A Weird Imagination

Fixing broken alternatives

Posted in Linux
apt apt-get debian debian sid distro liblapack3 linux package management ubuntu update-alternatives

The problem#

Trying to install the python-numpy package in Debian Unstable ("Sid") I got the following error on the liblapack3 package (seen also in this bug):

$ sudo apt-get install -f
Reading package lists... Done
Building dependency tree       
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
4 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Setting up liblapack3 (3.5.0-4) ...
update-alternatives: error: alternative liblapack.so.3gf can't be slave of liblapack.so.3: it is a master alternative
dpkg: error processing package liblapack3 (--configure):
 subprocess installed post-installation script returned error exit status 2
dpkg: dependency problems prevent configuration of python-numpy:
 python-numpy depends on liblapack3 | liblapack.so.3; however:
  Package liblapack3 is not configured yet.
  Package liblapack.so.3 is not installed.
  Package lapack3 which provides liblapack.so.3 is not installed.
  Package atlas3-base which provides liblapack.so.3 is not installed.
  Package liblapack3 which provides liblapack.so.3 is not configured yet.
  Package libatlas3-base which provides liblapack.so.3 is not installed.

The solution#

Run the following command to fix the error:

$ sudo update-alternatives --remove-all liblapack.so.3gf

And then rerun the install:

$ sudo apt-get install -f

The details#

The error#

The actual error is the following line:

update-alternatives: error: alternative liblapack.so.3gf can't be slave of liblapack.so.3: it is a master alternative

Searching for that error found this bug report which explains what went wrong: the most recent version of the package is incompatible with a very old version of the package which I must have had installed at some point in the past. If I had ever installed some version of it in the middle, then the problem would have been fixed by the automatic scripts, but for whatever reason the latest version no longer includes the code for cleaning up after that very old version.

So I had to do it myself instead.

update-alternatives#

The Debian Alternatives System allows for multiple packages to be installed that provide the same functionality. For example, you might have multiple versions of Java or multiple web browsers installed, and one of them has to be the default when you run java or x-www-browser.

The alternatives system is managed through the update-alternatives script. We can ask it for information about alternatives:

$ update-alternatives --display x-www-browser
x-www-browser - manual mode
  link currently points to /usr/bin/iceweasel
/usr/bin/chromium - priority 40
/usr/bin/epiphany-browser - priority 85
  slave x-www-browser.1.gz: /usr/share/man/man1/epiphany-browser.1.gz
/usr/bin/iceweasel - priority 70
  slave x-www-browser.1.gz: /usr/share/man/man1/iceweasel.1.gz
Current 'best' version is '/usr/bin/epiphany-browser'.

Which it gets from /var/lib/dpkg/alternatives/:

$ cat /var/lib/dpkg/alternatives/x-www-browser 
manual
/usr/bin/x-www-browser
x-www-browser.1.gz
/usr/share/man/man1/x-www-browser.1.gz

/usr/bin/chromium
40

/usr/bin/epiphany-browser
85
/usr/share/man/man1/epiphany-browser.1.gz
/usr/bin/iceweasel
70
/usr/share/man/man1/iceweasel.1.gz

The alternatives are handled via symlinks:1

$ /bin/ls -ld /usr/bin/x-www-browser
lrwxrwxrwx 1 root root 31 Mar  4  2010 /usr/bin/x-www-browser -> /etc/alternatives/x-www-browser
$ /bin/ls -ld /etc/alternatives/x-www-browser
lrwxrwxrwx 1 root root 18 Mar  4  2010 /etc/alternatives/x-www-browser -> /usr/bin/iceweasel

Dangling alternative#

Since the error message complained about the alternative for liblapack.so.3gf, let's take a look at it:

$ update-alternatives --display liblapack.so.3gf
update-alternatives: warning: alternative /usr/lib/atlas-base/atlas/liblapack.so.3gf (part of link group liblapack.so.3gf) doesn't exist; removing from list of alternatives
update-alternatives: warning: alternative /usr/lib/lapack/liblapack.so.3gf (part of link group liblapack.so.3gf) doesn't exist; removing from list of alternatives
liblapack.so.3gf - auto mode
  link currently points to /usr/lib/atlas-base/atlas/liblapack.so.3gf
No versions available.

It's pointing to files that don't exist, so it's clearly not doing any good. Let's get rid of it:

$ sudo update-alternatives --remove-all liblapack.so.3gf
update-alternatives: warning: alternative /usr/lib/atlas-base/atlas/liblapack.so.3gf (part of link group liblapack.so.3gf) doesn't exist; removing from list of alternatives
update-alternatives: warning: alternative /usr/lib/lapack/liblapack.so.3gf (part of link group liblapack.so.3gf) doesn't exist; removing from list of alternatives
update-alternatives: warning: /etc/alternatives/liblapack.so.3gf is dangling; it will be updated with best choice

Now if we check again, we can see that it's gone:

$ update-alternatives --display liblapack.so.3gf
update-alternatives: error: no alternatives for liblapack.so.3gf

Why did that happen?#

Debian Unstable (often referred to by its codename "Sid") is an unstable distribution, which basically means Debian doesn't guarantee that installs will work. As a result, it takes a bit more work to maintain than a stable distribution like Debian's stable release or Ubuntu which is a stable distribution that is based on Debian but stays more up-to-date by having a shorter release cycle.

In this case, a Debian Stable user would presumably have had the proper cleanup get done when performing an apt-get dist-upgrade to the new version of Debian Stable. I only encountered the issue because by using Debian Unstable I was taking responsibility for keeping my packages up to date; most likely this issue could have been avoided by doing apt-get purge when uninstalling the old version of liblapack3 to delete its configuration files when uninstalling it.

I currently use Debian Unstable on only one of my computers because it gives me things to fiddle with to learn the details of how things work, but on the rest I just use Ubuntu or Debian Stable so I don't have to worry about them working.

  1. These commands use /bin/ls instead of just ls because my alias for ls uses the -H option which dereferences links:

    $ alias ls
alias ls='ls --color=auto -FHbh'

    For example,

    $ /bin/ls -ldH /etc/alternatives/x-www-browser
-rwxr-xr-x 1 root root 110512 Mar 21 19:13 /etc/alternatives/x-www-browser

    doesn't display the link target because it follows the link. ↩

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