[R] Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?

[Duncan Murdoch]

On 19/01/2019 8:22 p.m., Peter Waltman wrote:
> I'm trying to install a devel package called gGnome (
> https://github.com/mskilab/gGnome). One of its dependencies is another
> package from the same group, called gTrack, which causes several warning
> messages to be generated because it overloads a couple of functions that
> are part of other packages that gTrack is dependent upon.  The specific
> warnings are provided below.  During the lazy-loading step of gGnome's
> install, gTrack is loaded, and when these warnings come up, they are
> converted to errors, causing the install to fail. This behavior is new to
> version 3.5.2, as I've been able to successfully install these packages
> with R versions 3.5.0 and 3.5.1. Is there a workaround for this for version
> 3.5.2?
> 
> Thanks!
> 
> Error message during gGnome install:
> 
>> install_github('mskilab/gGnome')
> Downloading GitHub repo mskilab/gGnome using master
> Skipping 3 packages not available: GenomicRanges, rtracklayer,
> VariantAnnotation
> ✔  checking for file
> ‘/tmp/Rtmp4hnMMO/remotes7fb938cd0553/mskilab-gGnome-81f661e/DESCRIPTION’ ...
> ─  preparing ‘gGnome’:
> ✔  checking DESCRIPTION meta-information ...
> ─  checking for LF line-endings in source and make files and shell scripts
> ─  checking for empty or unneeded directories
>     Removed empty directory ‘gGnome/inst/extdata/gTrack.js’
> ─  building ‘gGnome_0.1.tar.gz’
> 
> * installing *source* package ‘gGnome’ ...
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Error: package or namespace load failed for ‘gTrack’:
> * (converted from warning)* multiple methods tables found for ‘seqinfo<-’
> Error : package ‘gTrack’ could not be loaded
> ERROR: lazy loading failed for package ‘gGnome’
> * removing ‘/home/waltman/bin/R/3.5.2/lib/R/library/gGnome’
> Error in i.p(...) :
>    (converted from warning) installation of package
> ‘/tmp/Rtmp4hnMMO/file7fb929638ed8/gGnome_0.1.tar.gz’ had non-zero exit
> status

That message indicates that options("warn") is 2 or higher when the 
warning occurs.  What is its setting before you start the install?

Duncan Murdoch