[R-SIG-Mac] ncdf4 not auto-building on Mavericks -- can't tell why

[David W. Pierce]

Hello,

I'm the package maintainer for ncdf4, which provides an R interface
for netcdf files. I have successfully built and installed the package
on a OS X Mavericks machine I have access to, but the nightly build on
that platform for R failed with an error I'm trying to understand.

I'm sure it's documented somewhere who to contact about odd results on
the specific Mavericks machine used for the CRAN compiles, but I have
not been able to find that despite some searching. Does anyone know if
there's a contact who can be approached about the software environment
of that particular machine?

More technical details of the compiling problem follow.

The netcdf library has an accessory script that shows how it was
configured on the machine in question (the Mavericks machine in this
case). This shows:

------

This netCDF 4.1.3 has been built with the following features:

  --cc        -> gcc -arch i386 -std=gnu99
  --cflags    ->  -I/usr/local/include
  --libs      -> -L/usr/local/lib  -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl

-----

which is stating that the library compiled correctly using
-L/usr/local/lib -lhdf4_hl (among other libs). Yet the R build failed
with:

clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o
-Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5
-lm -lz -lcurl -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
ld: library not found for -lhdf5_hl
clang: error: linker command failed with exit code 1 (use -v to see invocation)

which claims that -lhdf5_hl was not found. The odd part is, if that
library was found when the netcdf library was compiled, why wasn't it
found when the R ncdf4 package was compiled with the same -L library
path flag? Am I missing something here?

Also, I know essentially nothing about Macs (hopefully some people
here can help me on this), but I see that the netcdf library was
compiled with "-arch i386", while the R package was compiled with
"clang -Wall -mtune=core2 -g -O2", which does not specify -arch i386.
Is it possible that the linker is reporting "hdf5_hl" not found
because the existing library is a 32-bit library but it's looking for
a 64-bit library? On Windows, for example,this would give an error
along the lines of "library is 32 bit not 64 bit" but I don't know how
OS X would handle this.

Thanks for any info,

--Dave

-- 
Dr. David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography, La Jolla, California, USA
(858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce at ucsd.edu