[Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?
??I think one option for me would be to switch to RBowtie instead of Rsubread, since this seems to have a windows binary. I would try this as soon as I have access to a windows system. -------- Vivek Bhardwaj PhD Candidate | International Max Planck Research School Max Planck Institute of Immunobiology and Epigenetics St?beweg 51, Freiburg
From: Bhardwaj, Vivek
Sent: Saturday, May 19, 2018 10:35 AM
To: Michael Lawrence; Martin Morgan
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?
Sent: Saturday, May 19, 2018 10:35 AM
To: Michael Lawrence; Martin Morgan
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?
@All thanks for your comments
I have provided Rsubread mapping wrapper as an optional step in the pipeline. Users can continue the analysis after mapping with their tool of choice as well. Therefore I added it in "suggests" and skip running it in the example and don't evaluate that chunk in the vignette.
I wouldn't want to skip supporting windows only because of an optional step, but I also prefer to keep that function as it allows users to perform end-to-end analysis in R if they wish to.
What would be the best option for me for now?
On 5/19/18 12:00 AM, Michael Lawrence wrote:
On Fri, May 18, 2018 at 2:26 PM, Martin Morgan
<martin.morgan at roswellpark.org><mailto:martin.morgan at roswellpark.org> wrote:
You can create a plain text file in the root directory of your package
.BBSoptions with the line
UnsupportedPlatform: win
Your package will not be available on Windows, losing about 1/2 your
potential audience.
I'm not sure how many people will endeavor to run that part of the
icetea pipeline on their Windows laptop. What about separating the
preprocessing and downstream exploratory stuff into two packages?
A better strategy is to figure out why you are
Suggests:'ing Rsubread, and find alternative cross-platform solutions.
I would not hesitate to add your voice to mine in asking the Rsubread
maintainer to make their package cross-platform compatible. While this
requires considerable work, it would benefit the Bioconductor community in
this and subsequent years.
Martin
On 05/18/2018 04:55 PM, Bhardwaj, Vivek wrote:
Hi All
My package is in review and the build is failing since a suggested package
(Rsubread) is not available on windows. Is there a way for me to instruct
the build machine on bioc to use: _R_CHECK_FORCE_SUGGESTS_ = FALSE ??
Best,
Vivek
--------
Vivek Bhardwaj
PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
St?beweg 51, Freiburg
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