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.sheph...@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-boun...@r-project.org> on behalf of Anna
Gogleva <gogleva....@gmail.com>
*Sent:* Monday, October 2, 2017 5:36:57 AM
*To:* bioc-devel@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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