?Thanks Stephanie, that's also a very helpful suggestion! I hadn't thought of using Docker containers.
________________________________ From: Stephanie Gogarten <sdmor...@uw.edu> Sent: April 24, 2020 4:34 PM To: Kieran O'Neill Cc: bioc-devel@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.jankev...@bham.ac.uk<mailto:a.jankev...@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, kone...@bcgsc.ca<mailto:kone...@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! [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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 sdmor...@uw.edu<mailto:sdmor...@uw.edu> she/her/hers [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
