[ncl-install] Problems build ncl 6.4.0 on Archlinux

[David Brown]

Hi Xavier and Kevin,

H5Rdereference is defined in libhdf5. It is referenced but not defined in
libhdf5_hl.

One thing that might be related to this problem is the fact that in HDF5
1.10.x H5Rdereference has become a macro that points to one of two
different function signatures: H5Rdereference1 or H5Rdereference2,
depending on various compiler flags and/or source code defines.
H5dereference2 has one more argument and is the newer version intended for
use with HDF5 1.10 and newer.
If you were compiling against 1.8.x header files but linking against 1.10
libraries, then that could be a scenario where H5Rdereference would show up
as an undefined symbol. I'm not sure if this is a plausible explanation,
but, if not, it is an interesting coincidence that this is one of only two
cases where a function name was changed to a macro in the migration from
1.8.x to 1.10.x.

See https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html

 -dave



On Mon, May 15, 2017 at 6:31 PM, Kevin Hallock <hallock at ucar.edu> wrote:

> 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
>
> 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
>
> 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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