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

[Stephanie Gogarten]

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>
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 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

she/her/hers

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