[Bioc-devel] external dependencies

Vincent Carey stvjc at channing.harvard.edu
Mon Oct 2 15:11:18 CEST 2017

I'd also comment that if you make the package visible I would be willing to
have a look at the issues involved in porting to windows.  No guarantees
but at least get some sense of context.

On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan <martin.morgan at roswellpark.org
> wrote:

> 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
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