>> Web: http://yihui.name
>>>
>>>
>>> On Fri, May 23, 2014 at 2:58 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>>> wrote:
>>> >
>>> >
>>> > ----- Original Message -----
>>> >> From: "Michael Lawrence" <lawrence.michael at gene.com>
>>> >> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
>>> >> Cc: "Michael Lawrence" <lawrence.michael at gene.com>,
>>> bioc-devel at r-project.org
>>> >> Sent: Friday, May 23, 2014 12:48:55 PM
>>> >> Subject: Re: [Bioc-devel] Bug tracker for Bioconductor?
>>> >>
>>> >> To support the decentralized model, it would be nice to have a
>>> >> standard way
>>> >> of directing users to the right bug tracker. Perhaps this could be
>>> >> specified as a URL in the DESCRIPTION and the Bioc package page could
>>> >> link
>>> >> to it.
>>> >
>>> > Already done; see for example the ACME package landing page:
>>> >
>>> > http://www.bioconductor.org/packages/release/bioc/html/ACME.html
>>> >
>>> > The URL is a clickable link. This could be the link to the github issue
>>> tracker. Note that you can have multiple URLs in the URL field, I believe
>>> comma separated. See also
>>> > http://www.bioconductor.org/developers/how-to/git-svn/#advertise
>>> >
>>> > Dan
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>
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