[R] Problems downloading and installing nlme under Linux Mint 15

John Sorkin JSorkin at grecc.umaryland.edu
Wed Jan 22 00:39:41 CET 2014


I am running R under Linux Mint 15 and trying to download and install
nlme. During the download I get an error message:
Warning message:
In install.packages("nlme") :
  installation of package ‘nlme’ had non-zero exit status

When I try to load the package, I get an error message 
> library(nlme)
Error: package ‘nlme’ was built before R 3.0.0: please re-install it
Why am I getting the error message, and what can I do to fix the
problem? Please see output of R session below.
Thank you,
John


>version
platform       i486-pc-linux-gnu           
arch           i486                        
os             linux-gnu                   
system         i486, linux-gnu             
status                                     
major          3                           
minor          0.1                         
year           2013                        
month          05                          
day            16                          
svn rev        62743                       
language       R                           
version.string R version 3.0.1 (2013-05-16)
nickname       Good Sport    


> install.packages("nlme")
Installing package into ‘/home/john/R/i486-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL
'http://watson.nci.nih.gov/cran_mirror/src/contrib/nlme_3.1-113.tar.gz'
Content type 'application/octet-stream' length 752188 bytes (734 Kb)
opened URL
==================================================
downloaded 734 Kb

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -O2 -pipe -g  -c chol.f -o chol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c corStruct.c -o corStruct.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c gnls.c -o gnls.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c nlme.c -o nlme.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c nlmefit.c -o nlmefit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c nls.c -o nls.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fvisibility=hidden
-fpic  -O2 -pipe -g  -c pdMat.c -o pdMat.o
gfortran   -fpic  -O2 -pipe -g  -c rs.f -o rs.o
gcc -std=gnu99 -shared -o nlme.so chol.o corStruct.o gnls.o init.o
matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran
-lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/john/R/i486-pc-linux-gnu-library/3.0/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error : package ‘lattice’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘nlme’
* removing ‘/home/john/R/i486-pc-linux-gnu-library/3.0/nlme’

The downloaded source packages are in
    ‘/tmp/Rtmpo7eFZf/downloaded_packages’
Warning message:
In install.packages("nlme") :
  installation of package ‘nlme’ had non-zero exit status
> library(nlme)
Error: package ‘nlme’ was built before R 3.0.0: please re-install it




John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 

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