[Bioc-devel] Bioconductor coding standards

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.

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