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Tasklist

FS#58189 - [netcdf] Out of date -- unable to build gdal-related content

Attached to Project: Community Packages
Opened by Joss Wright (tealeaf) - Tuesday, 10 April 2018, 15:57 GMT
Last edited by Doug Newgard (Scimmia) - Tuesday, 10 April 2018, 17:25 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To No-one
Architecture All
Severity Low
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:

netcdf 4.5.0-1 (x86_64) appears to be missing needed references for the latest version of gdal. This is making the "rgdal" library in R impossible to build with the latest netcdf/gdal as of 2018-04-10.

Additional info:

This can easily be fixed by updating the pkgver in the current netcdf PKGBUILD to 4.6.1 and removing the lines relating to the fix-tst_h_dimscales.patch, which now seems to be unnecessary. (I haven't tested this extensively, but attempting the patch reports it as already being applied in 4.6.1.)

Steps to reproduce:

Load R and attempt to install the "rgdal" package.

> install.packages("rgdal")
...
/usr/bin/ld: warning: libhdf5_hl.so.100, needed by /usr/lib/libnetcdf.so, not found (try using -rpath or -rpath-link)
/usr/lib/libnetcdf.so: undefined reference to `H5DSget_num_scales'
/usr/lib/libnetcdf.so: undefined reference to `H5DSset_scale'
/usr/lib/libnetcdf.so: undefined reference to `H5DSget_scale_name'
/usr/lib/libnetcdf.so: undefined reference to `H5LTopen_file_image'
/usr/lib/libnetcdf.so: undefined reference to `H5DSis_scale'
/usr/lib/libnetcdf.so: undefined reference to `H5DSdetach_scale'
/usr/lib/libnetcdf.so: undefined reference to `H5DSiterate_scales'
/usr/lib/libnetcdf.so: undefined reference to `H5DSattach_scale'

As mentioned, updating the PKGBUILD to update the sha256sums and pkgver fixes this and allows installation.
This task depends upon

Closed by  Doug Newgard (Scimmia)
Tuesday, 10 April 2018, 17:25 GMT
Reason for closing:  Fixed
Additional comments about closing:  hdf5 downgraded
Comment by Doug Newgard (Scimmia) - Tuesday, 10 April 2018, 16:33 GMT
With what version of hdf5? 1.10.2 has been pulled from testing because of this.
Comment by Joss Wright (tealeaf) - Tuesday, 10 April 2018, 17:10 GMT
Ah, it looks like I must have upgraded at the right moment to pull in hdf5 1.10.2-1.

Is it just this issue causing the downgrade to hdf5? Manually updating the pkgver in netcdf to 4.6.1 seems to have resolved it for me.
Comment by Doug Newgard (Scimmia) - Tuesday, 10 April 2018, 17:25 GMT
Multiple things would need rebuilt, but the issue goes a bit deeper: https://forum.hdfgroup.org/t/cmake-and-autotools-builds-differences/4277 and https://bugs.archlinux.org/task/58150

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