[Bioc-devel] Bioconductor coding standards

[Hervé Pagès]

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.

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
>>
>
>

-- 
Hervé Pagès

Program in Computational Biology
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