[Bioc-devel] Help with setting up a build environment to match

[Kieran O'Neill]

?Thanks Stephanie, that's also a very helpful suggestion! I hadn't thought of using Docker containers.

________________________________
From: Stephanie Gogarten <sdmorris using uw.edu>
Sent: April 24, 2020 4:34 PM
To: Kieran O'Neill
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Help with setting up a build environment to match

I have found the BIocnductor docker images very helpful in reproducing the build environment:
https://www.bioconductor.org/help/docker/

I used a combination of the examples under "modifying the images" to get a version of the docker images that would build my vignettes, and also install all dependencies needed to test my package. Then I mount the directory that contains my package repository when starting up a docker container:

docker run -it -v /Users/stephanie/Bioconductor:/home --user rstudio bioconductor_docker_genesis:devel bash

That gives me a shell prompt in which I can run "R CMD build" and "R CMD check". Since the docker container is viewing my local repository, I can make changes and then re-run the checks.

best wishes,
Stephanie

On Fri, Apr 24, 2020 at 2:03 PM Andris Jankevics <A.Jankevics using bham.ac.uk<mailto:A.Jankevics using bham.ac.uk>> wrote:
Hi,


Are you using R 4.00 on Ubuntu?

Travis error indicates that you are using class(), output of this command has changed.

https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq

BW,
Andris

On 24 Apr 2020 20:40, koneill using bcgsc.ca<mailto:koneill using bcgsc.ca> wrote:
A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build environment on Travis or the BioC build servers so  I can reproduce this error and debug it?


Thanks!




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--
Stephanie M. Gogarten, PhD
Team Lead, Sample QC and Analysis Software / TOPMed Data Coordinating Center<https://www.nhlbiwgs.org/group/dcc>
Senior Research Scientist / Genetic Analysis Center<https://www.biostat.washington.edu/research/centers/gac>
Department of Biostatistics<https://www.biostat.washington.edu/>
UNIVERSITY OF WASHINGTON

UW Tower Box 359461
4333 Brooklyn Ave NE, Seattle, WA 98195
206.221.0757
sdmorris using uw.edu<mailto:sdmorris using uw.edu>
she/her/hers

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