[Bioc-devel] Bioconductor coding standards

[Martin Morgan]

On 04/02/2013 05:09 PM, Hervé Pagès wrote:
> Hi Ulrich,
>
> On 04/02/2013 09:37 AM, Martin Morgan wrote:
>> 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.
>
> I would add that we also strongly suggest that you limit the line
> lengths to 80 chars, that you properly indent your code (typically
> by 2-space, 4-space, or 8-space increments, that's a matter of personal
> taste), that you put a space after the comma separating the function
> args, and that you do not put a space between the name of a function
> and the parentheses in a function call. Sounds obvious but many of the
> contributed packages we receive have code that is poorly formatted and
> hence hard to read.
>
> We also strongly suggest that class names start with a capital letter.

See

   http://bioconductor.org/developers/coding-style/

for the resurrected coding style.

Martin

>
> Thanks,
> H.
>
>> 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]]
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793