Hi I want to install the vegan package for R via terminal command - so far I have this:

This downloads the zipped file required (this part works)

wget -O ~/file/downloads/vegan_2.3-5.tar.gz "http://download.r-forge.r-project.org/src/contrib/vegan_2.3-5.tar.gz"  

I want this to then install that package so i can run it in R (this part doesn't work error message: syntax error near unexpected token `(' )

install.packages(~/file/downloads/vegan_2.3-5.tar.gz, repos = NULL, type="source")  

Thanks in advance

  • Can you be more specific than "this part doesn't work"? it doesn't give us much to go on – steeldriver May 28 '16 at 19:04
  • Use this terminal command to install the downloaded package R CMD INSTALL vegan_2.3-5.tar.gz – rcs May 28 '16 at 19:49
  • still get error with this but now it says: * installing to library ‘/usr/local/lib/R/site-library’ ERROR: dependency ‘permute’ is not available for package ‘vegan’ * removing ‘/usr/local/lib/R/site-library/vegan’ – Giles May 28 '16 at 20:14
  • Is there a reason you can't install vegan the standard way from within R? install.packages("vegan") should automatically pull on any dependencies. – amc Jun 14 '16 at 5:47
  • i prefer to do things via the command line rather than within R, makes things easier for larger script writing and install packages etc – Giles Jul 7 '16 at 18:45

Okay I've got the answer, thanks rcs for the install method. Basically vegan requires previous installation of permute. So these commands do the trick:

wget -O ~/downloads/permute_0.8-3.tar.gz "http://download.r-forge.r-project.org/src/contrib/permute_0.8-3.tar.gz"
wget -O ~/downloads/vegan_2.3-5.tar.gz "http://download.r-forge.r-project.org/src/contrib/vegan_2.3-5.tar.gz"
sudo R CMD INSTALL ~/downloads/permute_0.8-3.tar.gz
sudo R CMD INSTALL ~/downloads/vegan_2.3-5.tar.gz
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