[Bioc-devel] external dependencies

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Mon Oct 2 13:30:23 CEST 2017

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.


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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