[Bioc-devel] external dependencies

[Martin Morgan]

I want to add, though, that OS-specific functionality and system 
requirements greatly limit the utility of your package and, like the 
OS-specific dependencies your package depends on, serves as a kind of 
virus that makes any other package that uses yours also not operable on 
the unsupported OS. You're also introducing complexity into the build 
system and for potential users, and especially to your own package where 
you need to effectively navigate around idiosyncrasies of the 
third-party software.

So while technically possible, I'd take a deep dark look at the soul of 
your package and ask whether it is really necessary to do this. Maybe 
the functionality offered by the system dependency is not core to what 
your package offers, or an alternative cross-platform solution provides 
something that is 'good enough', or the author of the upstream 
dependency can be convinced to make their package more user friendly, or 
the specific functionality provided by the OS-specific software can be 
spun off to an independent R package.

I know that many Bioc developers are on linux or mac, but more than 1/2 
of our web and support site visitors are on Windows, so you're losing 
1/2 your audience and impact.
Martin


On 10/02/2017 08:40 AM, Anna Gogleva wrote:
> Dear Lori,
> 
> Thanks a lot for the clarification.
> I will incorporate os checks in my unit tests and examples.
> 
> Thanks,
> Anna
> 
> On 2 October 2017 at 12:30, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
> wrote:
> 
>> You can still submit to bioconductor despite this limitation.  You could
>> also do a os check in the examples and tests that fail on windows and make
>> a comment that this is the case.  If the program is not meant to run in
>> windows there is options to handle that as well and the review assigned to
>> you can assist you with this.  If you feel the package is otherwise ready
>> to submit to Bioconductor for review I would proceed.
>>
>>
>> https://github.com/Bioconductor/Contributions
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Anna
>> Gogleva <gogleva.a.a at gmail.com>
>> *Sent:* Monday, October 2, 2017 5:36:57 AM
>> *To:* bioc-devel at r-project.org
>> *Subject:* [Bioc-devel] external dependencies
>>
>> Dear Bioconductor Team,
>>
>> I have written a package and was planning to submit it to Bioconductor one
>> day. The package provides a set of wrapper functions around several
>> existing command line tools to construct scalable and reproducible
>> pipelines for secretome prediction.
>>
>> The package requires several external system dependencies to be installed
>> in order to work (listed in the SystemRequirements filed). I have a
>> top-level README describing in detail how to install the required
>> dependencies and a shell script to automate this process. The thing is,
>> some of the external dependencies were not designed to work on Windows -
>> causing certain unit tests and examples to fail during the automatic R CMD
>> check on Windows.
>>
>> I have run R CMD check on Mac and Linux and the package passes without
>> errors, warnings or notes. It also satisfies the remaining requirements
>> from the recommended package checklist.
>>
>> What would be the best way to proceed? Would it be still ok to submit the
>> package though it is not fully functional on Windows due to unavailability
>> of certain external dependencies?
>>
>> Thank you for your advice,
>>
>> Anna Gogleva
>>
>>          [[alternative HTML version deleted]]
>>
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