[R] rimage package broken with fedora upgrade
John Kornak
john.kornak at ucsf.edu
Sun Dec 31 03:55:30 CET 2006
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'
>
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