Started having a problem installing packages where R can't find base unix
commands. I've put an example below (other packages have identical "command not
found" errors, sometimes with different commands e.g. sh) and my
PATH/.Renviron(where the problem likely is). I'm on MacOS. Thanks in advance
for any assistance!
> install.packages("hdf5r",
configure.args="--with-hdf5=/usr/local/Cellar/hdf5/1.10.5_1/bin/h5cc")
trying URL
'https://www.stats.bris.ac.uk/R/bin/macosx/el-capitan/contrib/3.6/hdf5r_1.3.0.tgz'
Content type 'application/x-gzip' length 4332333 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
sh: tar: command not found
Error: file
�/var/folders/ll/jmydhb6n7jqg5rv_c58jxkkh0000gn/T//RtmpnssBh2/downloaded_packages/hdf5r_1.3.0.tgz�
is not a macOS binary package
In addition: Warning messages:
1: In system(paste0("tar zxf \"", path.expand(what), "\" -C \"",
path.expand(where), :
error in running command
2: 'tar' returned non-zero exit code 127
PATH:
> Sys.getenv("PATH")
[1] "/bin;/usr/bin;/usr/local/bin"
.Renviron (could anyone explain why "Sys.getenv" doesn't output the contents of
Renviron, trying to understand how they link)
.RenvironR_LIBS=~/R/library
PAGER=/usr/local/bin/less
PATH=/Users/gordon.beattie/Downloads/R_packages/gliph-master/gliph/bin
PATH=/usr/local/bin
PATH=/usr/local/bin
PATH=/usr/bin
PATH=/bin
PATH=/usr/sbin
PATH=/sbin
PATH=/Users/gordon.beattie/.virtualenvs/r-reticulate/bin
PATH=/Users/gordon.beattie/.virtualenvs/r-reticulate/bin
PATH=/usr/bin:/bin:/usr/sbin
PATH=/sbin
PATH=/usr/local/bin
[[alternative HTML version deleted]]
______________________________________________
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.
