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

[Waldir Leoncio Netto]

Thank you Charlotte, that was it!

On Thu, 2020-05-07 at 11:39 +0200, Charlotte Soneson wrote:

Hi Waldir,


try to delete the travis cache (under More Options - Caches) and restart the build. That helped for me.


Best,

Charlotte


On 7 May 2020, at 11:33, Waldir Leoncio Netto <w.l.netto using medisin.uio.no<mailto:w.l.netto using medisin.uio.no>> wrote:


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

travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=

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,

Waldir


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