[ncl-install] Problems build ncl 6.4.0 on Archlinux

Mon May 15 20:31:19 MDT 2017

On Monday, 15 May 2017 20:18:15 -05 David Brown wrote:
> 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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Hi Kevin and David!

Thanks for your help, but not build yet. I tried build ncl with hdf5 1.10.0 
(disabling hdf-eos5 because it not build with this version) and the error is:

NclNewHDF5.c:1499:55: error: incompatible type for argument 3 of 
‘H5Rdereference2’
      dataset_id = H5Rdereference(attr_id, H5R_OBJECT, &rbuf[i]);
                                                       ^
NclNewHDF5.c:1499:19: error: too few arguments to function ‘H5Rdereference2’
      dataset_id = H5Rdereference(attr_id, H5R_OBJECT, &rbuf[i]);

My question here is if ncl is compatible with hdf5 1.10.x, I think that Kevin 
is right if build ncl using hdf5 1.8.x while some dependencies (like gdal, 
netcdf) are built with 1.10.x version, and it maybe causing a conflict.

Regards,
Xavier CLL
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