[Bioc-devel] Help with creating first Bioconductor package

Stephanie M. Gogarten sdmorris at u.washington.edu
Fri Nov 14 18:33:15 CET 2014

On 11/14/14, 9:20 AM, Laurent Gatto wrote:
> Dear January,
> On 14 November 2014 10:51, January Weiner wrote:
>> Dear all,
>> I am building my first Bioconductor package and, before wasting
>> everyone's time with a faulty submission, I would like to clarify
>> certain things.
>> 1) The package seems to fulfill the requirements of the Bioconductor
>> Package Guidelines and passes all checks except one "consideration":
>> CONSIDER: Indenting lines with a multiple of 4 spaces;
>> I love to indent my code with 2 spaces, is it a problem? Or do I have
>> to reformat all code before release? This is doable, but it would
>> complicate my workflow and if I am allowed to avoid it, I will. I see
>> that not all Bioconductor packages stick to this formatting (many even
>> use tabs instead of spaces).
> I don't think this is a reason for rejection, as long as all other
> aspects of the formatting are fine (for instance miles-long lines).

Emacs and RStudio both have 2 spaces as the default, so you will be in 
good company.  My own package is not even internally consistent, as it 
contains code written by multiple people, all using text editors with 
different indentation defaults.  Sometimes I get the urge to go through 
the (many) .R files and reformat it all, but it never makes it to the 
top of the to-do list.

>> 2) Another problem I have is the testing package on other platforms. I
>> do not have a Windows machine to test my package. Could someone help
>> me and test my package (build, check and BiocCheck) on Windows and
>> MacOS? Otherwise -- how do you check your packages? You keep an up to
>> date R development environment on three platforms?
> As mentioned by Julian, you could use http://win-builder.r-project.org/
> for Windows. But I don't think you are expected to check it on all
> platforms before submission. If your package contains straightforward R
> code, there is no reason to anticipate issues on other platforms.

I don't have a Windows machine either, so I rely on the Bioc build 
system to alert me if something goes wrong on Windows but not the other 


More information about the Bioc-devel mailing list