[R] install.packages problem with R 3.1.0 on a multiuser linux system

eugene eugene.dedits at gmail.com
Wed Jun 11 22:53:25 CEST 2014


Hello R users. 


I have a problem with R installation on one of my systems: install.packages returns 
different errors. Here is an example: 

*********************************************************************
~# /share/apps/r/3.1.0/bin/R

R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> install.packages('animation')
Warning in install.packages("animation") :
  'lib = "/share/apps/r/3.1.0/lib64/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/3.1
to install packages into?  (y/n) y
--- Please select a CRAN mirror for use in this session ---
CRAN mirror
…………..
….. list of mirrors ……
………..
89: USA (PA 2)                   90: USA (TN)
91: USA (TX 1)                   92: USA (WA 1)
93: USA (WA 2)                   94: Venezuela
95: Vietnam

Selection: 89
trying URL 'http://cran.mirrors.hoobly.com/src/contrib/animation_2.2.tar.gz'
Content type 'application/x-gzip' length 321316 bytes (313 Kb)
opened URL
==================================================
downloaded 313 Kb

* installing *source* package ‘animation’ ...
** package ‘animation’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
Error in load(zfile, envir = envir) : empty (zero-byte) input file
ERROR: lazydata failed for package ‘animation’
* removing ‘/home/user.name/R/x86_64-unknown-linux-gnu-library/3.1/animation’

The downloaded source packages are in
	‘/tmp/RtmpP4ug6j/downloaded_packages’
Warning message:
In install.packages("animation") :
  installation of package ‘animation’ had non-zero exit status
*********************************************************************


If I try to install different package, I get different error:
*********************************************************************
> install.packages('car')
Installing package into ‘/home/user.name/R/x86_64-unknown-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://cran.mirrors.hoobly.com/src/contrib/car_2.0-20.tar.gz'
Content type 'application/x-gzip' length 582567 bytes (568 Kb)
opened URL
==================================================
downloaded 568 Kb

* installing *source* package ‘car’ ...
** package ‘car’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
Error in readRDS(pfile) : error reading from connection
ERROR: lazydata failed for package ‘car’
* removing ‘/home/user.name/R/x86_64-unknown-linux-gnu-library/3.1/car’

The downloaded source packages are in
	‘/tmp/RtmpP4ug6j/downloaded_packages’
Warning message:
In install.packages("car") :
  installation of package ‘car’ had non-zero exit status
*********************************************************************

The most weird part: as another user on the same system I can install all these packages 
without any problems. 

So it looks like there is something about user environment that breaks install.packages. 


I would appreciate any help with this issue. 


Thanks,
E. 



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