gordon beattie
2019-Oct-15 13:09 UTC
[R] R unable to locate base unix commands (tar, sh etc)
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]]
peter dalgaard
2019-Oct-18 00:13 UTC
[R] R unable to locate base unix commands (tar, sh etc)
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 at 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 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.-- 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 at cbs.dk Priv: PDalgd at gmail.com
stephen sefick
2019-Oct-18 01:14 UTC
[R] R unable to locate base unix commands (tar, sh etc)
I work on a Mac now. I believe .profile gets sourced first and then .bashrc. I set PATH in my .bashrc. I set a git token in .Renviron and a blank .Rprofile because I use packrat quite often. I have no problem with my environment at a shell or in Rstudio. I would start by commenting where you set the PATH in the multiple files until you find the order they are sourced. Or look in .profile and .bashrc to find and replace the semi colons with colons? I do not understand how a PATH variable would be set in .Rprofile. I agree with pd about the semicolons. What happens when you type tar at a command prompt? FWIW, Stephen On Thu, Oct 17, 2019, 20:13 peter dalgaard <pdalgd at gmail.com> wrote:> 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 at 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 > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at 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. > > -- > 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 at cbs.dk Priv: PDalgd at gmail.com > > ______________________________________________ > R-help at 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. >[[alternative HTML version deleted]]