[Bioc-devel] nightly build errors while checking tests

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Apr 29 01:24:40 CEST 2021

Hi Kelly,

It looks like the most recent versions of rgl are causing problems (the 
package was updated twice in less than a week on CRAN):


Here is what I did:

- I went on merida1 (our Mac builder for the release builds) and was 
able to reproduce the error we see on the build report for slingshot 
using the latest rgl (0.106.8).

- However after downgrading rgl to version 0.105.22 (archived on CRAN 
here https://cran.r-project.org/src/contrib/Archive/rgl/), I was able to 
run 'R CMD check' on slingshot without problem.

You have a unit test in slingshot ("3D plotting functions work as 
expected") that uses rgl. This test fails with the latest rgl and when 
run in the context of 'R CMD check'. Note however that it doesn't fail 
when I try to run the tests interactively by doing 
test_check("slingshot") at the command line.

Unfortunately the slingshot.Rcheck/tests/testthat.Rout.fail file 
produced by 'R CMD check' does not provide any details about the failure 
so debugging this to understand exactly what's going on would require 
more time and effort than what I'm able to offer at the moment.

Anyways, an easy workaround is to simply skip the problematic test on 
Mac for now. I think you can do this by adding something like this at 
the beginning of the test:

   if (Sys.info()[["sysname"]] == "Darwin")
     skip('latest rgl is causing problem on Mac')

Hope this helps,


On 4/28/21 12:24 PM, Kelly Street wrote:
> Hello,
> I've recently noticed that the nightly builds for the slingshot package
> (both release and devel versions) are failing on merida1, but I can't
> figure out why. It has something to do with the tests, but I am unable to
> reproduce the error. Here is the build report for the release version:
> http://bioconductor.org/checkResults/release/bioc-LATEST/slingshot/merida1-checksrc.html
> R CMD check provides this output:
> * checking tests ...
>    Running ‘testthat.R’
> Running the tests in ‘tests/testthat.R’ failed.
> Complete output:
>    > library(testthat)
>    > library(slingshot)
>    Loading required package: princurve
>    >
>    > test_check("slingshot")
> And the slingshot.Rcheck/tests/testthat.Rout.fail output is similar:
> R version 4.0.5 (2021-03-31) -- "Shake and Throw"
> Copyright (C) 2021 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin17.0 (64-bit)
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>> library(testthat)
>> library(slingshot)
> Loading required package: princurve
>> test_check("slingshot")
> There's not a lot of information to go on, so has anybody else seen this
> kind of behavior? I went through the list of packages with errors in the
> nightly builds and didn't see anything exactly like this, although
> the paxtoolsr package was failing in a similar way (seemingly due to a Java
> issue?). Any help would be greatly appreciated.
> Thanks,
> Kelly Street
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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