[R-SIG-Mac] Installing biOps fails with "Symbol not found: _TIFFClose"

Dominic Steinitz dominic at steinitz.org
Sat Feb 16 17:37:41 CET 2013

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.

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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