Fantastic - that was it! Thanks so much! On Sun, Jan 20, 2019 at 7:29 AM Martin Morgan <[email protected]> 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" < > [email protected] on behalf of [email protected]> 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 > > ______________________________________________ > [email protected] 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. > > [[alternative HTML version deleted]] ______________________________________________ [email protected] 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.
