Message-ID: <DM6PR05MB52128C7C620A7DFA4B8DA18AF99E0@DM6PR05MB5212.namprd05.prod.outlook.com>
Date: 2019-01-20T12:29:19Z
From: Martin Morgan
Subject: Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?
In-Reply-To: <957dbbbf-38a9-98a4-699a-23f00525beff@gmail.com>
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 at r-project.org on behalf of murdoch.duncan at 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 at 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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