[R] R unable to locate base unix commands (tar, sh etc)

[peter dalgaard]

Semicolons in PATH on a Unix derivative like MacOS could well do that to you. It is not clear how they got there, but apparently not from your ~/.Environ file. However, multiple settings of the same PATH variable in .Environment is not something I'd think would work. Persumably the last setting wins, but I'm not sure of that. 

-pd

> On 15 Oct 2019, at 15:09 , gordon beattie <gordo2b using hotmail.co.uk> wrote:
> 
> 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
> 
> 
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> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com