[ncl-install] Problems build ncl 6.4.0 on Archlinux

[Kevin Hallock]

Hi Xavier,

First of all, thank you for maintaining this package on the AUR. I use Arch Linux at home, so it’s great to see someone supporting this!

I tried makepkg’ing the PKGBUILD you provided, but I encountered the same H5Rdereference error. I noticed that the hdf5_18 package is listed as a dependency, and then noticed that /usr/lib/hdf5_18 does not include libhdf5_hl.so. Someone reported this for a previous version of hdf5_18, but it doesn’t appear to have been fixed since then: https://bugs.archlinux.org/task/51902 <https://bugs.archlinux.org/task/51902> 

I also found that the newer hdf5 package was installed as a dependency for both gdal and netcdf, with its libs and includes directly in /usr/lib and /usr/include (as opposed to /usr/{lib,include}/hdf5_18 for hdf5_18); the libs and includes seem to be duplicated between the two packages (except the libhdf5_hl.so* files mentioned above), so I wonder if perhaps having both of these installed is causing a conflict?

Also, I noticed that the Site.local you provided has “-I/usr/include/hdf5_18” in IncSearch, but no corresponding “-L/usr/lib/hdf5_18” in LibSearch. I tried adding “-L/usr/lib/hdf5_18”, but the build still failed.

For what it’s worth, /usr/lib/hdf5_18/libhdf5.so does seem have a reference to H5Rdereference:
$ nm -D /usr/lib/hdf5_18/libhdf5.so | grep H5Rdereference
000000000016cfb0 T H5Rdereference

I hope this helps!
Kevin

PS - I currently run NCL 6.4.0 on Arch using conda: http://ncl.ucar.edu/Download/conda.shtml <http://ncl.ucar.edu/Download/conda.shtml> 

> On May 15, 2017, at 3:06 PM, Xavier Corredor Llano <xcorredorl at unal.edu.co> wrote:
> 
> hi everyone, 
> 
> I'm the maintainer of the NCL packages for Archlinux [1], I have some issues for build the new version 6.4.0, the error is:
> 
> NclNewHDF5.o: In function `_checkH5attribute':
> NclNewHDF5.c:(.text+0x2818): undefined reference to `H5Rdereference'
> NclNewHDF5.c:(.text+0x3552): undefined reference to `H5Rdereference'
> NclNewHDF5.o: In function `_region2string':
> NclNewHDF5.c:(.text+0x4c89): undefined reference to `H5Rdereference'
> NclNewHDF5.o: In function `_mem2string':
> NclNewHDF5.c:(.text+0x4de1): undefined reference to `H5Rdereference'
> NclNewHDF5.o: In function `_readH5dataInfo':
> NclNewHDF5.c:(.text+0x64aa): undefined reference to `H5Rdereference'
> collect2: error: ld returned 1 exit status
> make[4]: *** [Makefile:707: ncl] Error 1
> make[4]: Leaving directory '/build/ncl/src/ncl_ncarg-6.4.0/ni/src/ncl'
> 
> using hdf5 version 1.8.18, the build instructions (PKGBUILD) and completed build log can found in [2].
> 
> Thanks for any help!
> 
> Xavier
> 
> [1] https://aur.archlinux.org/packages/ncl/
> [2] https://drive.google.com/drive/folders/0B2KQf7Dbx7DUNkZXRVRwOEVLcm8_______________________________________________
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