[SOLVED] update alternatives problem while installing lapack

Tonystark · 07-22-2013, 04:05 AM

I am trying to install lapack in my new system, HP pavilion g6-2313AX 64 bit using ubntu 12.04. I am using synaptic to install lapack.

sudo apt-get install liblapack-dev

This is giving the following error :

Setting up liblapack-dev (3.3.1-1) ...
update-alternatives: error: alternative path /usr/lib/lapack/liblapack.so doesn't exist.
dpkg: error processing liblapack-dev (--configure):
subprocess installed post-installation script returned error exit status 2
Errors were encountered while processing:
liblapack-dev
E: Sub-process /usr/bin/dpkg returned an error code (1)

Can anyone please tell me why this error is occuring and wat could be the reason.? I am stuck here for 2 days and your help is much appreciated.

evo2 · 07-22-2013, 08:51 PM

Hi,

that file should be provided by the liblapack-dev package. Please try to reconfigure it using the following command. If it does not work please post the full output of the command inside [code] tags.

Code:

sudo dpkg --configure --pending

Also please post the output of the following:

Code:

dpkg -l 'liblapack*'

Evo2.

Tonystark · 07-23-2013, 06:21 AM

Thanks a lot for your reply. This is the output I got for the respective commands you suggested me to use.

Code:

sudo dpkg --configure --pending

Code:

[sudo] password for itachi: 
Setting up liblapack-dev (3.3.1-1) ...
update-alternatives: error: alternative path /usr/lib/lapack/liblapack.so doesn't exist.
dpkg: error processing liblapack-dev (--configure):
 subprocess installed post-installation script returned error exit status 2
Errors were encountered while processing:
 liblapack-dev

Code:

dpkg -l 'liblapack*'
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name           Version        Description
+++-==============-==============-============================================
un  liblapack-3.so <none>         (no description available)
un  liblapack-3gf. <none>         (no description available)
iF  liblapack-dev  3.3.1-1        library of linear algebra routines 3 - stati
un  liblapack.so.3 <none>         (no description available)
ii  liblapack3gf   3.3.1-1        library of linear algebra routines 3 - share

This is the output I got. Can you further help me from here? Thanks in advance

.

evo2 · 07-23-2013, 07:41 PM

Hi,

something seems to have gotten screwed up, since liblapack-dev should be unpacked, but the error reported is that /usr/lib/lapack/liblapack.so doesn't exist. Did you try deleting something by hand?

Anyway an easy fix may be just to remove and reinstall the relevant packages. Eg

Code:

sudo apt-get remove --purge liblapack-dev liblapack3gf

When running this take note of any other packages that are uninstalled. Then reinstall the packages.

Eg

Code:

sudo apt-get install liblapack-dev liblapack3gf

and any other pacakges that were removed.

If there are any problems with the above please post the commands that you ran and the full output.

Cheers,

Evo2.

Tonystark · 07-24-2013, 02:15 PM

Thanks a lot once again. You have been really patient in helping me. Yes, I ran couple of commands and I think I did delete something by hand. I was meddling with it and now am facing few issues. I did some linking and unlinking as well. But the problem is I did not keep track of all the commands. That is wat I mentioned in my first post. I will run the commands and post the output.

Tonystark · 07-24-2013, 02:20 PM

Everything seems to be connected with ROS-fuerte, so am planning to remove ROS completely and reinstall it. Is it advised? Please check the command below.

Code:

sudo apt-get remove --purge liblapack3gf 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libboost-thread1.46-dev ros-fuerte-std-msgs ros-fuerte-geometry-experimental
  libcaca-dev python-pyside.qtopengl libboost-filesystem1.46.1 libtorque2
  libp11-kit-dev libxaw7-dev yaml-cpp ros-fuerte-robot-model ros-fuerte-xacro
  python-sphinx libboost-regex1.46-dev libzzip-dev
  libboost-program-options1.46-dev python3.2-minimal
  python-pyside.qtdeclarative libfreeimage3 libtinyxml-dev libassimp2
  libilmbase6 libnetpbm10-dev ros-fuerte-catkin ros-fuerte-bullet
  libboost-graph-parallel1.46-dev python-pyside.phonon librtmp-dev
  libboost-graph-parallel1.46.1 libgpg-error-dev nvidia-cg-toolkit
  libpyside-py3-1.1 ros-fuerte-dynamic-reconfigure ros-fuerte-bond-core
  libcppunit-1.12-1 liblog4cxx10-dev ros-fuerte-nodelet-core sphinx-doc
  python-pyside.qtuitools ros-fuerte-filters ros-fuerte-ros-comm
  libboost-graph1.46-dev libboost-all-dev libasound2-dev libtinyxml2.6.2
  libgnutls-openssl27 python-matplotlib-data libboost-system1.46.1
  libpython3.2 libboost-date-time-dev libyaml-dev phonon
  ros-fuerte-driver-common ros-fuerte-executive-smach libavfilter2 libgl2ps0
  libncurses5-dev libboost-python1.46.1 libboost-mpi1.46-dev
  libboost-signals1.46.1 libboost-signals-dev libav-tools libsdl-image1.2-dev
  ros-fuerte-image-common libboost-program-options1.46.1 libshiboken-dev
  libavdevice53 docgenerator libboost-date-time1.46.1 libboost-thread-dev
  ros-fuerte-orocos-kinematics-dynamics libwxgtk2.8-dev libxxf86vm-dev
  libqhull-dev libavahi-client-dev python-qt4-dev libgl2ps-dev
  libboost-test1.46.1 libapr1-dev python3.2 ros-fuerte-rospack libaprutil1-dev
  libboost-iostreams1.46.1 libopenmpi-dev libboost-program-options-dev
  ros-fuerte-visualization-common libcurl4-openssl-dev ros-fuerte-genpy
  libboost-wave1.46.1 libboost-test-dev libboost-wave-dev libgnutlsxx27
  libusb-1.0-0-dev libboost-graph1.46.1 libpyside1.1 python-pyside.qttest
  liblog4cxx10 libsdl1.2-dev libjs-underscore libboost-graph-parallel-dev
  libsdl-image1.2 libboost-date-time1.46-dev libboost-serialization-dev
  libboost-system-dev python-qt4 ros-fuerte-roscpp-core python-pyside.qtwebkit
  libtinfo-dev libapiextractor-dev python-tz python-sip libgtest-dev
  libfltk1.1 libgenrunner-dev libboost1.46-dev ros-fuerte-python-qt-binding
  python-pyside.qtcore libfreeimage-dev libboost-regex-dev
  python-pyside.qtnetwork x11proto-xf86vidmode-dev python-pyside.qtgui
  libvtk5.8 libopenmpi1.3 libcppunit-dev libxt-dev libxmu-dev
  x11proto-scrnsaver-dev libgenrunner0.6 libopenexr6 libnetcdf-dev
  libboost-iostreams1.46-dev libidn11-dev libboost-math-dev libtasn1-3-dev
  ros-fuerte-common-rosdeps sphinx-common libeigen3-dev libhdf5-serial-1.8.4
  ffmpeg libpostproc52 ros-fuerte-common-msgs ros-fuerte-langs
  ros-fuerte-pluginlib ros-fuerte-common-tutorials libboost-thread1.46.1
  libxpm-dev libboost-math1.46-dev libzzip-0-13 tcl8.5-dev ros-fuerte-swig-wx
  libboost-python1.46-dev ros-fuerte-geometry-tutorials libvtk5-dev shiboken
  ros-fuerte-stage libphonon4 ros-fuerte-robot-model-visualization
  python-pyside.qtsql libqtassistantclient4 python-pyside.qtsvg
  python-pyside.qthelp libnuma1 libgcrypt11-dev libboost-signals1.46-dev
  uuid-dev libassimp-dev phonon-backend-gstreamer gccxml libboost-mpi-dev
  libboost-mpi1.46.1 python-pyside.qtxml ros-fuerte-bfl libpyside-dev
  wx-common libibverbs1 libwxbase2.8-dev ros-fuerte-ros-tutorials
  python-sip-dev libboost-system1.46-dev python-empy libhdf5-serial-dev
  libxmu-headers libboost-filesystem-dev libfltk1.1-dev libpulse-dev
  libnetpbm10 ros-fuerte-protobuf ros-fuerte-robot-model-tutorials
  libibverbs-dev libboost-serialization1.46-dev tk8.5-dev libicu-dev
  libboost-wave1.46-dev libgnutls-dev libboost-dev wx2.8-headers
  ros-fuerte-genlisp ros-fuerte-gencpp libboost-math1.46.1
  python-pyside.qtscript libapiextractor0.10 libdbus-1-dev generatorrunner
  freeglut3-dev libavahi-common-dev libopenjpeg2 python-jinja2
  libshiboken-py3-1.1 mpi-default-dev libxss-dev libcg libqhull5
  libboost-iostreams-dev libboost-mpi-python-dev libboost-regex1.46.1
  ros-fuerte-physics-ode python-pyside openmpi-common
  libboost-filesystem1.46-dev ros-fuerte-diagnostics freeglut3
  ros-fuerte-common libshiboken1.1 libboost-test1.46-dev ros-fuerte-ros
  libboost-graph-dev libbz2-dev ros-fuerte-geometry libnetcdf6 libjs-sphinxdoc
  ros-fuerte-langs-dev ros-fuerte-actionlib python-pyparsing ros-fuerte-genmsg
  libboost-python-dev libldap2-dev
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  libatlas3gf-base
The following packages will be REMOVED:
  liblapack3gf* python-matplotlib* ros-fuerte-desktop-full*
  ros-fuerte-diagnostics-monitors* ros-fuerte-executive-smach-visualization*
  ros-fuerte-flann* ros-fuerte-geometry-visualization*
  ros-fuerte-image-pipeline* ros-fuerte-image-transport-plugins*
  ros-fuerte-laser-pipeline* ros-fuerte-navigation* ros-fuerte-opencv2*
  ros-fuerte-pcl* ros-fuerte-perception-pcl* ros-fuerte-rx*
  ros-fuerte-simulator-gazebo* ros-fuerte-slam-gmapping*
  ros-fuerte-vision-opencv* ros-fuerte-visualization*
  ros-fuerte-visualization-tutorials*
The following NEW packages will be installed:
  libatlas3gf-base
0 upgraded, 1 newly installed, 20 to remove and 0 not upgraded.
Need to get 6,191 kB of archives.
After this operation, 881 MB disk space will be freed.

evo2 · 07-24-2013, 06:53 PM

Hi,

AFAIK those ros-fuerte packages are not official Debian packages, so if you need them and don't have explicit access to the corresponding .deb files you should not remove them.

As I see it, I still think the easiest way to solve this (since I don't know exactly what was broken) is still to reinstall the liblapack-dev and liblapack3gf packages. But we don't want to remove all the ros-fuerte packages in the process. So, I think you should try to do this but telling dpkg to remove these packages but not those that depend on them. This leaves apt in a somewhat "broken" state since you will briefly have packages installed with missing dependencies - but only very briefly, since immediately after, you reinstall them.

Remove:

Code:

dpkg --purge --ignore-depends=liblapack-dev,liblapack3gf liblapack-dev liblapack3gf

Reinstall:

Code:

apt-get --fix-broken install

Cheers,

Evo2.

Tonystark · 07-24-2013, 11:35 PM

Thanks for your help. It worked just fine

.