Bug#992405: buster->bullseye: octave left unconfigured due to naming of shared lib libopenblas

Thu Nov 4 11:50:31 GMT 2021

Hi,

I’m putting back the bug in Cc. Please keep it on future replies.

My comments below.

Le mardi 02 novembre 2021 à 18:07 +0100, reuss andras a écrit :
> Yes, I do, I have a /var/log/dpkg.log.3.gz from August.
> 
> Here is the output
> 
> /var/log$ zcat dpkg.log.3.gz |grep openblas
> 2021-08-17 17:13:31 status unpacked libopenblas0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 17:13:31 install libopenblas0:amd64 <none> 0.3.13+ds-3
> 2021-08-17 17:13:31 status half-installed libopenblas0:amd64 0.3.13+ds-3
> 2021-08-17 17:13:32 status unpacked libopenblas0:amd64 0.3.13+ds-3
> 2021-08-17 18:14:37 configure libopenblas0-pthread:amd64 0.3.13+ds-3 <none>
> 2021-08-17 18:14:37 status unpacked libopenblas0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 18:14:37 status half-configured libopenblas0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 18:14:37 status installed libopenblas0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 19:47:41 configure libopenblas0:amd64 0.3.13+ds-3 <none>
> 2021-08-17 19:47:41 status unpacked libopenblas0:amd64 0.3.13+ds-3
> 2021-08-17 19:47:41 status half-configured libopenblas0:amd64 0.3.13+ds-3
> 2021-08-17 19:47:41 status installed libopenblas0:amd64 0.3.13+ds-3
> 2021-08-17 20:25:58 install libopenblas-pthread-dev:amd64 <none> 0.3.13+ds-3
> 2021-08-17 20:25:58 status half-installed libopenblas-pthread-dev:amd64 0.3.13+ds-3
> 2021-08-17 20:25:59 status unpacked libopenblas-pthread-dev:amd64 0.3.13+ds-3
> 2021-08-17 20:26:01 upgrade libopenblas-dev:amd64 0.3.5+ds-3 0.3.13+ds-3
> 2021-08-17 20:26:01 status half-configured libopenblas-dev:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status unpacked libopenblas-dev:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status half-installed libopenblas-dev:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status unpacked libopenblas-dev:amd64 0.3.13+ds-3
> 2021-08-17 20:26:01 upgrade libopenblas-base:amd64 0.3.5+ds-3 0.3.13+ds-3
> 2021-08-17 20:26:01 status half-configured libopenblas-base:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status unpacked libopenblas-base:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status half-installed libopenblas-base:amd64 0.3.5+ds-3
> 2021-08-17 20:26:01 status unpacked libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 21:30:33 configure libopenblas-pthread-dev:amd64 0.3.13+ds-3 <none>
> 2021-08-17 21:30:33 status unpacked libopenblas-pthread-dev:amd64 0.3.13+ds-3
> 2021-08-17 21:30:33 status half-configured libopenblas-pthread-dev:amd64 0.3.13+ds-3
> 2021-08-17 21:30:34 status installed libopenblas-pthread-dev:amd64 0.3.13+ds-3
> 2021-08-17 21:30:45 configure libopenblas-base:amd64 0.3.13+ds-3 <none>
> 2021-08-17 21:30:45 status unpacked libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 21:30:45 status half-configured libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 21:30:45 status installed libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 21:32:24 configure libopenblas-dev:amd64 0.3.13+ds-3 <none>
> 2021-08-17 21:32:24 status unpacked libopenblas-dev:amd64 0.3.13+ds-3
> 2021-08-17 21:32:24 status half-configured libopenblas-dev:amd64 0.3.13+ds-3
> 2021-08-17 21:32:24 status installed libopenblas-dev:amd64 0.3.13+ds-3
> 2021-08-17 22:39:10 status installed libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:39:10 remove libopenblas-base:amd64 0.3.13+ds-3 <none>
> 2021-08-17 22:39:10 status half-configured libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:39:10 status half-installed libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:39:10 status config-files libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:39:10 status not-installed libopenblas-base:amd64 <none>
> 2021-08-17 22:48:32 install libopenblas64-0-pthread:amd64 <none> 0.3.13+ds-3
> 2021-08-17 22:48:32 status half-installed libopenblas64-0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 22:48:33 status unpacked libopenblas64-0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 22:48:33 install libopenblas64-0:amd64 <none> 0.3.13+ds-3
> 2021-08-17 22:48:33 status half-installed libopenblas64-0:amd64 0.3.13+ds-3
> 2021-08-17 22:48:33 status unpacked libopenblas64-0:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 configure libopenblas64-0-pthread:amd64 0.3.13+ds-3 <none>
> 2021-08-17 22:48:34 status unpacked libopenblas64-0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 status half-configured libopenblas64-0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 status installed libopenblas64-0-pthread:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 configure libopenblas64-0:amd64 0.3.13+ds-3 <none>
> 2021-08-17 22:48:34 status unpacked libopenblas64-0:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 status half-configured libopenblas64-0:amd64 0.3.13+ds-3
> 2021-08-17 22:48:34 status installed libopenblas64-0:amd64 0.3.13+ds-3
> 2021-08-17 22:52:30 install libopenblas-base:amd64 <none> 0.3.13+ds-3
> 2021-08-17 22:52:30 status half-installed libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:52:30 status unpacked libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:52:30 configure libopenblas-base:amd64 0.3.13+ds-3 <none>
> 2021-08-17 22:52:30 status unpacked libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:52:30 status half-configured libopenblas-base:amd64 0.3.13+ds-3
> 2021-08-17 22:52:30 status installed libopenblas-base:amd64 0.3.13+ds-3
> 
> and 
> 
> /var/log/apt$ sudo zcat term.log.3.gz|grep openblas
> 
> Selecting previously unselected package libopenblas0-pthread:amd64.
> Preparing to unpack .../4-libopenblas0-pthread_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas0-pthread:amd64 (0.3.13+ds-3) ...
> Selecting previously unselected package libopenblas0:amd64.
> Preparing to unpack .../5-libopenblas0_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas0:amd64 (0.3.13+ds-3) ...
> Setting up libopenblas0-pthread:amd64 (0.3.13+ds-3) ...
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode
> Setting up libopenblas0:amd64 (0.3.13+ds-3) ...
> Selecting previously unselected package libopenblas-pthread-dev:amd64.
> Preparing to unpack .../01-libopenblas-pthread-dev_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas-pthread-dev:amd64 (0.3.13+ds-3) ...
> Preparing to unpack .../05-libopenblas-dev_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas-dev:amd64 (0.3.13+ds-3) over (0.3.5+ds-3) ...
> Preparing to unpack .../06-libopenblas-base_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas-base:amd64 (0.3.13+ds-3) over (0.3.5+ds-3) ...
> Setting up libopenblas-pthread-dev:amd64 (0.3.13+ds-3) ...
> update-alternatives: warning: alternative /usr/lib/x86_64-linux-gnu/openblas/libblas.so (part of link group libblas.so-x86_64-linux-gnu) doesn't exist; removing from list of alternatives
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
> update-alternatives: warning: alternative /usr/lib/x86_64-linux-gnu/openblas/liblapack.so (part of link group liblapack.so-x86_64-linux-gnu) doesn't exist; removing from list of alternatives
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode
> Setting up libopenblas-base:amd64 (0.3.13+ds-3) ...
> update-alternatives: warning: alternative /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3 (part of link group liblapack.so.3-x86_64-linux-gnu) doesn't exist; removing from list of alternatives
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
> update-alternatives: warning: alternative /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 (part of link group libblas.so.3-x86_64-linux-gnu) doesn't exist; removing from list of alternatives
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
> Setting up libopenblas-dev:amd64 (0.3.13+ds-3) ...
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> Removing libopenblas-base:amd64 (0.3.13+ds-3) ...
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> Selecting previously unselected package libopenblas64-0-pthread:amd64.
> Preparing to unpack .../libopenblas64-0-pthread_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas64-0-pthread:amd64 (0.3.13+ds-3) ...
> Selecting previously unselected package libopenblas64-0:amd64.
> Preparing to unpack .../libopenblas64-0_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas64-0:amd64 (0.3.13+ds-3) ...
> Setting up libopenblas64-0-pthread:amd64 (0.3.13+ds-3) ...
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas64-pthread/libblas64.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas64.so.3 (libblas64.so.3-x86_64-linux-gnu) in auto mode
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas64-pthread/liblapack64.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack64.so.3 (liblapack64.so.3-x86_64-linux-gnu) in auto mode
> update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas64-pthread/libopenblas64.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas64.so.0 (libopenblas64.so.0-x86_64-linux-gnu) in auto mode
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> Setting up libopenblas64-0:amd64 (0.3.13+ds-3) ...
> Selecting previously unselected package libopenblas-base:amd64.
> Preparing to unpack .../libopenblas-base_0.3.13+ds-3_amd64.deb ...
> Unpacking libopenblas-base:amd64 (0.3.13+ds-3) ...
> Setting up libopenblas-base:amd64 (0.3.13+ds-3) ...
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> /usr/bin/octave-cli: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> 
> 
> Yes, I do have /usr/local/lib with a few dirs inside.
> drwxr-sr-x 3 root staff 4096 Mar 12  2019 luarocks
> drwxrwsr-x 3 root staff 4096 Aug 17 21:46 ocaml
> drwxrwsr-x 4 root staff 4096 Aug 17 23:12 python2.7
> drwxr-sr-x 3 root staff 4096 Aug 17 17:10 python3.9
> drwxrwsr-x 3 root staff 4096 Nov 11  2017 R
> drwxr-sr-x 3 root staff 4096 Aug 17 21:46 xemacs
> 
> 
> 1. I removed my manual symlink and 
> 2. apt-get install libopenblas-dev --reinstall
> 3. run ldconfig as root
> 4. started octave:
> /usr/libexec/octave/6.2.0/exec/x86_64-pc-linux-gnu/octave-gui: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
> 
> :(
> 
> So I recovered my initial solution, but I am ready to restart.
> 
> Tell me what do you need for the debugging, I would be glad to assist you.

Actually I had read your initial message to quickly. It seems that the
problem is that the /usr/lib/x86_64-linux-gnu/libopenblas.so.0 symlink
is missing.

Please remove your workaround again, and run the following:

 sudo dpkg-reconfigure libopenblas0-pthread

Then please check whether the symlink is back:

 ls -l /usr/lib/x86_64-linux-gnu/libopenblas.so.0

-- 
⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁  Debian Developer
⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org

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