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

[Simon Urbanek]

For posterity: this message got apparently suck in some queue - the issue has been resolved off-list in the mean time where simply HDF5 binary was not installed on the build machine.

Cheers,
Simon

On Jun 20, 2014, at 6:14 PM, David W. Pierce <dpierce at ucsd.edu> wrote:

> 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
> 
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