CODEWITHSUNDEEP
rubuntuinstall.packages
Tom
Tom

Reputation: 603

R: package installation trouble in Ubuntu

I'm running on Ubuntu 16.04 (on a Lenovo ThinkPak T450). I have installed R version 3.4.1, installed by following the instructions here via Rbloggers.

From here, I would like to start installing packages, but if I run R from the command line without root privileges, I cannot access a CRAN mirror. That is, when I run install.packages('dplyr') (or any install.packages('blah')) I get the following error 

--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Can't find a usable init.tcl in the following directories: 
    /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library ./tcl8.5.18/library

With that error, no CRAN mirror dialog box appears and hence no installation of packages. Note: this error does not happen when I start R with root privileges (i.e., start via > sudo R), but I do not want to install packages as root.

Thanks in advance for any help you can send my way!

Edit: Specifying the repo also results in error (in the file paths below, I replaced my user-name with user-name).

E.g.: install.packages('Rcpp',repos='http://cran.us.r-project.org') terminates with:

installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so':
  /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp’

E.g., install.packages('dplyr',repos='http://cran.us.r-project.org') terminates with:

installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so':
  /home/user-name/anaconda3/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so)
ERROR: lazy loading failed for package ‘dplyr’
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr’

Upvotes: 1

Views: 675

Answers (1)

Tom
Tom

Reputation: 603

As pointed out by DirkEddelbuettel in the comments, the issue was a mixing of Anaconda and R. To fix this problem:

  • I uninstalled the R packages from Anaconda by first looking at > conda list and realizing that the package was r-base; hence running > conda remove r-base.

  • Next, by looking at the output of > which R, it was clear that we were still trying to execute from the ../anaconda3/bin/.. directory. I suspect there is a quick way to change this via an export or bashrc amendment (or something similar), but for me, the quickest work-around was to run > sudo apt-get install r-base r-base-dev, which took all of 0.2 seconds as they were already installed, but it did affect the directory which the system looks in to the appropriate one, for me this is /usr/bin/R/.

From here I've been able to install everything I've needed.

Note: Thinking back, I suspect the "mixing" happened when I installed rpy2 via conda.

Upvotes: 1

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