Hi Vivek, I'd say don't worry about R CMD check failing with the Single Package Builder on Windows for now. When your package gets accepted, we'll set _R_CHECK_FORCE_SUGGESTS_ to FALSE on Windows so your package will be supported on this platform despite having Rsubread in Suggests.
Note that this not unprecedented: we're already doing this for VariantTools (suggests gmapR, which is no supported on Windows either) and singleCellTK (suggests Rsubread). The way we do this is by adding a .BBSoptions file to the package source tree with the following line in it: CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&& Of course, you'll have to make sure that the code in the man pages, vignettes and unit tests can run without Rsubread being installed. Cheers, H. On 05/19/2018 02:49 AM, Bhardwaj, Vivek 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=lfZWGGarfZUEkLuLxuYCQktiBKaASsMbNpCwLMzfFrM&s=8onp29q_vGi-gvujeRnxw0EL-gvcJNBKB7_FPrP4zYg&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=lfZWGGarfZUEkLuLxuYCQktiBKaASsMbNpCwLMzfFrM&s=8onp29q_vGi-gvujeRnxw0EL-gvcJNBKB7_FPrP4zYg&e= [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=lfZWGGarfZUEkLuLxuYCQktiBKaASsMbNpCwLMzfFrM&s=8onp29q_vGi-gvujeRnxw0EL-gvcJNBKB7_FPrP4zYg&e=
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