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Re: netcdf Transition

On 31-07-15 00:15, Sebastiaan Couwenberg wrote:
> On 30-07-15 14:03, Sebastiaan Couwenberg wrote:
>> There are a couple of easy to solve FTBFS that cannot find the hdf5
>> library that will need a patch add the HDF5 variant specific library
>> path. For those issues bugs haven't been filed yet, for all other bugs
>> related to the netcdf transition see:
>> https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=netcdf-split-c-f-cxx;users=debian-gis@lists.debian.org
> To address the hdf5 linking issues I've patched nc-config & netcdf.pc to
> include the HDF5 library & include paths as mentiond in the 'HDF5
> linking issues with new NetCDF packages' thread [1]. These changes will
> be included in netcdf (1:4.4.0~rc2-1~exp4) which I haven't uploaded yet,
> but only use for my rebuilds at the moment.

netcdf (1:4.4.0~rc2-1~exp4) has been uploaded to experimental, it
includes the nc-config & netcdf.pc changes, and also switches back to
the HDF5 serial variant because we cannot provide only the MPI variant.
Providing both is a bit too much work to do properly before the GCC 5
related transitions start.

To not require the build dependency changes for the netcdf-cxx-legacy
and netcdf-fortran -dev packages, we should consider having
libnetcdf-dev recommend the language specific -dev packages.

I've started a new round of rebuilds with the updated netcdf packages,
and it looks much better than the first round.

adios (1.8.0-4~exp1) was uploaded to unstable recently, it includes the
build-dependency on libnetcdff-dev (netcdf-fortran) which is not
available in unstable yet. The buildds cannot build it, so the build
dependency needs to be removed in unstable. It reported this issue in

ncview (2.1.5+ds1-1) still FTBFS because it didn't consider the
/usr/bin/cc symlink to gcc acceptable. I've added a patch in
ncview (2.1.5+ds1-2) to disable these unhelpfull configure checks.

I didn't manage to finish the round of rebuild before GCC 5 was made the
default compiler in unstable causing dependency installation issues.
Except gmt (5.1.2+dfsg1-1 / 5.1.2+dfsg1-2~exp1) all remaining packages
built successfully in the last round, so I expect them to still do with
the updated netcdf packages. I also suspect the gmt FTBFS is fixed now
without needing the changes in experimental.

While I'd liked to have finished my last round of rebuilds, I'd think
we're ready for the netcdf transition.

Transition: netcdf

 libnetcdfc7   (1:4.1.3-7.2) -> libnetcdf7       (1:4.4.0~rc2-1~exp4)
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4-1 (4.2.1-1~exp4) [cxx4]
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4   (4.2-1~exp4)   [legacy]
 libnetcdff5   (1:4.1.3-7.2) -> libnetcdff6      (4.4.2-1~exp5)

The status of the most recent rebuilds is as follows. Entries tagged
with [+] build successfully after applying the patch from the bugreport.

 netcdf-cxx         (4.2.1-1~exp4)                       OK
 netcdf-cxx-legacy  (4.2-1~exp4)                         OK
 netcdf-fortran     (4.4.2-1~exp5)                       OK

 adios              (1.8.0-4~exp1)                       OK [+]
 cdftools           (3.0-1 / 3.0-2~exp1)                 FTBFS / OK
 cmor               (2.9.1-5 / 2.9.1-6)                  OK / OK
 dx                 (1:4.4.4-7)                          OK
 etsf-io            (1.0.3-4 / 1.0.4-1~exp1)             OK / OK [+]
 exodusii           (6.02.dfsg.1-5 / 6.02.dfsg.1-6)      OK / OK
 ferret-vis         (6.9.3-1 / 6.9.3-2~exp1)             FTBFS / OK
 gdal               (1.10.1+dfsg-9 / 1.11.2+dfsg-1~exp4) OK / OK
 gnudatalanguage    (0.9.5-2)                            OK
 grace              (1:5.1.25-1)                         OK
 grads              (2:2.0.2-5 / 2:2.0.2-6)              OK / OK
 gri                (2.12.23-8)                          FTBFS [#790526]
 kst                (2.0.3-4)                            OK
 libpdl-netcdf-perl (4.20-1)                             OK [+]
 magics++           (2.24.7-3 / 2.24.7-4)                FTBFS / OK
 minc               (2.2.00-6)                           OK [+]
 nco                (4.5.1-1)                            OK
 ncview             (2.1.5+ds1-2)                        OK
 netcdf4-python     (1.1.9-1 / 1.1.9-2~exp2)             OK / OK
 oasis3      (3.mct+dfsg.121022-3 / 3.mct+dfsg.121022-5) OK / OK [+]
 octave-octcdf      (1.1.8-1)                            OK
 ovito              (2.3.3+dfsg1-1)                      OK
 python-scientific  (2.9.4-3)                            OK
 r-cran-ncdf4       (1.13-1)                             OK
 r-cran-rnetcdf     (1.6.3-1-1)                          OK
 ruby-netcdf        (                          OK
 v-sim              (3.7.2-1)                            OK
 vtk                (5.8.0-17.5 / 5.10.1+dfsg-1)         OK / OK [+]

 cdo                (1.6.6+dfsg.1-3 / 1.6.6+dfsg.1-4)    OK / OK
 gmt                (5.1.2+dfsg1-1 / 5.1.2+dfsg1-2~exp1) TODO / TODO
 metview            (4.5.6-3 / 4.5.6-4exp1)              TODO / TODO [+]
 ncl                (6.3.0-3~exp1 / 6.3.0-3)             TODO / TODO
 vtk6               (6.2.0+dfsg1-2)                      TODO [+]

Kind Regards,


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