Hi
I found a completely GUI based way to fix the problem. If you have taken an
update-manager
update of sagemath-upstream-binary 5.1 -> 5.4 and it leaves the package in
an unconfigured
state, you can open Software Centre, search for sagemath, choose
sagemath-upstream-binary,
click Remove, and then when it is done click Install.
(update-manager does not try to remove it first, and the upgrade will not
work while there is an
unconfigured package. I suspect this might work with synaptic as well. Note
that if the user
ran sudo sage after update-manager failed to configure the package, then I
think that is
what caused the second half of the problem: root-owned files in .sage/tmp.
These I guess
will have to be moved on the command line.)
Regards,
Jan
On 15 November 2012 22:01, Jan Groenewald <j...@aims.ac.za> wrote:
> Hi
>
> Solution to the Sagemath PPA upgrades to 5.4 via update-manager which does
> not read $HOME=/root/ correctly, and so
> 1) fails to configure the package and 2) possibly writes files owned by
> root into the user's .sage.
>
> The Sagemath PPA has been updated to 5.4ubuntu1, which does not present
> the problem with update-manager installations.
> Future upgrades from 5.1 to 5.4ubuntu1 should work as expected.
>
> However, installations which were already upgraded from 5.1 to 5.4 with
> the PPA can only be fixed by running this in a terminal to fix the package
> manager:
>
> sudo dpkg --configure sagemath-upstream-binary
>
> Update manager will then continue to pull the new 5.4ubuntu1 and that
> should work.
> If problems persist due to sage startup showing permission errors, then
> run this as the user:
>
> sudo mv /home/`whoami`/.sage/tmp{.,broken-permissions}
>
> Regards,
> Jan
>
>
>
>
> On 15 November 2012 01:20, JJS137 <john.spit...@gmail.com> wrote:
>
>> Hi Jan,
>> You were correct - the launcher problem went away following my reboot
>> this morning.
>> Many Thanks for your assistance!
>> Cheers,
>> John
>>
>>
>> On Wednesday, November 14, 2012 4:24:25 PM UTC+11, Jan Groenewald wrote:
>>
>>> Hi John,
>>>
>>> I'm guessing whatever launcher problem you have will go away
>>> once you've rebooted.
>>>
>>> Regards,
>>> Jan
>>>
>>>
>>> On 14 November 2012 07:19, JJS137 <john.s...@gmail.com> wrote:
>>>
>>>> Hi Jan,
>>>> I ran the second command but it did not find anything to do. The
>>>> Launcher had some issue because the first command actually started Sage in
>>>> my browser (Firefox). That instance worked fine. The launcher still has a
>>>> problem, but the sign in page is presented when using the standard URL.
>>>> Many Thanks,
>>>> John
>>>>
>>>>
>>>>
>>>> On Tuesday, November 13, 2012 10:55:29 AM UTC+11, JJS137 wrote:
>>>>>
>>>>> The Sage 5.4 installation on Ubuntu 12.04 LTS using Update Manager
>>>>> fails with the following messages:
>>>>>
>>>>> installArchives() failed: (Reading database ...
>>>>> (Reading database ... 5%%
>>>>> (Reading database ... 10%%
>>>>> (Reading database ... 15%%
>>>>> (Reading database ... 20%%
>>>>> (Reading database ... 25%%
>>>>> (Reading database ... 30%%
>>>>> (Reading database ... 35%%
>>>>> (Reading database ... 40%%
>>>>> (Reading database ... 45%%
>>>>> (Reading database ... 50%%
>>>>> (Reading database ... 55%%
>>>>> (Reading database ... 60%%
>>>>> (Reading database ... 65%%
>>>>> (Reading database ... 70%%
>>>>> (Reading database ... 75%%
>>>>> (Reading database ... 80%%
>>>>> (Reading database ... 85%%
>>>>> (Reading database ... 90%%
>>>>> (Reading database ... 95%%
>>>>> (Reading database ... 100%%
>>>>> (Reading database ... 717630 files and directories currently
>>>>> installed.)
>>>>> Preparing to replace libav-tools 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libav-tools_4%%3a0.8.4-**0ub**untu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libav-tools ...
>>>>> Preparing to replace libpostproc52 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libpostproc52_4%%3a0.8.4-**0**ubuntu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libpostproc52 ...
>>>>> Preparing to replace libavfilter2 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libavfilter2_4%%3a0.8.4-**0u**buntu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libavfilter2 ...
>>>>> Preparing to replace libswscale2 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libswscale2_4%%3a0.8.4-**0ub**untu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libswscale2 ...
>>>>> Preparing to replace libavdevice53 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libavdevice53_4%%3a0.8.4-**0**ubuntu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libavdevice53 ...
>>>>> Preparing to replace libavformat53 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libavformat53_4%%3a0.8.4-**0**ubuntu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libavformat53 ...
>>>>> Preparing to replace libavcodec53 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libavcodec53_4%%3a0.8.4-**0u**buntu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libavcodec53 ...
>>>>> Preparing to replace libavutil51 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../libavutil51_4%%3a0.8.4-**0ub**untu0.12.04.1_i386.deb) ...
>>>>> Unpacking replacement libavutil51 ...
>>>>> Preparing to replace libproxy1-plugin-**networkmanage**r
>>>>> 0.4.7-0ubuntu4 (using .../libproxy1-plugin-**networkma**
>>>>> nager_0.4.7-0ubuntu4.**1_i386.**deb) ...
>>>>> Unpacking replacement libproxy1-plugin-**networkmanage**r ...
>>>>> Preparing to replace libproxy1-plugin-gsettings 0.4.7-0ubuntu4 (using
>>>>> .../libproxy1-plugin-**gsettings**_0.4.7-0ubuntu4.1_**i386.deb) ...
>>>>> Unpacking replacement libproxy1-plugin-gsettings ...
>>>>> Preparing to replace libproxy1 0.4.7-0ubuntu4 (using
>>>>> .../libproxy1_0.4.7-0ubuntu4.**1**_i386.deb) ...
>>>>> Unpacking replacement libproxy1 ...
>>>>> Preparing to replace ffmpeg 4:0.8.3-0ubuntu0.12.04.1 (using
>>>>> .../ffmpeg_4%%3a0.8.4-**0ubuntu0**.12.04.1_all.deb) ...
>>>>> Unpacking replacement ffmpeg ...
>>>>> Preparing to replace sagemath-upstream-binary 5.1 (using
>>>>> .../sagemath-upstream-binary_**5**.4_i386.deb) ...
>>>>> Unpacking replacement sagemath-upstream-binary ...
>>>>> Preparing to replace python-libproxy 0.4.7-0ubuntu4 (using
>>>>> .../python-libproxy_0.4.7-**0ubu**ntu4.1_all.deb) ...
>>>>> Unpacking replacement python-libproxy ...
>>>>> Processing triggers for man-db ...
>>>>> Processing triggers for bamfdaemon ...
>>>>> Rebuilding /usr/share/applications/bamf.**i**ndex...
>>>>> Processing triggers for desktop-file-utils ...
>>>>> Processing triggers for gnome-menus ...
>>>>> Setting up libavutil51 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libavcodec53 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libavformat53 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libavdevice53 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libswscale2 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libavfilter2 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libpostproc52 (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libav-tools (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up libproxy1 (0.4.7-0ubuntu4.1) ...
>>>>> Setting up libproxy1-plugin-**networkmanage**r (0.4.7-0ubuntu4.1) ...
>>>>> Setting up libproxy1-plugin-gsettings (0.4.7-0ubuntu4.1) ...
>>>>> Setting up ffmpeg (4:0.8.4-0ubuntu0.12.04.1) ...
>>>>> Setting up sagemath-upstream-binary (5.4) ...
>>>>> Removing previous path, rm -rf /usr/lib/sage (new path
>>>>> /usr/lib/sagemath)
>>>>> Running Sage once as root to set paths
>>>>> Error: environment variable $HOME is not set.
>>>>> Error setting environment variables by sourcing
>>>>> '/usr/lib/sagemath/spkg/bin/**sa**ge-env';
>>>>> possibly contact sage-devel (see http://groups.google.com/**group**
>>>>> /sage-devel <http://groups.google.com/group/sage-devel>).
>>>>> dpkg: error processing sagemath-upstream-binary (--configure):
>>>>> subprocess installed post-installation script returned error exit
>>>>> status 1
>>>>> No apport report written because MaxReports is reached already
>>>>> Setting up python-libproxy (0.4.7-0ubuntu4.1) ...
>>>>> Processing triggers for libc-bin ...
>>>>> ldconfig deferred processing now taking place
>>>>> Errors were encountered while processing:
>>>>> sagemath-upstream-binary
>>>>> Error in function:
>>>>> SystemError: E:Sub-process /usr/bin/dpkg returned an error code (1)
>>>>> Setting up sagemath-upstream-binary (5.4) ...
>>>>> Removing previous path, rm -rf /usr/lib/sage (new path
>>>>> /usr/lib/sagemath)
>>>>> Running Sage once as root to set paths
>>>>> Error: environment variable $HOME is not set.
>>>>> Error setting environment variables by sourcing
>>>>> '/usr/lib/sagemath/spkg/bin/**sa**ge-env';
>>>>> possibly contact sage-devel (see http://groups.google.com/**group**
>>>>> /sage-devel <http://groups.google.com/group/sage-devel>).
>>>>> dpkg: error processing sagemath-upstream-binary (--configure):
>>>>> subprocess installed post-installation script returned error exit
>>>>> status 1
>>>>>
>>>>> Is there a work around or fix for this problem?
>>>>>
>>>>> --
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>>>> .
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> .~.
>>> /V\ Jan Groenewald
>>> /( )\ www.aims.ac.za
>>> ^^-^^
>>>
>>> --
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>>
>>
>
>
>
> --
> .~.
> /V\ Jan Groenewald
> /( )\ www.aims.ac.za
> ^^-^^
>
>
--
.~.
/V\ Jan Groenewald
/( )\ www.aims.ac.za
^^-^^
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