[rkward-users] RKward-error updating packages

Sourav Chakraborty schakra1 at my.uno.edu
Mon May 16 20:56:15 UTC 2011 

Hi,

I am having problems updating R packages from rkward.

It has been going for a while now. Can't remember if it is just two
weeks or more.

I use ubuntu 10.04 and rkward daily build ppa.

Attached is the error message. Hope this will troubleshoot the issue.

Best,
Sourav Chakraborty, Ph.D. 
The Ohio State University


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R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i486-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options (repos=c (CRAN="http://cran.case.edu"))
> install.packages (pkgs=c ("Rcmdr", "abind", "caTools", "car", "effects", "lmtest", "multcomp", "mvtnorm", "relimp", "rgl", "sandwich", "sm", "strucchange", "strucchange", "zoo"), lib="/usr/local/lib/R/site-library")
trying URL 'http://cran.case.edu/src/contrib/Rcmdr_1.6-4.tar.gz'
Content type 'application/x-gzip' length 2796047 bytes (2.7 Mb)
opened URL
==================================================
downloaded 2.7 Mb

trying URL 'http://cran.case.edu/src/contrib/abind_1.3-0.tar.gz'
Content type 'application/x-gzip' length 19140 bytes (18 Kb)
opened URL
==================================================
downloaded 18 Kb

trying URL 'http://cran.case.edu/src/contrib/caTools_1.11.tar.gz'
Content type 'application/x-gzip' length 62232 bytes (60 Kb)
opened URL
==================================================
downloaded 60 Kb

trying URL 'http://cran.case.edu/src/contrib/car_2.0-10.tar.gz'
Content type 'application/x-gzip' length 359388 bytes (350 Kb)
opened URL
==================================================
downloaded 350 Kb

trying URL 'http://cran.case.edu/src/contrib/effects_2.0-12.tar.gz'
Content type 'application/x-gzip' length 119190 bytes (116 Kb)
opened URL
==================================================
downloaded 116 Kb

trying URL 'http://cran.case.edu/src/contrib/lmtest_0.9-27.tar.gz'
Content type 'application/x-gzip' length 273943 bytes (267 Kb)
opened URL
==================================================
downloaded 267 Kb

trying URL 'http://cran.case.edu/src/contrib/multcomp_1.2-6.tar.gz'
Content type 'application/x-gzip' length 930101 bytes (908 Kb)
opened URL
==================================================
downloaded 908 Kb

trying URL 'http://cran.case.edu/src/contrib/mvtnorm_0.9-999.tar.gz'
Content type 'application/x-gzip' length 318839 bytes (311 Kb)
opened URL
==================================================
downloaded 311 Kb

trying URL 'http://cran.case.edu/src/contrib/relimp_1.0-2.tar.gz'
Content type 'application/x-gzip' length 12949 bytes (12 Kb)
opened URL
==================================================
downloaded 12 Kb

trying URL 'http://cran.case.edu/src/contrib/rgl_0.92.798.tar.gz'
Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://cran.case.edu/src/contrib/sandwich_2.2-6.tar.gz'
Content type 'application/x-gzip' length 881767 bytes (861 Kb)
opened URL
==================================================
downloaded 861 Kb

trying URL 'http://cran.case.edu/src/contrib/sm_2.2-4.1.tar.gz'
Content type 'application/x-gzip' length 154467 bytes (150 Kb)
opened URL
==================================================
downloaded 150 Kb

trying URL 'http://cran.case.edu/src/contrib/strucchange_1.4-4.tar.gz'
Content type 'application/x-gzip' length 788769 bytes (770 Kb)
opened URL
==================================================
downloaded 770 Kb

trying URL 'http://cran.case.edu/src/contrib/zoo_1.6-5.tar.gz'
Content type 'application/x-gzip' length 892136 bytes (871 Kb)
opened URL
==================================================
downloaded 871 Kb

* installing *source* package ‘abind’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (abind)
* installing *source* package ‘caTools’ ...
** libs
g++ -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c GifTools.cpp -o GifTools.o
GifTools.cpp: In function ‘int imreadGif(const char*, int, bool, uchar**, int&, int&, int&, int*, int&, char**)’:
GifTools.cpp:598: warning: case label value is less than minimum value for type
GifTools.cpp:608: warning: case label value is less than minimum value for type
gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c runfunc.c -o runfunc.o
g++ -shared -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/caTools/libs
** R
** preparing package for lazy loading
Error : package 'bitops' was built before R 2.10.0: please re-install it
ERROR: lazy loading failed for package ‘caTools’
* removing ‘/usr/local/lib/R/site-library/caTools’
* installing *source* package ‘car’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (car)
* installing *source* package ‘effects’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : package 'colorspace' was built before R 2.10.0: please re-install it
ERROR: lazy loading failed for package ‘effects’
* removing ‘/usr/local/lib/R/site-library/effects’
* installing *source* package ‘mvtnorm’ ...
** libs
gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c miwa.c -o miwa.o
gfortran   -fpic  -O3 -pipe  -g -c mvt.f -o mvt.o
gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c randomF77.c -o randomF77.o
gfortran   -fpic  -O3 -pipe  -g -c tvpack.f -o tvpack.o
gfortran   -fpic  -O3 -pipe  -g -c tvpackAPI.f -o tvpackAPI.o
gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c tvpackAux.c -o tvpackAux.o
gcc -shared -o mvtnorm.so miwa.o mvt.o randomF77.o tvpack.o tvpackAPI.o tvpackAux.o -lgfortran -lm -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/mvtnorm/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (mvtnorm)
* installing *source* package ‘relimp’ ...
** R
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (relimp)
* installing *source* package ‘rgl’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries , headers 
checking GL/gl.h usability... no
checking GL/gl.h presence... no
checking for GL/gl.h... no
checking GL/glu.h usability... no
checking GL/glu.h presence... no
checking for GL/glu.h... no
configure: error: missing required header GL/gl.h
ERROR: configuration failed for package ‘rgl’
* removing ‘/usr/local/lib/R/site-library/rgl’
* installing *source* package ‘sm’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (sm)
* installing *source* package ‘zoo’ ...
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (zoo)
* installing *source* package ‘Rcmdr’ ...
** libs
gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c ismdi.c -o ismdi.o
gcc -shared -o Rcmdr.so ismdi.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rcmdr/libs
** R
** inst
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
The Commander GUI is launched only in interactive sessions

* DONE (Rcmdr)
* installing *source* package ‘lmtest’ ...
** libs
gfortran   -fpic  -O3 -pipe  -g -c pan.f -o pan.o
gcc -shared -o lmtest.so pan.o -lgfortran -lm -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/lmtest/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (lmtest)
* installing *source* package ‘multcomp’ ...
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (multcomp)
* installing *source* package ‘sandwich’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (sandwich)
* installing *source* package ‘strucchange’ ...
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (strucchange)

The downloaded packages are in
	‘/tmp/RtmpBMLKoN/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = c("Rcmdr", "abind", "caTools", "car",  :
  installation of package 'caTools' had non-zero exit status
2: In install.packages(pkgs = c("Rcmdr", "abind", "caTools", "car",  :
  installation of package 'effects' had non-zero exit status
3: In install.packages(pkgs = c("Rcmdr", "abind", "caTools", "car",  :
  installation of package 'rgl' had non-zero exit status
> system ("chown sc /home/sc/.rkward/package_archive/*")
chown: cannot access `/home/sc/.rkward/package_archive/*': No such file or directory
> q ()

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