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

[Martin Morgan]

Looks like you're using remotes::install_github(), which in turn uses remotes::install().

The README

  https://github.com/r-lib/remotes/blob/254c67ed6502e092a316553f2a44f04b0e595b64/README.md

says "Setting R_REMOTES_NO_ERRORS_FROM_WARNINGS=true avoids stopping the installation for warning messages. Warnings usually mean installation errors, so by default remotes stops for a warning. However, sometimes other warnings might happen, that could be ignored by setting this environment variable.

So I'd guess

  Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)

before installing the package would address this problem.

Martin Morgan

On 1/20/19, 6:58 AM, "R-help on behalf of Duncan Murdoch" <r-help-bounces using r-project.org on behalf of murdoch.duncan using gmail.com> wrote:

    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
    
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