Just a point of comparison to the results others got for how biOps
compiles under Snow Leopard:
Here are the warnings and notices I got when compiling, using the
R-gui's Package Installer to compile from source:
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking fftw3.h usability... no
checking fftw3.h presence... no
checking for fftw3.h... no
configure: WARNING: Can't find fftw3 header
I haven't exercised many of the functions in the package yet, but this
seems to be a better result than Simon got.
Carl
---- S. Urbanek's results ----
The package has some issues with detecting TIFF and more over references
it even though its detection fails -- the error log says:
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.12/biOps.Rcheck/biOps/libs/i386/biOps.so':
dlopen(/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.12/biOps.Rcheck/biOps/libs/i386/biOps.so,
6): Symbol not found: _TIFFClose
Referenced from:
/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.12/biOps.Rcheck/biOps/libs/i386/biOps.so
Expected in: dynamic lookup
ERROR: loading failed
While the configuration fails to detect TIFF (because it's using the
wrong flags) and yet it still does reference it in the code (but not at
link time):
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 tiff.h usability... yes
checking tiff.h presence... yes
checking for tiff.h... yes
[...]
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o biO
ps.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 shenca
stan.o tiffio.o translation.o utils.o -lm -ljpeg -lfftw3
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
There are apparently two bugs in biOps:
1) the TIFF detection uses wrong flags - it fails to add dependencies:
configure:2624: checking for TIFFOpen in -ltiff
configure:2659: gcc -arch x86_64 -std=gnu99 -o conftest -g -O2
conftest.c -ltiff >&5
Undefined symbols:
"_jpeg_read_raw_data", referenced from:
_jpeg_read_raw_data_encap in libtiff.a(tif_ojpeg.o)
_TIFFjpeg_read_raw_data in libtiff.a(tif_jpeg.o)
"_jpeg_write_scanlines", referenced from:
_TIFFjpeg_write_scanlines in libtiff.a(tif_jpeg.o)
"_jpeg_write_tables", referenced from:
_TIFFjpeg_write_tables in libtiff.a(tif_jpeg.o)
"_inflateSync", referenced from:
_PixarLogDecode in libtiff.a(tif_pixarlog.o)
_ZIPDecode in libtiff.a(tif_zip.o)
[...]
so it's missing -ljpeg -lz
In fact it's checking jpeg and TIFF in the inverse order, so chances are
if check for libz was added first, then jpeg and then tiff that it might
work properly.
2) it is still referencing libTIFF in the package even though it did not
link against libTIFF (I didn't dig deeper to see why - likely issue with
setting a conditional or not respecting it).
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