Generally the guidelines are at https://bioconductor.org/developers/how-to/git/
and you'll access 'devel' as the master branch and release as the RELEASE_3_10 branch of git clone g...@git.bioconductor.org:packages/netDx 'We' do not offer a faster way to iterate on the nightly builds; the traditional approach, usually 'good enough' for most packages, is to maintain an installation of the relevant R / Bioconductor platforms, e.g., R-devel / Bioc 3-11 for 'devel and R-3.6.2 / Bioc 3-10 for release for the current cycle, following instructions and links at https://bioconductor.org/developers/how-to/useDevel/ You could also try managing the two versions using the Bioconductor/Bioconductor_docker image http://bioconductor.org/help/docker/ and Travis etc images (I don't have expertise on this, maybe someone else on the list can provide detail) but my overall experience is that these layers introduce the risk that one ends up debugging the tool rather than the package. Regardless, the basic process is to make and commit changes locally, then on a clean local checkout build and check cd /tmp git clone path/to/updated/repo R CMD build repo R CMD check repo_x.y.z.tar.gz or similar, depending on your development system. If there are obscure errors then one might visit http://bioconductor.org/developers/how-to/troubleshoot-build-report/ for inspiration. Martin From: Shraddha Pai <shraddhapai.ne...@gmail.com> Reply-To: "shraddha....@utoronto.ca" <shraddha....@utoronto.ca> Date: Monday, February 24, 2020 at 10:31 PM To: Martin Morgan <mtmorgan.b...@gmail.com> Cc: Bioc-devel <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Deleting netDx.examples package from BioC Hi Martin, Great, thank you. I will set the number of cores to one for the examples (must have had something running in parallel). I was unable to find the BioC github repo for netDx in the devel branch - what is the URL for that? It would help me ascertain if my push indeed synchronized with BioC github repo. Also is there another build process I could use to get quicker feedback on issues, so I can resolve them sooner? If I understand correctly, waiting for the nightly build means having the turnaround time of a day to know whether or not a fix worked. Best,Shraddha On Sat, Feb 22, 2020 at 7:49 AM Martin Morgan <mailto:mtmorgan.b...@gmail.com> wrote: We've removed netDx.examples from the build manifest and from our git repository; these changes will propagate through the system over the next couple of days. Thanks for pointing this out! The builds are nightly, and summarized from this page http://bioconductor.org/checkResults/ This is the report for your package http://bioconductor.org/checkResults/3.11/bioc-LATEST/netDx/tokay2-checksrc.html Note the 'snapshot' date (the time the nightly builds started) and the time the page was generated (after the completion of nightly builds of all packages). Any commit after the snapshot date won't be included in the build report. Looks like there is a (obscure!) problem on the Linux builder -- parallel evaluation is often challenging to make robust, because the builder is heavily used, and a better strategy is usually to tackle more modest analyses in examples. Martin On 2/21/20, 2:43 PM, "Bioc-devel on behalf of Shraddha Pai" <mailto:bioc-devel-boun...@r-project.org on behalf of mailto:shraddhapai.ne...@gmail.com> wrote: Hello BioC team, My package netDx was recently accepted to BioC (yay!). Its original companion package netDx.examples was, as well. However, the latter is now outdated because I'm pulling the data for the examples directly from BioConductor. How can I delete the netDx.examples package from BioConductor? https://bioconductor.org/packages/devel/data/experiment/html/netDx.examples.html Separately, I am also refreshing my memory about how feedback from the build process works after a package is submitted, so I may have questions after reading the instructions... Thank you, Shraddha -- -- Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto [[alternative HTML version deleted]] _______________________________________________ mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- -- Shraddha Pai, PhD http://shraddhapai.com/ ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
