[Bioc-devel] external dependencies

Anna Gogleva gogleva.a.a at gmail.com
Mon Oct 2 14:40:18 CEST 2017

Dear Lori,

Thanks a lot for the clarification.
I will incorporate os checks in my unit tests and examples.


On 2 October 2017 at 12:30, Shepherd, Lori <Lori.Shepherd at roswellpark.org>

> 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]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list