[Bioc-devel] Failing Travis build on bioc-devel

Waldir Leoncio Netto w@|@netto @end|ng |rom med|@|n@u|o@no
Thu May 7 11:33:14 CEST 2020

Dear fellow developers,

I have a package which has been failing on Travis CI's bioc-devel build since the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still working fine.

The error happens when installing the SummarizedExperiment dependency (or, apparently, when installing its dependency, GenomicRanges). Here is the relevant part of the log:

* installing *source* package ‘SummarizedExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘GenomicRanges’:
 .onLoad failed in loadNamespace() for 'XVector', details:
  call: NULL
  error: (converted from warning) undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Error: package ‘GenomicRanges’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘SummarizedExperiment’
* removing ‘/home/travis/R/Library/SummarizedExperiment’
* restoring previous ‘/home/travis/R/Library/SummarizedExperiment’
Error in i.p(...) :
  (converted from warning) installation of package ‘SummarizedExperiment’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .

Your build has been stopped.

I was wondering if anyone else went through this or can offer a solution.

Best regards,

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