Switching aligners is very likely going to affect the results. You could have Rbowtie as the built-in aligner, and then provide Rsubread support as a simple add-on package.
On Sat, May 19, 2018 at 2:49 AM, Bhardwaj, Vivek <bhard...@ie-freiburg.mpg.de> wrote: > ??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 > Stübeweg 51, Freiburg > ________________________________ > From: Bhardwaj, Vivek > Sent: Saturday, May 19, 2018 10:35 AM > To: Michael Lawrence; Martin Morgan > Cc: bioc-devel@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.mor...@roswellpark.org><mailto:martin.mor...@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 > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
