Bug#676657: [libatlas3gf-base] update-alternatives doesn't provide libblas.so.3gf

darkestkhan darkestkhan at gmail.com
Fri Jun 8 15:31:10 UTC 2012 

Package: libatlas3gf-base
Version: 3.8.4-5
Severity: grave
Tags: patch

Here is full log from today morning upgrade:
-------------
$ sudo aptitude safe-upgrade -t sid
Resolving dependencies...
The following packages will be upgraded:
  autopoint bzip2 dctrl-tools dnsmasq-base firebird2.5-common
firebird2.5-common-doc fonts-opensymbol gettext gettext-base
initramfs-tools libasprintf0c2
  libatlas3-base libatlas3gf-base libbrlapi0.5 libbz2-1.0 libbz2-dev
libfbclient2 libgettextpo0 libgnutls-dev libgnutls-openssl27
libgnutls26
  libgnutlsxx27 libreoffice libreoffice-base libreoffice-base-core
libreoffice-calc libreoffice-common libreoffice-core libreoffice-draw
  libreoffice-emailmerge libreoffice-filter-binfilter
libreoffice-filter-mobiledev libreoffice-help-en-us
libreoffice-impress libreoffice-java-common
  libreoffice-math libreoffice-report-builder-bin
libreoffice-style-galaxy libreoffice-writer libtasn1-3 libtasn1-3-dev
libx86-1 python-tz python-uno
  shared-mime-info ttf-opensymbol uno-libs3 ure xfonts-mathml
49 packages upgraded, 0 newly installed, 0 to remove and 104 not upgraded.
Need to get 129 MB of archives. After unpacking 1,779 kB will be used.
Do you want to continue? [Y/n/?] e
Retrieving bug reports... Done
Parsing Found/Fixed information... Done
Extracting templates from packages: 100%
(Reading database ... 415903 files and directories currently installed.)
Preparing to replace libbz2-dev:amd64 1.0.6-2 (using
.../libbz2-dev_1.0.6-3_amd64.deb) ...
Unpacking replacement libbz2-dev:amd64 ...
Preparing to replace bzip2 1.0.6-2 (using .../bzip2_1.0.6-3_amd64.deb) ...
Unpacking replacement bzip2 ...
Preparing to replace libbz2-1.0:amd64 1.0.6-2 (using
.../libbz2-1.0_1.0.6-3_amd64.deb) ...
Unpacking replacement libbz2-1.0:amd64 ...
Processing triggers for man-db ...
Setting up libbz2-1.0:amd64 (1.0.6-3) ...
(Reading database ... 415903 files and directories currently installed.)
Preparing to replace gettext 0.18.1.1-8 (using
.../gettext_0.18.1.1-9_amd64.deb) ...
Unpacking replacement gettext ...
Preparing to replace libgettextpo0:amd64 0.18.1.1-8 (using
.../libgettextpo0_0.18.1.1-9_amd64.deb) ...
Unpacking replacement libgettextpo0:amd64 ...
Preparing to replace libasprintf0c2:amd64 0.18.1.1-8 (using
.../libasprintf0c2_0.18.1.1-9_amd64.deb) ...
Unpacking replacement libasprintf0c2:amd64 ...
Preparing to replace gettext-base 0.18.1.1-8 (using
.../gettext-base_0.18.1.1-9_amd64.deb) ...
Unpacking replacement gettext-base ...
Preparing to replace libgnutls-dev 2.12.19-1 (using
.../libgnutls-dev_2.12.19-2_amd64.deb) ...
Unpacking replacement libgnutls-dev ...
Preparing to replace libgnutlsxx27:amd64 2.12.19-1 (using
.../libgnutlsxx27_2.12.19-2_amd64.deb) ...
Unpacking replacement libgnutlsxx27:amd64 ...
Preparing to replace libtasn1-3-dev 2.12-1 (using
.../libtasn1-3-dev_2.13-2_amd64.deb) ...
Unpacking replacement libtasn1-3-dev ...
Preparing to replace libtasn1-3:amd64 2.12-1 (using
.../libtasn1-3_2.13-2_amd64.deb) ...
Unpacking replacement libtasn1-3:amd64 ...
Preparing to replace libgnutls-openssl27:amd64 2.12.19-1 (using
.../libgnutls-openssl27_2.12.19-2_amd64.deb) ...
Unpacking replacement libgnutls-openssl27:amd64 ...
Preparing to replace libgnutls26:amd64 2.12.19-1 (using
.../libgnutls26_2.12.19-2_amd64.deb) ...
Unpacking replacement libgnutls26:amd64 ...
Preparing to replace libfbclient2:amd64 2.5.2~svn+54545.ds4-1 (using
.../libfbclient2_2.5.2~svn+54604.ds4-1_amd64.deb) ...
Unpacking replacement libfbclient2:amd64 ...
Preparing to replace firebird2.5-common 2.5.2~svn+54545.ds4-1 (using
.../firebird2.5-common_2.5.2~svn+54604.ds4-1_all.deb) ...
Unpacking replacement firebird2.5-common ...
Preparing to replace firebird2.5-common-doc 2.5.2~svn+54545.ds4-1
(using .../firebird2.5-common-doc_2.5.2~svn+54604.ds4-1_all.deb) ...
Unpacking replacement firebird2.5-common-doc ...
Preparing to replace ure 3.5.4-2 (using .../archives/ure_3.5.4-3_amd64.deb) ...
Unpacking replacement ure ...
Preparing to replace uno-libs3 3.5.4-2 (using
.../uno-libs3_3.5.4-3_amd64.deb) ...
Unpacking replacement uno-libs3 ...
Preparing to replace libreoffice-calc 1:3.5.4-2 (using
.../libreoffice-calc_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-calc ...
Preparing to replace libreoffice-writer 1:3.5.4-2 (using
.../libreoffice-writer_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-writer ...
Preparing to replace libreoffice-base 1:3.5.4-2 (using
.../libreoffice-base_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-base ...
Preparing to replace libreoffice-base-core 1:3.5.4-2 (using
.../libreoffice-base-core_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-base-core ...
Preparing to replace libreoffice-java-common 1:3.5.4-2 (using
.../libreoffice-java-common_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-java-common ...
Preparing to replace libreoffice-impress 1:3.5.4-2 (using
.../libreoffice-impress_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-impress ...
Preparing to replace libreoffice-draw 1:3.5.4-2 (using
.../libreoffice-draw_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-draw ...
Preparing to replace python-uno 1:3.5.4-2 (using
.../python-uno_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement python-uno ...
Preparing to replace libreoffice-common 1:3.5.4-2 (using
.../libreoffice-common_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-common ...
Preparing to replace libreoffice 1:3.5.4-2 (using
.../libreoffice_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice ...
Preparing to replace libreoffice-math 1:3.5.4-2 (using
.../libreoffice-math_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-math ...
Processing triggers for install-info ...
install-info: warning: no info dir entry in
`/usr/share/info/adacontrol_ug.info.gz'
Processing triggers for man-db ...
Processing triggers for doc-base ...
Processing 1 changed doc-base file...
Registering documents with dhelp...
Processing triggers for desktop-file-utils ...
Processing triggers for menu ...
Processing triggers for mime-support ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for gnome-icon-theme ...
Processing triggers for shared-mime-info ...
Setting up uno-libs3 (3.5.4-3) ...
Setting up ure (3.5.4-3) ...
(Reading database ... 415903 files and directories currently installed.)
Preparing to replace libreoffice-core 1:3.5.4-2 (using
.../libreoffice-core_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-core ...
Preparing to replace libreoffice-filter-binfilter 1:3.5.4-2 (using
.../libreoffice-filter-binfilter_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-filter-binfilter ...
Preparing to replace fonts-opensymbol 2:102.2+LibO3.5.4-2 (using
.../fonts-opensymbol_2%3a102.2+LibO3.5.4-3_all.deb) ...
Unpacking replacement fonts-opensymbol ...
Preparing to replace ttf-opensymbol 2:102.2+LibO3.5.4-2 (using
.../ttf-opensymbol_2%3a102.2+LibO3.5.4-3_all.deb) ...
Unpacking replacement ttf-opensymbol ...
Preparing to replace libreoffice-report-builder-bin 1:3.5.4-2 (using
.../libreoffice-report-builder-bin_1%3a3.5.4-3_amd64.deb) ...
Unpacking replacement libreoffice-report-builder-bin ...
Preparing to replace libreoffice-filter-mobiledev 1:3.5.4-2 (using
.../libreoffice-filter-mobiledev_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-filter-mobiledev ...
Preparing to replace libreoffice-style-galaxy 1:3.5.4-2 (using
.../libreoffice-style-galaxy_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-style-galaxy ...
Preparing to replace libx86-1 1.1+ds1-7 (using
.../libx86-1_1.1+ds1-9_amd64.deb) ...
Unpacking replacement libx86-1:amd64 ...
Preparing to replace libbrlapi0.5:amd64 4.3-3 (using
.../libbrlapi0.5_4.4-1_amd64.deb) ...
Unpacking replacement libbrlapi0.5:amd64 ...
Preparing to replace autopoint 0.18.1.1-8 (using
.../autopoint_0.18.1.1-9_all.deb) ...
Unpacking replacement autopoint ...
Preparing to replace dctrl-tools 2.22.1 (using
.../dctrl-tools_2.22.2_amd64.deb) ...
Unpacking replacement dctrl-tools ...
Preparing to replace dnsmasq-base 2.62-1 (using
.../dnsmasq-base_2.62-2_amd64.deb) ...
Unpacking replacement dnsmasq-base ...
Preparing to replace initramfs-tools 0.105 (using
.../initramfs-tools_0.106_all.deb) ...
Unpacking replacement initramfs-tools ...
Preparing to replace libatlas3-base 3.8.4-4 (using
.../libatlas3-base_3.8.4-5_amd64.deb) ...
update-alternatives: error: no alternatives for libblas.so.3gf.
dpkg: warning: subprocess old pre-removal script returned error exit status 2
dpkg - trying script from the new package instead ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide
/usr/lib/libblas.so.3 (libblas.so.3) in auto mode.
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide
/usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode.
dpkg: ... it looks like that went OK.
Unpacking replacement libatlas3-base ...
Preparing to replace libatlas3gf-base 3.8.4-4 (using
.../libatlas3gf-base_3.8.4-5_amd64.deb) ...
update-alternatives: error: no alternatives for libblas.so.3gf.
dpkg: warning: subprocess old pre-removal script returned error exit status 2
dpkg - trying script from the new package instead ...
dpkg: ... it looks like that went OK.
Unpacking replacement libatlas3gf-base ...
Preparing to replace libreoffice-emailmerge 1:3.5.4-2 (using
.../libreoffice-emailmerge_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-emailmerge ...
Preparing to replace libreoffice-help-en-us 1:3.5.4-2 (using
.../libreoffice-help-en-us_1%3a3.5.4-3_all.deb) ...
Unpacking replacement libreoffice-help-en-us ...
Preparing to replace python-tz 2011h-1 (using .../python-tz_2012c-1_all.deb) ...
Unpacking replacement python-tz ...
Preparing to replace shared-mime-info 0.90-1.1 (using
.../shared-mime-info_1.0-1_amd64.deb) ...
Unpacking replacement shared-mime-info ...
Preparing to replace xfonts-mathml 5 (using .../xfonts-mathml_6_all.deb) ...
Unpacking replacement xfonts-mathml ...
Processing triggers for desktop-file-utils ...
Processing triggers for mime-support ...
Processing triggers for fontconfig ...
Processing triggers for man-db ...
Processing triggers for doc-base ...
Processing 2 changed doc-base files...
Registering documents with dhelp...
Setting up libbz2-dev:amd64 (1.0.6-3) ...
Setting up bzip2 (1.0.6-3) ...
Setting up libgettextpo0:amd64 (0.18.1.1-9) ...
Setting up libasprintf0c2:amd64 (0.18.1.1-9) ...
Setting up gettext-base (0.18.1.1-9) ...
Setting up gettext (0.18.1.1-9) ...
Setting up libtasn1-3:amd64 (2.13-2) ...
Setting up libgnutls26:amd64 (2.12.19-2) ...
Setting up libgnutlsxx27:amd64 (2.12.19-2) ...
Setting up libgnutls-openssl27:amd64 (2.12.19-2) ...
Setting up libtasn1-3-dev (2.13-2) ...
Setting up libgnutls-dev (2.12.19-2) ...
Setting up firebird2.5-common-doc (2.5.2~svn+54604.ds4-1) ...
Setting up firebird2.5-common (2.5.2~svn+54604.ds4-1) ...
Setting up libfbclient2:amd64 (2.5.2~svn+54604.ds4-1) ...
Setting up fonts-opensymbol (2:102.2+LibO3.5.4-3) ...
Setting up ttf-opensymbol (2:102.2+LibO3.5.4-3) ...
Setting up libx86-1:amd64 (1.1+ds1-9) ...
Setting up libbrlapi0.5:amd64 (4.4-1) ...
Setting up autopoint (0.18.1.1-9) ...
Setting up dctrl-tools (2.22.2) ...
Setting up dnsmasq-base (2.62-2) ...
Setting up initramfs-tools (0.106) ...
update-initramfs: deferring update (trigger activated)
Setting up libatlas3-base (3.8.4-5) ...
update-alternatives: using /usr/lib/atlas-base/atlas/libblas.so.3 to
provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode.
update-alternatives: warning: skip creation of /usr/lib/libblas.so.3gf
because associated file /usr/lib/atlas-base/libblas.so.3 (of link
group libblas.so.3) doesn't exist.
update-alternatives: using /usr/lib/atlas-base/atlas/liblapack.so.3 to
provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode.
Setting up libatlas3gf-base (3.8.4-5) ...
Setting up python-tz (2012c-1) ...
Setting up shared-mime-info (1.0-1) ...
Setting up xfonts-mathml (6) ...
Setting up libreoffice-style-galaxy (1:3.5.4-3) ...
Setting up libreoffice-common (1:3.5.4-3) ...
Setting up libreoffice-core (1:3.5.4-3) ...
Setting up libreoffice-base-core (1:3.5.4-3) ...
Setting up libreoffice-calc (1:3.5.4-3) ...
Setting up libreoffice-writer (1:3.5.4-3) ...
Setting up libreoffice-java-common (1:3.5.4-3) ...
Setting up libreoffice-base (1:3.5.4-3) ...
Setting up libreoffice-draw (1:3.5.4-3) ...
Setting up libreoffice-impress (1:3.5.4-3) ...
Setting up python-uno (1:3.5.4-3) ...
Setting up libreoffice-math (1:3.5.4-3) ...
Setting up libreoffice-report-builder-bin (1:3.5.4-3) ...
Setting up libreoffice-filter-mobiledev (1:3.5.4-3) ...
Setting up libreoffice (1:3.5.4-3) ...
Setting up libreoffice-filter-binfilter (1:3.5.4-3) ...
Setting up libreoffice-emailmerge (1:3.5.4-3) ...
Setting up libreoffice-help-en-us (1:3.5.4-3) ...
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.2.0-2-amd64
Processing triggers for menu ...
Press return to continue.
-------------------
Note these lines:
-----
Preparing to replace libatlas3gf-base 3.8.4-4 (using
.../libatlas3gf-base_3.8.4-5_amd64.deb) ...
update-alternatives: error: no alternatives for libblas.so.3gf.
dpkg: warning: subprocess old pre-removal script returned error exit status 2
dpkg - trying script from the new package instead ...
dpkg: ... it looks like that went OK.
-----
This causes things like this:
darkestkhan at khaganate ~ $ mnemosyne
Uncaught exception!
Traceback (innermost last):
  File "/usr/bin/mnemosyne", line 146, in <module>
    debug_file=options.debug_file)
  File "/usr/lib/python2.7/dist-packages/mnemosyne/libmnemosyne/__init__.py",
line 146, in initialise
    self.register_components()
  File "/usr/lib/python2.7/dist-packages/mnemosyne/libmnemosyne/__init__.py",
line 199, in register_components
    exec("from %s import %s" % (module_name, class_name))
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/mnemosyne/pyqt_ui/statistics_wdgts_plotting.py",
line 7, in <module>
    from matplotlib.figure import Figure
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line
134, in <module>
    from matplotlib.rcsetup import (defaultParams,
  File "/usr/lib/pymodules/python2.7/matplotlib/rcsetup.py", line 19,
in <module>
    from matplotlib.colors import is_color_like
  File "/usr/lib/pymodules/python2.7/matplotlib/colors.py", line 52, in <module>
    import numpy as np
  File "/usr/lib/pymodules/python2.7/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/lib/pymodules/python2.7/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib/pymodules/python2.7/numpy/lib/__init__.py", line 13,
in <module>
    from polynomial import *
  File "/usr/lib/pymodules/python2.7/numpy/lib/polynomial.py", line
17, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/usr/lib/pymodules/python2.7/numpy/linalg/__init__.py", line
48, in <module>
    from linalg import *
  File "/usr/lib/pymodules/python2.7/numpy/linalg/linalg.py", line 23,
in <module>
    from numpy.linalg import lapack_lite
 ImportError: libblas.so.3gf: cannot open shared object file: No such
file or directory
----
BUGFIX:
running
$ sudo ln -s /usr/lib/libblas.so.3 /usr/lib/libblas.so.3gf
seems to fix the problem.

darkestkhan

--- System information. ---
Architecture: amd64
Kernel:       Linux 3.2.0-2-amd64

Debian Release: wheezy/sid
  650 testing         ftp.debian.org
  600 unstable        ftp.debian.org

--- Package information. ---
Depends             (Version) | Installed
=============================-+-===========
libatlas3-base                | 3.8.4-5


Package's Recommends field is empty.

Package's Suggests field is empty.

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