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

[Martin Morgan]

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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-- 
--
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