rimage package broken with fedora upgrade - R-help

Sat, Dec 30, 2006 6:55 PM #

Dear R list members

I would be grateful if anyone could guide me to a solution for fixing my 
rimage package problem described below.

I recently upgraded my machine from fedora core 3 to fedora core 6 and 
then upgraded R from version 2.3.1 from version 2.4.1.

I then fired up R, tried to load the rimage library and received the 
following messages:

  > library(rimage)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
         unable to load shared library 
'/usr/lib/R/library/rimage/libs/rimage.so':
   /usr/lib/R/library/rimage/libs/rimage.so: cannot restore segment prot 
after reloc: Permission denied
Error in library(rimage) : .First.lib failed for 'rimage'
 >

I tried removing and re-installing rimage. The install seemed to go well 
but I received the identical error messages upon loading. (I provide the 
output from the package re-install at the very end of this email in case 
it is useful.)

I am running R version 2.4.1 and fc6 on a dual boot (with XP) Pentium 4 
Dell Dimension 8250. I have both fftw-2.1.5 and fftw-3.1.2 on my machine 
within /usr/local and .

rimage was working fine on the same machine before I upgraded from R 
2.3.1 and fc3.

I searched online but was unable to find any relevant posts.

Thanks again

John

John Kornak,PhD
Assistant Professor
Departments of Radiology, and Epidemiology & Biostatistics
University of California, San Francisco
Box 0946
San Francisco, CA 94143
Tel: (415) 353-4740
fax: (415) 353-9423
Email: john.kornak at ucsf.edu

#############################################

 > install.packages("rimage")
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rimage_0.5-7.tar.gz'
Content type 'application/x-gzip' length 331029 bytes
opened URL
==================================================
downloaded 323Kb

* Installing *source* package 'rimage' ...
checking for g++... g++
checking for C++ compiler default output... 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 g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking fftw.h usability... yes
checking fftw.h presence... yes
checking for fftw.h... yes
checking jpeglib.h usability... yes
checking jpeglib.h presence... yes
checking for jpeglib.h... yes
checking for inline... inline
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -c equalize.cpp -o equalize.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c fftw_access_func.c 
-o fftw_access_func.o
g++ -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -c freqfilters.cpp -o freqfilters.o
g++ -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -c interface.cpp -o interface.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c jpegio.c -o jpegio.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c laplacian.c -o 
laplacian.o
laplacian.c: In function ?laplacian?:
laplacian.c:14: warning: implicit declaration of function ?clearFrame?
g++ -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -c matrix.cpp -o matrix.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c smooth.c -o smooth.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -g -O2 
-I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c sobel.c -o sobel.o
g++ -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o rimage.so equalize.o 
fftw_access_func.o freqfilters.o interface.o jpegio.o laplacian.o 
matrix.o smooth.o sobel.o -ljpeg -lfftw  -L/usr/lib/R/lib -lR
** R
** data
** help
  >>> Building/Updating help pages for package 'rimage'
      Formats: text html latex example
   cat                               text    html    latex   example
   clipping                          text    html    latex   example
   equalize                          text    html    latex   example
   fftImg                            text    html    latex   example
   fftw                              text    html    latex
   highpass                          text    html    latex   example
   imageType                         text    html    latex   example
   imagematrix                       text    html    latex   example
   laplacian                         text    html    latex   example
   logo                              text    html    latex   example
   lowpass                           text    html    latex   example
   meanImg                           text    html    latex   example
   minImg                            text    html    latex   example
   normalize                         text    html    latex   example
   plot.imagematrix                  text    html    latex   example
   print.imagematrix                 text    html    latex   example
   read.jpeg                         text    html    latex   example
   rgb2grey                          text    html    latex   example
   sobel                             text    html    latex   example
   sobel.h                           text    html    latex   example
   sobel.v                           text    html    latex   example
   thresholding                      text    html    latex   example
** building package indices ...
* DONE (rimage)

The downloaded packages are in
         /tmp/RtmprJeHV4/downloaded_packages
 > library(rimage)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
         unable to load shared library 
'/usr/lib/R/library/rimage/libs/rimage.so':
   /usr/lib/R/library/rimage/libs/rimage.so: cannot restore segment prot 
after reloc: Permission denied
Error in library(rimage) : .First.lib failed for 'rimage'
 >

Oleg Sklyar

Sat, Dec 30, 2006 7:51 PM #

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Jonathan Baron

Sun, Dec 31, 2006 7:32 AM #

Responding to the original post, which I did not save.

I had the same problem, but, unfortunately, a slightly different error 
message.  My error message said:

Error in dyn.load(x, as.logical(local), as.logical(now)) : 
        unable to load shared library
'/usr/lib/R/library/rimage/libs/rimage.so':
  libfftw.so.2: cannot open shared object file: No such file or
directory
Error in library(rimage) : .First.lib failed for 'rimage'

So I took the hint and said

yum install libfftw.so.2

and this installed libfftw,
which cured the problem.

But you did not get this error message about libfftw.

Jon