Bug#755539: transition: hdf5
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: transition
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Dear Release Team,
The last hdf5 release package in experimental (1.8.13+docs-2)
introduced a soname bump (7 -> 8) due to the MPIPOSIX API removal, plus
significant path changes to allow the co-installation of the different
flavors (serial, mpich, openmpi) of the library.
Almost all affected source packages need to be adapted to acknowledge
the new paths for the hdf5 headers and libraries, depending on the
flavor of the library used for the build. For most of them the
fix is trivial and consists in adding proper --with-hdf5 configure
option or setting C[PP]FLAGS and LDFLAGS at configure step.
For example, with cmake build system:
include /usr/share/mpi-default-dev/debian_defaults
export CMAKE_INCLUDE_PATH=/usr/include/hdf5/$(ARCH_DEFAULT_MPI_IMPL)
export CMAKE_LIBRARY_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/$(ARCH_DEFAULT_MPI_IMPL)
With configure scripts:
- --with-hdf5=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
or
- --with-hdf5-include=/usr/include/hdf5/serial
- --with-hdf5-lib=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
Other trivial cases:
export CPPFLAGS += -I/usr/include/hdf5/serial
export LDFLAGS += -Wl,-L/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
Affected packages are:
adios
armadillo
aster
cdo
cmor
code-saturne
dolfin (not in testing)
exodusii
flann
gdal
getdp (not in testing)
gmsh
gnudatalanguage (not in testing)
gpiv
gpivtools
grads
h5py
h5utils
hdf-eos5
insighttoolkit4
jhdf
libcgns
libgpiv
libmatio
libpdl-io-hdf5-perl (not in testing)
libvigraimpex
magics++
mathgl
med-fichier
meep
meep-lam4
meep-mpich2
meep-mpi-default
meep-openmpi
minc
mpb
ncl
netcdf
nexus
oasis3
octave
octave-bim
octave-msh
ovito
paraview
petsc
pygpiv
pytables
python-shogun
r-cran-hdf5
ruby-hdfeos5
salome-kernel
scilab
shogun
silo-llnl
slepc (not in testing)
stimfit
syrthes
tessa (not in testing)
vtk
vtk6
xdmf
xmds2 (not in testing)
yorick-hdf5
I've tested a build against hdf5 1.8.13+docs-2 for all of them. Here are
the cases where the fix is not trivial:
FTBFS in sid:
gnudatalanguage (blocked by plplot which is in a really bad state)
cmor (missing build-deps in debian/control)
Use deprecated MPIPOSIX API:
h5py
silo-llnl
Minor patch to the build system needed:
hdf-eos5
jhdf
libpdl-io-hdf5-perl
r-cran-hdf5
ruby-hdfeos5
scilab
syrthes
Really weird build system (ymake)
ncl
There are also some cases where the build dependency on libhdf5-*dev
seems useless:
magics++
oasis3
slepc
Now that I've achieved all these test builds I think it is time to
request a transition slot.
Ben file proposal:
title = "hdf5";
is_affected = .build-depends ~ /libhdf5-((mpi|mpich|mpich2|openmpi|serial)-)?dev/ | .depends ~ /libhdf5-((cpp|mpich|mpich2|openmpi)-)?7/ | .depends ~ /libhdf5-((cpp|mpich|openmpi)-)?8/;
is_good = .depends ~ /libhdf5-((cpp|mpich|openmpi)-)?8/;
is_bad = .depends ~ /libhdf5-((cpp|mpich|mpich2|openmpi)-)?7/;
Please tell me when I can upload to unstable.
Many thanks in advance,
_g.
- -- System Information:
Debian Release: jessie/sid
APT prefers testing
APT policy: (500, 'testing'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 3.14-1-486
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
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