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

[Peter Waltman]

Fantastic - that was it! Thanks so much!

On Sun, Jan 20, 2019 at 7:29 AM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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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