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Re: netcdf Transition

To followup on the rebuilds done by Ross, I've also started a round of

At the same time I've fixed my ben setup for experimental, so we can now
also track which packages in experimental are fixed already:


Thanks to Alastair several reverse dependencies already have fixed
versions available in experimental. They're still built against the old
libraries because the new netcdf packages hadn't been built with netcdf
(>= yet, that's been corrected with the recent uploads to

etsf-io (1.0.3-4 / 1.0.4-1~exp1) initially FTBFS, but succeeds when the
build dependency on libnetcdff-dev is added. I've forwarded the patches
in #793823.

gnudatalanguage (0.9.5-2) still FTBFS due to missing libraries:

 /usr/bin/ld: cannot find -lhdf5_hl
 /usr/bin/ld: cannot find -lhdf5
 /usr/bin/ld: cannot find -lcurl

These are build dependencies of netcdf, so libnetcdf-dev should pull in
their -dev packages. I've added the dependencies in netcdf
(1:4.4.0~rc2-1~exp2), but that only resolves the missing curl library.

gri (2.12.23-8) FTBFS due to #790526, this RC bug has scheduled it for
removal from testing. gri (2.12.23-8) built successfully when Ross
tested it.

libpdl-netcdf-perl (4.20-1) FTBFS because it doesn't search the
Multi-Arch library paths for netcdf.so. Exporting the Multi-Arch library
path allows the build to succeed. I've forwarded the patch in #nnnnnn.

magics++ (2.24.7-3) FTBFS because it's missing NetCDF C++, adding the
libnetcdf-c++4-dev build dependency did not resolve it, so
libnetcdf-cxx-legacy-dev was tried instead and it allows the build to
succeed. Patch forwarded in #793882.

minc (2.2.00-6) FTBFS because a NetCDF related test fails:

 FAIL: testminctools.sh

 Converted file to MINC2.0 format.
 ncvarid: ncid 65536: NetCDF: Variable not found
 Version: 1 (netCDF)
 FAIL testminctools.sh (exit status: 3)

I've patched minc (2.2.00-6) to report verbose test output and ignore
any test failures to allow the build to succeed. The patch is forwarded
in #793885 in which I also asked the maintainer to help fix the test

nco (4.5.1-1) FTBFS with some errors:

 libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. \
   -I/usr/include -D_FORTIFY_SOURCE=2 -I/usr/include -g -O2 \
   -fstack-protector-strong -Wformat -Werror=format-security -std=c99 \
   -D_BSD_SOURCE -D_POSIX_SOURCE -c nco_bnr.c  -fPIC -DPIC \
   -o .libs/nco_bnr.o
 In file included from /usr/include/string.h:635:0,
                  from nco_att_utl.h:22,
                  from nco_att_utl.c:10:
 nco_sng_utl.h:79:3: error: expected identifier or '(' before
    strdup /* [fnc] Duplicate string */
 In file included from /usr/include/string.h:635:0,
                  from nco_netcdf.h:46,
                  from nco_aux.h:22,
                  from nco_aux.c:19:
 nco_sng_utl.h:79:3: error: expected identifier or '(' before
    strdup /* [fnc] Duplicate string */

This FTBFS issue has been reported in #793891 and will need to be
resolved to not hinder the netcdf transition.


The bugs filed for the netcdf transition have been usertagged for easy
reference, see:


Transition: netcdf

 libnetcdfc7   (1:4.1.3-7.2) -> libnetcdf7       (1:4.4.0~rc2-1~exp2)
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4-1 (4.2.1-1~exp3) [cxx4]
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4   (4.2-1~exp3)   [legacy]
 libnetcdff5   (1:4.1.3-7.2) -> libnetcdff6      (4.4.2-1~exp4)

The status of the most recent rebuilds is as follows.

 adios              (1.8.0-2 / 1.8.0-3)                  OK / 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 [patch]
 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)                            FTBFS
 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
 kst                (2.0.3-4)                            OK
 libpdl-netcdf-perl (4.20-1)                             OK [patch]
 magics++           (2.24.7-3)                           OK [patch]
 minc               (2.2.00-6)                           OK [patch]
 nco                (4.5.1-1)                            FTBFS
 ncview             (2.1.5+ds1-1)                        TODO
 netcdf4-python     (1.1.8-2)                            TODO
 oasis3      (3.mct+dfsg.121022-3 / 3.mct+dfsg.121022-4) TODO / TODO
 octave-octcdf      (1.1.8-1)                            TODO
 ovito              (2.3.3+dfsg1-1)                      TODO
 python-scientific  (2.9.4-3)                            TODO
 r-cran-ncdf4       (1.13-1)                             TODO
 r-cran-rnetcdf     (1.6.3-1-1)                          TODO
 ruby-netcdf        (0.6.6-2)                            TODO
 v-sim              (3.7.2-1)                            TODO
 vtk                (5.8.0-17.5)                         TODO

 cdo                (1.6.6+dfsg.1-3)                     TODO
 gmt                (5.1.2+dfsg1-1)                      TODO
 metview            (4.5.6-1)                            TODO
 ncl                (6.3.0-3~exp1)                       TODO
 vtk6               (6.2.0+dfsg1-1                       TODO

Kind Regards,


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