[Bioc-devel] Bioconductor coding standards

[Martin Morgan]

On 04/02/2013 09:04 AM, Alejandra Gonzalez-Beltran wrote:
> Hi Ulrich,
>
> While not for Bioconductor, this Google's R style guide might be useful:
>
> http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html

Bioc doesn't dictate coding style. The use of '.' in any kind of symbol is 
potentially confusing with S3 dispatch. The IRanges package is perhaps the most 
consistently coded of those produced by our group.

The url http://wiki.fhcrc.org/bioc/Coding_Standards was on a wiki that became 
unmaintainable due to spam; we'll try to resurrect that page.

Martin

>
> Best wishes,
>
> Alejandra
>
>
> On 26 March 2013 11:48, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Tue, Mar 26, 2013 at 7:27 AM, Ulrich Bodenhofer <
>> bodenhofer at bioinf.jku.at
>>> wrote:
>>
>>> On 03/26/2013 12:18 PM, Laurent Gatto wrote:
>>>
>>>> On 26 March 2013 09:26, Ulrich Bodenhofer <bodenhofer at bioinf.jku.at>
>>>> wrote:
>>>>
>>>>> Dear colleagues,
>>>>>
>>>>> One of my students is currently working on a package that we plan to
>>>>> submit
>>>>> to Bioconductor. I want him to adhere to the Bioconductor coding
>>>>> standards
>>>>> which I thought were available at
>>>>> http://wiki.fhcrc.org/bioc/**Coding_Standards<
>> http://wiki.fhcrc.org/bioc/Coding_Standards>.
>>>>>
>>>>
>>>>
>> Hi, Ulrich.
>>
>> This is the correct URL, I believe.  I think the wiki is just down right
>> now.  I'd expect that someone will get to it when it gets closer to
>> business hours in Seattle.
>>
>>
>>> However, it turned out that the
>>>>> site is down or has been moved. I searched for them and only found
>>>>> https://phssec1.fhcrc.org/**secureplone/www.bioconductor.**
>>>>> org/developers/OLD/devwiki/**CodingStandards<
>> https://phssec1.fhcrc.org/secureplone/www.bioconductor.org/developers/OLD/devwiki/CodingStandards
>>>
>>>>> which is somehow what I expect, but seems quite old (last edited 7
>> years
>>>>> ago). So where have the guidelines gone?
>>>>
>>>>
>> Yep, that is old and probably appropriately ignored.
>>
>> Sean
>>
>>
>>
>>> Thanks in advance for your any kind
>>>>> of help!
>>>>
>>>>   What about http://bioconductor.org/**developers/package-guidelines/<
>> http://bioconductor.org/developers/package-guidelines/>
>>>>
>>>> Laurent
>>>>
>>>>   Of course, I know this page, but this is not what I was looking for.
>>> While the package guidelines pagedeals with the structure and design of
>>> packages, I was looking for guidelines how to write code, i.e.
>> indentation,
>>> spacing, line length, etc.
>>>
>>
>>          [[alternative HTML version deleted]]
>>
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