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 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
