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> 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 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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 she/her/hers [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
