Comments (5)
Hello,
I attempted to replicate your error, and it appears that bactaxR skips the installation of ggtree, which is hosted on bioconductor. If you don't already have ggtree installed, try running the following (you may then need to re-start R/RStudio; additionally, if you do already have ggtree installed, perhaps uninstall it using remove.packages, re-install it, and possibly re-start your session):
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggtree")
Afterwards, try loading devtools (library(devtools)
) and installing bactaxR again (install_github("lmc297/bactaxR")
)
Good luck, and just let me know if this works or not!
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Hi ntromas,
I seem to have had the same issue as yourself. The remotes package of R (which contains install_github) has a default to convert warning messages to errors as seen with (converti depuis l'avis). If you change the default by using:
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)
That should work. All the warnings are for in this case is that the dependencies are built under different R versions which isn't a problem.
Hope that helps
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Hi dv332247,
Thanks so much for finding a possible fix with Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)
. I/none of the friends I've forced to test the package over the past few days have been gotten an error, so I was having difficulties replicating it. I'll update the manual with your suggestion in case others run into the same problem.
LC
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