Your message dated Fri, 4 Nov 2016 21:34:27 +0100
with message-id <144f2c16-847d-80a7-368d-cd17c56c8...@debian.org>
and subject line Fixed a long time ago
has caused the Debian Bug report #675936,
regarding E: Could not perform immediate configuration on 'libhdf5-serial-dev'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
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--
675936: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=675936
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: libhdf5-serial-dev
Version: 1.8.8-9
Severity: serious
Justification: Package fails to install
Hi,
the likelihood of this bug being reported to the wrong package is quite
high, but I'll do it nevertheless, as this is were I noticed the
problem. Here is the commented log:
(all done on a more or less up-to-date i386 wheezy)
% sudo apt-get install python-h5py
[sudo] password for michael:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
python-scientific libgl2ps0 libgps19 libvo-aacenc0 dcmtk libxp-dev
libvo-amrwbenc0 libhal1 libgl2ps-dev
qt-assistant-compat libyajl1 libmysqlclient18 libarmadillo3 libexiv2-12
libfreexl1 libdapclient3 libdapserver7
libkml0 libspatialite3
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
hdf5-helpers hdf5-tools libarmadillo3 libdapclient3 libdapserver7 libexiv2-12
libfreexl1 libgeos-3.3.1
libgeos-c1 libhdf5-7 libhdf5-dev libhdf5-serial-dev libkml0 libmysqlclient18
libspatialite3 mysql-common
octave3.2 octave3.2-headers
Suggested packages:
libhdf5-doc octave3.2-info octave3.2-doc octave3.2-htmldoc octave3.2-emacsen
The following packages will be REMOVED:
caret gdal-bin itksnap libgdal1-1.7.0 libhdf5-openmpi-1.8.4
libhdf5-openmpi-dev libkwwidgets1-dev
libkwwidgets1.0.1009 libminc-dev libminc2-1 libnetcdf-dev libnetcdf6
libshogun8 libvtk5-dev libvtk5-qt4-dev
libvtk5.6 libvtk5.8 libvtk5.8-qt4 libvtkgdcm2.0 mayavi2 merkaartor mitools
odin python-insighttoolkit3
python-netcdf python-surfer python-vtk python-vtkgdcm qlandkartegt tcl-vtk
The following NEW packages will be installed:
hdf5-helpers libarmadillo3 libdapclient3 libdapserver7 libexiv2-12 libfreexl1
libgeos-3.3.1 libhdf5-7
libhdf5-dev libhdf5-serial-dev libkml0 libmysqlclient18 libspatialite3
python-h5py
The following packages will be upgraded:
hdf5-tools libgeos-c1 mysql-common octave3.2 octave3.2-headers
5 upgraded, 14 newly installed, 31 to remove and 909 not upgraded.
Need to get 20.3 MB of archives.
After this operation, 770 MB disk space will be freed.
Do you want to continue [Y/n]?
Get:1 http://ftp2.de.debian.org/debian/ wheezy/main hdf5-tools i386 1.8.8-9
[629 kB]
Get:2 http://ftp2.de.debian.org/debian/ wheezy/main hdf5-helpers i386 1.8.8-9
[32.8 kB]
Get:3 http://ftp2.de.debian.org/debian/ wheezy/main libhdf5-dev i386 1.8.8-9
[2,492 kB]
Get:4 http://ftp2.de.debian.org/debian/ wheezy/main libhdf5-serial-dev i386
1.8.8-9 [24.3 kB]
Get:5 http://ftp2.de.debian.org/debian/ wheezy/main octave3.2-headers i386
3.2.4-12+b1 [596 kB]
Get:6 http://ftp2.de.debian.org/debian/ wheezy/main octave3.2 i386 3.2.4-12+b1
[9,509 kB]
Get:7 http://ftp2.de.debian.org/debian/ wheezy/main libhdf5-7 i386 1.8.8-9
[1,331 kB]
Get:8 http://ftp2.de.debian.org/debian/ wheezy/main libdapclient3 i386
3.11.1-10 [165 kB]
Get:9 http://ftp2.de.debian.org/debian/ wheezy/main libdapserver7 i386
3.11.1-10 [99.9 kB]
Get:10 http://ftp2.de.debian.org/debian/ wheezy/main mysql-common all
5.5.23+dfsg-2 [74.4 kB]
Get:11 http://ftp2.de.debian.org/debian/ wheezy/main libmysqlclient18 i386
5.5.23+dfsg-2 [1,026 kB]
Get:12 http://ftp2.de.debian.org/debian/ wheezy/main libfreexl1 i386 1.0.0b-1
[22.0 kB]
Get:13 http://ftp2.de.debian.org/debian/ wheezy/main libarmadillo3 i386
1:3.2.0+dfsg-2 [18.9 kB]
Get:14 http://ftp2.de.debian.org/debian/ wheezy/main libexiv2-12 i386 0.23-1
[798 kB]
Get:15 http://ftp2.de.debian.org/debian/ wheezy/main libgeos-3.3.1 i386 3.3.1-1
[667 kB]
Get:16 http://ftp2.de.debian.org/debian/ wheezy/main libgeos-c1 i386 3.3.1-1
[173 kB]
Get:17 http://ftp2.de.debian.org/debian/ wheezy/main python-h5py i386
2.0.1-2+b1 [1,276 kB]
Get:18 http://ftp2.de.debian.org/debian/ wheezy/main libkml0 i386 1.3.0~r863-4
[496 kB]
Get:19 http://ftp2.de.debian.org/debian/ wheezy/main libspatialite3 i386
3.0.0~beta20110817-3 [870 kB]
Fetched 20.3 MB in 17s (1,135 kB/s)
E: Could not perform immediate configuration on 'libhdf5-serial-dev'. Please
see man 5 apt.conf under APT::Immediate-Configure for details. (2)
It looked like a dependency nightmare was causing this, and it needed
the equivalent of the following to get it to work. In summary: Remove
anything that is remotely netcdf/hdf-related and bring it back by hand.
% sudo dpkg --remove libhdf5-openmpi-dev octave3.2-headers libminc-dev
libminc2-1 libnetcdf6 hdf5-tools libshogun8 libgdal1-1.7.0 octave-optim
octave-specfun octave-gsl octave-psychtoolbox-3 octave-image octave-control
octave-miscellaneous octave-signal octave-statistics octave-audio octave-struct
caret libminc2-1 python-netcdf libvtk5.6 libvtk5.8 libnetcdf-dev merkaartor
gdal-bin qlandkartegt python-insighttoolkit3 python-vtkgdcm itksnap
libvtkgdcm2.0 tcl-vtk mitools python-vtk odin libvtk5-dev libkwwidgets1.0.1009
libvtk5.8-qt4 mayavi2 libkwwidgets1-dev libvtk5-qt4-dev python-surfer
octave3.2
...
% sudo dpkg -i /var/cache/apt/archives/libhdf5-serial-dev_1.8.8-9_i386.deb
/var/cache/apt/archives/libhdf5-dev_1.8.8-9_i386.deb
/var/cache/apt/archives/libhdf5-7_1.8.8-9_i386.deb
...
dpkg: dependency problems prevent configuration of libhdf5-dev:
libhdf5-dev depends on hdf5-helpers; however:
Package hdf5-helpers is not installed.
...
% sudo apt-get install -f
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
units libcxsparse2.2.3 libcamd2.2.0 psychtoolbox-3-lib libglpk0 libarpack2
libspatialite2
python-scientific libxerces-c28 libfreenect0.0 libgl2ps0 libgps19 libogdi3.2
libqrupdate1 libvo-aacenc0 dcmtk
libxp-dev libgeos-3.2.2 octave3.2-common psychtoolbox-3-common libdap11
libvo-amrwbenc0 libhal1 libepsilon0
libhdf4-0-alt libgeos-c1 libgl2ps-dev qt-assistant-compat libyajl1 libsysfs2
libccolamd2.7.1
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
hdf5-helpers
The following NEW packages will be installed:
hdf5-helpers
0 upgraded, 1 newly installed, 0 to remove and 641 not upgraded.
2 not fully installed or removed.
Need to get 0 B/32.8 kB of archives.
After this operation, 98.3 kB of additional disk space will be used.
Do you want to continue [Y/n]?
And now I could install the intended package:
% sudo apt-get install python-h5py
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
units libcxsparse2.2.3 libcamd2.2.0 psychtoolbox-3-lib libglpk0 libarpack2
libspatialite2
python-scientific libxerces-c28 libfreenect0.0 libgl2ps0 libgps19 libogdi3.2
libqrupdate1 libvo-aacenc0 dcmtk
libxp-dev libgeos-3.2.2 octave3.2-common psychtoolbox-3-common libdap11
libvo-amrwbenc0 libhal1 libepsilon0
libhdf4-0-alt libgeos-c1 libgl2ps-dev qt-assistant-compat libyajl1 libsysfs2
libccolamd2.7.1
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
python-h5py
0 upgraded, 1 newly installed, 0 to remove and 641 not upgraded.
Need to get 0 B/1,276 kB of archives.
After this operation, 4,357 kB of additional disk space will be used.
Retrieving bug reports... Done
Parsing Found/Fixed information... Done
Selecting previously unselected package python-h5py.
(Reading database ... 415379 files and directories currently installed.)
Unpacking python-h5py (from .../python-h5py_2.0.1-2+b1_i386.deb) ...
Setting up python-h5py (2.0.1-2+b1) ...
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: i386 (i686)
Kernel: Linux 3.2.0-2-686-pae (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
--- End Message ---
--- Begin Message ---
Version: 1.8.13+docs-8
Hi,
This bug was fixed when all the libhdf5*-dev flavors were made
co-installable.
Thanks,
_g.
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--- End Message ---
