[Bioc-devel] Deleting netDx.examples package from BioC

[Shraddha Pai]

Hi Martin, Great, this is all very helpful.
Thanks especially for the workflow to set up a Docker instance and run the
build test.
Best,Shraddha


On Mon, Feb 24, 2020 at 2:34 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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 git using 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.neuro using gmail.com>
> Reply-To: "shraddha.pai using utoronto.ca" <shraddha.pai using utoronto.ca>
> Date: Monday, February 24, 2020 at 10:31 PM
> To: Martin Morgan <mtmorgan.bioc using gmail.com>
> Cc: Bioc-devel <bioc-devel using 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.bioc using 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-bounces using r-project.org on behalf of mailto:
> shraddhapai.neuro using 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
>
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>
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>
>
>
> --
> --
> 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
>
>

-- 
--
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

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