On 16/02/2013 16:37, Dominic Steinitz wrote:
I have searched the archives and while I can find reports of this
problem, I was unable to find any information on what to do to fix
it. Apologies if this is already documented somewhere (and if so
please point me at it). Let me know if should post any more
information to help resolve this.
You should have contacted the package maintainer as per the R posting
guide. But
>> checking for TIFFOpen in -ltiff... no
is the clue. See what config.log has to say ....
[I have no idea whether you actually have libtiff installed and if so
where you got it from. This will typically work with a dynamically
linked libtiff: statically linked ones usually need -ljpeg -lz as well,
and some need more (see packages tiff and rtiff for approaches that
currently work with static libtiff as provided on r.research.att.com/libs).]
Many thanks, Dominic.
install.packages("biOps", type="source")
trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/biOps_0.2.1.1.tar.gz'
Content type 'application/x-gzip' length 1166265 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb
* installing *source* package 'biOps' ...
** package 'biOps' successfully unpacked and MD5 sums checked
checking for gcc... gcc -arch i386 -std=gnu99
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 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for TIFFOpen in -ltiff... no
checking for jpeg_destroy_compress in -ljpeg... yes
checking for fftw_plan_dft in -lfftw3... no
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking jpeglib.h usability... yes
checking jpeglib.h presence... yes
checking for jpeglib.h... yes
checking tiff.h usability... yes
checking tiff.h presence... yes
checking for tiff.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/fft_filters.R
config.status: creating R/fft_funcs.R
config.status: creating R/tiff.R
config.status: creating R/jpeg.R
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c arithmetics.c -o arithmetics.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c canny.c -o canny.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c convolution.c -o convolution.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c crop.c -o crop.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c edge_detection.c -o edge_detection.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c fft_filters.c -o fft_filters.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c fft_funcs.c -o fft_funcs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c filter.c -o filter.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c gaussian.c -o gaussian.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c interpolation.c -o interpolation.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c isodata.c -o isodata.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c isodata_cluster.c -o isodata_cluster.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c jpegio.c -o jpegio.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c kdtree.c -o kdtree.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c kmeans.c -o kmeans.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c kmeans_enhanced.c -o kmeans_enhanced.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c kmeans_kdtree.c -o kmeans_kdtree.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c logics.c -o logics.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c luts.c -o luts.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c marr_hildreth.c -o marr_hildreth.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c minification.c -o minification.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c mirroring.c -o mirroring.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c morphology.c -o morphology.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c noise_gen.c -o noise_gen.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c rotate.c -o rotate.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c scale.c -o scale.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c shencastan.c -o shencastan.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c tiffio.c -o tiffio.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c translation.c -o translation.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG
-I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o biOps.so arithmetics.o canny.o convolution.o crop.o
edge_detection.o fft_filters.o fft_funcs.o filter.o gaussian.o interpolation.o
isodata.o isodata_cluster.o jpegio.o kdtree.o kmeans.o kmeans_enhanced.o
kmeans_kdtree.o logics.o luts.o marr_hildreth.o minification.o mirroring.o
morphology.o noise_gen.o rotate.o scale.o shencastan.o tiffio.o translation.o
utils.o -lm -ljpeg -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps/libs/i386/biOps.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps/libs/i386/biOps.so,
6): Symbol not found: _TIFFClose
Referenced from:
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps/libs/i386/biOps.so
Expected in: flat namespace
in
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps/libs/i386/biOps.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing
'/Library/Frameworks/R.framework/Versions/2.15/Resources/library/biOps'
The downloaded source packages are in
'/private/var/folders/3p/m593dprn5snbjz6sc45c77f80000gn/T/RtmpKEonYx/downloaded_packages'
Warning message:
In install.packages("biOps", type = "source") :
installation of package 'biOps' had non-zero exit status
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--
Brian D. Ripley, [email protected]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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