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
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