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-boun...@r-project.org on behalf of murdoch.dun...@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@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 ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
