[Bug 1165868] Re: kazam crashed with IndexError in cb_volume2_changed(): list index out of range

2013-04-18 Thread melchiaros
** Also affects: kazam
   Importance: Undecided
   Status: New

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Title:
  kazam crashed with IndexError in cb_volume2_changed(): list index out
  of range

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[Bug 1135345] Re: kazam crashed with AttributeError in setup_pipeline(): 'Screencast' object has no attribute 'videosrc'

2013-04-18 Thread melchiaros
** Also affects: kazam
   Importance: Undecided
   Status: New

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Title:
  kazam crashed with AttributeError in setup_pipeline(): 'Screencast'
  object has no attribute 'videosrc'

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[Bug 1094097] Re: Xorg crashed with SIGSEGV in mieqMoveToNewScreen()

2013-04-18 Thread melchiaros
Sorry Bryce, but I could not provide.

I have switch some weeks ago with the affected system back to quantal,
because one think I want to do was not pssible with raring. I have had
known that it works with quantal.

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[Bug 1094097] Re: Xorg crashed with SIGSEGV in mieqMoveToNewScreen()

2013-04-18 Thread melchiaros
Could anybody else answer the question from comment #11 ?

Thnaks

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[Bug 1170322] [NEW] firefox is not able to zoom on a specific single website

2013-04-18 Thread melchiaros
Public bug reported:

I have accessed tohe following website:

http://www.bonnerbueroservice.de/

and tried to zoom in.

It does not do.

Neiter STRG + + nor a zoom with the capabilities from the menu -
View- Zoom

give a success.

ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: firefox 20.0+build1-0ubuntu0.12.10.3
ProcVersionSignature: Ubuntu 3.5.0-28.47-generic 3.5.7.9
Uname: Linux 3.5.0-28-generic x86_64
NonfreeKernelModules: fglrx
AddonCompatCheckDisabled: False
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
AudioDevicesInUse:
 USERPID ACCESS COMMAND
 /dev/snd/controlC1:  user   2166 F pulseaudio
 /dev/snd/controlC0:  user   2166 F pulseaudio
BuildID: 20130329030352
Channel: Unavailable
Date: Thu Apr 18 13:52:51 2013
ExecutablePath: /usr/lib/firefox/firefox
ForcedLayersAccel: False
IfupdownConfig:
 # interfaces(5) file used by ifup(8) and ifdown(8)
 auto lo
 iface lo inet loopback
InstallationDate: Installed on 2013-01-13 (94 days ago)
InstallationMedia: Ubuntu 12.10 Quantal Quetzal - Release amd64 (20121017.5)
IpRoute:
 default via 192.168.1.1 dev wlan0  proto static 
 169.254.0.0/16 dev wlan0  scope link  metric 1000 
 192.168.1.0/24 dev wlan0  proto kernel  scope link  src 192.168.1.12  metric 9
MarkForUpload: True
PrefSources:
 prefs.js
 
[Profile]/extensions/https-everywh...@eff.org/defaults/preferences/preferences.js
Profiles: Profile0 (Default) - LastVersion=20.0/20130329030352 (In use)
RelatedPackageVersions:
 rhythmbox-mozilla 2.97-1ubuntu6.1
 totem-mozilla 3.4.3-0ubuntu5
RunningIncompatibleAddons: False
SourcePackage: firefox
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 04/27/2012
dmi.bios.vendor: Insyde
dmi.bios.version: F.02
dmi.board.asset.tag: Base Board Asset Tag
dmi.board.name: 1885
dmi.board.vendor: Hewlett-Packard
dmi.board.version: 66.11
dmi.chassis.asset.tag: Chassis Asset Tag
dmi.chassis.type: 10
dmi.chassis.vendor: Hewlett-Packard
dmi.chassis.version: Chassis Version
dmi.modalias: 
dmi:bvnInsyde:bvrF.02:bd04/27/2012:svnHewlett-Packard:pnHP655NotebookPC:pvr07981000521000260:rvnHewlett-Packard:rn1885:rvr66.11:cvnHewlett-Packard:ct10:cvrChassisVersion:
dmi.product.name: HP 655 Notebook PC
dmi.product.version: 07981000521000260
dmi.sys.vendor: Hewlett-Packard

** Affects: firefox
 Importance: Undecided
 Status: New

** Affects: firefox (Ubuntu)
 Importance: Undecided
 Status: New


** Tags: amd64 apport-bug quantal running-unity

** Also affects: firefox
   Importance: Undecided
   Status: New

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  firefox is not able to zoom on a specific single website

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[Bug 1082109] Re: In 12.10 autodocktools doesn't start

2013-04-13 Thread melchiaros
** Tags added: quantal

** Tags added: natty

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Title:
  In 12.10 autodocktools doesn't start

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[Bug 839691] Re: autodocktools are not able to start

2013-04-13 Thread melchiaros
*** This bug is a duplicate of bug 1082109 ***
https://bugs.launchpad.net/bugs/1082109

** This bug has been marked a duplicate of bug 1082109
   In 12.10 autodocktools doesn't start

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[Bug 1025237] Re: software center is not able to find many server packages

2013-04-13 Thread melchiaros
** Tags added: precise

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  software center is not able to find many server packages

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[Bug 1168307] Re: cannot upgrade to v13.04

2013-04-12 Thread melchiaros
In VarLogDistupgradeMainLog.txt:

2013-04-12 02:01:36,097 ERROR openCache() failed: 'E:Could not open file
/var/lib/apt/lists/dl.google
.com_linux_talkplugin_deb_dists_stable_main_binary-amd64_Packages - open
(24: Too many open files), E:Could not open file
/var/lib/apt/lists/dl.google
.com_linux_chrome_deb_dists_stable_main_binary-i386_Packages - open (24:
Too many open files), E:Could not open file /var/lib/apt/lists

.
..
..


may  more of this and finally the line

2013-04-12 02:01:36,097 ERROR self.prepared() failed

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  cannot upgrade to v13.04 - ERROR openCache() failed

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[Bug 1168307] Re: cannot upgrade to v13.04

2013-04-12 Thread melchiaros
Hi grumpycat

and apologiese for this issue. It is neasty when such a deep system
operation fail.

I have looked into the logs the bugreporting system apport has
automatically attached here.

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  cannot upgrade to v13.04 - ERROR openCache() failed

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[Bug 1168307] Re: cannot upgrade to v13.04

2013-04-12 Thread melchiaros
I know I have seen such issue a short time ago from a other user.  I
will give this a search on launchpad during today.

** Summary changed:

- cannot upgrade to v13.04
+ cannot upgrade to v13.04 - ERROR openCache() failed

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[Bug 1168307] Re: cannot upgrade to v13.04 - ERROR openCache() failed

2013-04-12 Thread melchiaros
grumpycat,

are you willing to spend some time on this for hunting down the issue?
It may be take some time and may be it will be discontinious.

greetings

malchiaros

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  cannot upgrade to v13.04 - ERROR openCache() failed

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[Bug 1168307] Re: cannot upgrade to v13.04 - ERROR openCache() failed

2013-04-12 Thread melchiaros
Aha,

I have found the other report.

I close the older as dublicate of this here, because there was no user
response.

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  cannot upgrade to v13.04 - ERROR openCache() failed

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[Bug 1159502] Re: Not Able to upgrade from 12.10 to 13.04 - cache not open

2013-04-12 Thread melchiaros
*** This bug is a duplicate of bug 1168307 ***
https://bugs.launchpad.net/bugs/1168307

** This bug has been marked a duplicate of bug 1168307
   cannot upgrade to v13.04 - ERROR openCache() failed

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Title:
  Not Able to upgrade from 12.10 to 13.04 - cache not open

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[Bug 1125630] Re: kdegraphics-strigi-analyzer_Size mismatch on upgrade

2013-04-12 Thread melchiaros
In main.log

2013-02-15 01:23:56,704 ERROR IOError in cache.commit(): 'Failed to fetch 
http://sg.archive.ubuntu.com/ubuntu/pool/universe/k/kdegraphics-strigi-analyzer/kdegraphics-strigi-analyzer_4.9.2-0ubuntu1_amd64.deb
 Size mismatch
'. Retrying (currentTry: 0)
2013-02-15 01:23:57,280 ERROR IOError in cache.commit(): 'Failed to fetch 
http://sg.archive.ubuntu.com/ubuntu/pool/universe/k/kdegraphics-strigi-analyzer/kdegraphics-strigi-analyzer_4.9.2-0ubuntu1_amd64.deb
 Size mismatch
'. Retrying (currentTry: 1)
2013-02-15 01:23:57,852 ERROR IOError in cache.commit(): 'Failed to fetch 
http://sg.archive.ubuntu.com/ubuntu/pool/universe/k/kdegraphics-strigi-analyzer/kdegraphics-strigi-analyzer_4.9.2-0ubuntu1_amd64.deb
 Size mismatch
'. Retrying (currentTry: 2)
2013-02-15 01:23:57,853 ERROR giving up on fetching after maximum retries
2013-02-15 06:43:58,034 DEBUG enabling apt cron job
2013-02-15 06:43:58,035 DEBUG abort called

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  kdegraphics-strigi-analyzer_Size mismatch on upgrade

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[Bug 1125630] Re: kdegraphics-strigi-analyzer_Size mismatch on upgrade

2013-04-12 Thread melchiaros
With this the upgrade-process simple fails(properly) on a missing
package on a sg server or discontinious internaet connection, or server
downtime, or...

there are many possibilities.

A workarround is to switch in software-sources to the main servers.

Fromthere the dist-upgrade should work.

greetings

melchiaros

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[Bug 1099257] Re: fail to update ubuntu-one indicator

2013-04-12 Thread melchiaros
Could you disable your ppa 's and restest?

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  fail to update ubuntu-one indicator

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[Bug 1084854] Re: upgrade crashes on code 1.

2013-04-12 Thread melchiaros
** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = New

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Title:
  upgrade crashes on code 1.

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[Bug 1084854] Re: upgrade crashes on code 1.

2013-04-12 Thread melchiaros
Sorry, Sanjay, but it must be always the whole files.

There is no shortening allowed.

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: New = Incomplete

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[Bug 1073739] Re: swap not mounted after upgrade to 12.10

2013-04-12 Thread melchiaros
** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = Confirmed

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Title:
  swap not mounted after upgrade to 12.10

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[Bug 1070684] Re: Fatal error during do-dist-upgrade 12.04 - 12.10

2013-04-12 Thread melchiaros
It is not best practice to attach the logs as archive, but acceptable.

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Expired = New

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Title:
  Fatal error during do-dist-upgrade 12.04 - 12.10 - cron apt-get
  upgrade disturbes dist-upgrade

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[Bug 1070684] Re: Fatal error during do-dist-upgrade 12.04 - 12.10

2013-04-12 Thread melchiaros
@ Jon

Your suggestion is verry helpfull.

I adapt the summary to your intentnion.

Could you copy out the specific lines(polease keep the ammout small for
readability) from the logs out here to the comments, so that I am able
to follow completely.

best

melchiaros

** Summary changed:

- Fatal error during do-dist-upgrade 12.04 - 12.10
+ Fatal error during do-dist-upgrade 12.04 - 12.10 - cron apt-get upgrade 
disturbes dist-upgrade

** Tags added: dist-upgrade precise precise2quantal

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  Fatal error during do-dist-upgrade 12.04 - 12.10 - cron apt-get
  upgrade disturbes dist-upgrade

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[Bug 1070675] Re: install error kubuntu 10.12

2013-04-12 Thread melchiaros
The attachments made seems not to be from the dist-upgrade folder. But
may be that is because the report is for lucid(I don't know which files
are to expect fromthere).

@Brian

In commet '10

you seems to be satisfied with the logs Morgan has provided.

In respect to this I set the status of the report back to confirmed,
because it affects multiple users.


** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Expired = Confirmed

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  install error kubuntu 10.12

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[Bug 1070675] Re: install error kubuntu 10.12

2013-04-12 Thread melchiaros
Is this report really on lucid, or is there a typo in the summary?

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[Bug 1168390] [NEW] requestsync crashed with PasswordSetError in save(): cancelled by username

2013-04-12 Thread melchiaros
Public bug reported:

I have runned requestsync without giving acces to the gnupg keyring.

On this requestsync crashed.

To sign a sync request seems not really needed, becaue a launchpad token
is used in parallel for identification and launchpad access.


Steps to reproduce:
-

1.Give to command line

requestsync conservation-code -d sid -s -e

2.See a gnupg-keyring authenification popup occure.
3. Abort the authentificaiton to the keyring.
4.See the launchpad quthentification token website come up in firefox.
5, Give a unlimited authentificaiton token from launchpad
6. See the gnupg- keyring authentificaiton popup occure again.
7.Denie the access  to the keyring again without providing any passphrase and 
use the abort button of the authentication dialog.
8. See the crash.

ProblemType: Crash
DistroRelease: Ubuntu 12.10
Package: ubuntu-dev-tools 0.143ubuntu0.2
ProcVersionSignature: Ubuntu 3.5.0-28.47-generic 3.5.7.9
Uname: Linux 3.5.0-28-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
CrashCounter: 1
Date: Fri Apr 12 14:30:12 2013
ExecutablePath: /usr/bin/requestsync
InstallationDate: Installed on 2013-01-13 (88 days ago)
InstallationMedia: Ubuntu 12.10 Quantal Quetzal - Release amd64 (20121017.5)
InterpreterPath: /usr/bin/python2.7
MarkForUpload: True
PackageArchitecture: all
ProcCmdline: /usr/bin/python /usr/bin/requestsync conservation-code -d sid -s -e
PythonArgs: ['/usr/bin/requestsync', 'conservation-code', '-d', 'sid', '-s', 
'-e']
SourcePackage: ubuntu-dev-tools
Title: requestsync crashed with PasswordSetError in save(): cancelled by 
username
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo vboxusers

** Affects: ubuntu-dev-tools (Ubuntu)
 Importance: Undecided
 Status: New


** Tags: amd64 apport-crash need-duplicate-check quantal running-unity

** Information type changed from Private to Public

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[Bug 1031753] Re: tracker-miner-fs crashed with SIGSEGV in g_str_hash()

2013-04-12 Thread melchiaros
** Bug watch added: GNOME Bug Tracker #676489
   https://bugzilla.gnome.org/show_bug.cgi?id=676489

** Changed in: tracker
   Importance: Critical = Unknown

** Changed in: tracker
   Status: Invalid = Unknown

** Changed in: tracker
 Remote watch: GNOME Bug Tracker #687108 = GNOME Bug Tracker #676489

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  tracker-miner-fs crashed with SIGSEGV in g_str_hash()

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore

2013-04-12 Thread melchiaros
Have you used a cd to do the distribuntion upgrade?

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Title:
  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore

2013-04-12 Thread melchiaros
In VarLogDistupgradeAptLog.txt

there could be found:

Investigating (0) linux-generic [ i386 ]  3.5.0.28.44 - 3.8.0.18.34  ( 
kernel )
Broken linux-generic:i386 Depends on linux-image-generic [ i386 ]  3.5.0.28.44 
- 3.8.0.18.34  ( kernel ) (= 3.8.0.18.34)

at the end of the log.

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Title:
  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore -
  affects kernel

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore

2013-04-12 Thread melchiaros
This corresponds with the first enty for the kernel in
VarLogDistupgradeAptLog.txt:

linux-headers-generic:i386 Depends on linux-headers-3.8.0-18-generic [
i386 ]  none  ( none ) can't be satisfied!

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  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore -
  affects kernel

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore

2013-04-12 Thread melchiaros
This corresponds further with the end that can be found in
VarLogDistupgradeMainlog.txt:


2013-04-12 15:35:02,609 DEBUG openCache()
2013-04-12 15:35:02,610 DEBUG failed to SystemUnLock() (E:Not locked) 
2013-04-12 15:35:09,731 DEBUG /openCache(), new cache size 41732
2013-04-12 15:35:09,731 DEBUG need_server_mode(): run in 'desktop' mode, 
(because of pkg 'ubuntu-desktop')
2013-04-12 15:35:13,089 DEBUG Running KeepInstalledSection rules
2013-04-12 15:35:14,371 DEBUG Kernel uname: '3.5.0-28-generic' 
2013-04-12 15:35:14,433 DEBUG ./get_kernel_list.sh returns: ['linux-generic', 
'linux-image-generic', 'linux-virtual', 'linux-image-virtual', 'linux-rt', 
'linux-image-rt']
2013-04-12 15:35:14,434 DEBUG linux-generic kernel already installed
2013-04-12 15:35:14,434 DEBUG Upgrading 'linux-generic' (Upgrading kernel from 
base-installer)

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  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore -
  affects kernel

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore

2013-04-12 Thread melchiaros
I do not know the content of the package ubuntu-minimal, but the logs
show that the generic kernel is affected, which makes this here a
serious thing.

A adapt the summary to this.

** Summary changed:

- during dist upgrade from 12.10 to 13.04 b2... got the errore messagge 
essential package 'ubuntu-minimal' can not be found anymore
+ during dist upgrade from 12.10 to 13.04 b2... got the errore messagge 
essential package 'ubuntu-minimal' can not be found anymore - affects kernel

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  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore -
  affects kernel

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[Bug 1070675] Re: install error kubuntu 10.12

2013-04-12 Thread melchiaros
So, than...

** Summary changed:

- install error kubuntu 10.12
+ upgrade error kubuntu 12.04 - 12.10

** Tags added: dist-upgrade kubuntu precise precise2quantal

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Title:
  upgrade error kubuntu 12.04 - 12.10 - failed on libdrm2

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[Bug 1070675] Re: upgrade error kubuntu 12.04 - 12.10

2013-04-12 Thread melchiaros
@ Morgan

If we do here something that you know is not correct, please bring up a
correction to us. That really helps.

greetings

melchiaros

** Summary changed:

- upgrade error kubuntu 12.04 - 12.10
+ upgrade error kubuntu 12.04 - 12.10 - failed on libdrm2

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[Bug 1168404] Re: during dist upgrade from 12.10 to 13.04 b2... got the errore messagge essential package 'ubuntu-minimal' can not be found anymore - affects kernel

2013-04-12 Thread melchiaros
Thank you for the workarround.

Can you provide the excatly command or commands workflow you have used.
That may be helpfull to user users that might run in this issue. At best
in a style that they could more or less directly copy and paste.

Thank you in advance

melchiaros

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  during dist upgrade from 12.10 to 13.04 b2... got the errore messagge
  essential package 'ubuntu-minimal' can not be found anymore -
  affects kernel

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[Bug 1156194] Re: update-manager still informs that Ubuntu12.10 is beta(5 month after final)

2013-04-12 Thread melchiaros
I have set to notify about every release, but I have done this through
software-sources.

I have done this just before running

update-manager -d

---
I have just hurried through a (new)vm.

I have set again to notify about every new release and runned this time:

update-manager

you see, without the -d switch

This brings up update-manger with the notification about Quantal. Using
the upgrade button brings up a normal text that not point to any
developmet/beta whatever not ready think.

So,...

it might be seen as enough.

On the other hand:

Do you know what the server people see if the use a pure command line
system?! - AFAIR the -d switch is recommend in the wiki pages to use
for server systems.

To prevent:

I do not watn test this(little small laptop in moment - a little bit
overloaded with vm's).


greetings

melchiaros



** Changed in: update-manager (Ubuntu)
   Status: Incomplete = New

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Title:
  update-manager still informs that Ubuntu12.10 is beta(5 month after
  final)

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[Bug 1165011] Re: Please backport concavity 0.1-2 (universe) from raring

2013-04-12 Thread melchiaros
Refering to the

https://wiki.ubuntu.com/UbuntuBackports

the status for the Precise backport will be set to confirmed.

** Changed in: precise-backports
   Status: New = Confirmed

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  Please backport concavity 0.1-2 (universe) from raring

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[Bug 1165011] Re: Please backport concavity 0.1-2 (universe) from raring

2013-04-12 Thread melchiaros
A testinstallation of the binary and debug packages builded in pbuilder
for Ubuntu12.04 is now also performed on Ubuntu12.04.

A function test was also successfull.

The summary of this report will be adapted to this.

** Description changed:

  Please backport concavity 0.1-2 (universe) from raring to quantal and
  precise.
  
  Reason for the backport:
  
  One of the major issues for drug development in any way is to have a clue 
what kind of substances could bound to a protein.
  For in silico prediction on this(e.g. with AutoDock) it is helpfull to reduce 
the protein surface to just
  that parts where an interaction is possible at all. This are the ligand 
binding sides of a protein.
  That is where concavity fits. It arises a precision up to 80%, which is 
remarkable more that other
  programs/algorithms archive. The most establisched ones are arround 60% 
precision is ligand binding side prediction.
  So, concavity makes a remarkable advance in this area and should be brought 
to those parts of the community who reside on stable release Quantal and LTS 
Precise.
  
  Testing:
  
  Mark off items in the checklist [X] as you test them, but please leave the 
checklist so that backporters can quickly evaluate the state of testing.
  
  You can test-build the backport in your PPA with backportpackage:
  $ backportpackage -u ppa:lp username/ppa name -s raring -d quantal 
concavity
  
  * quantal:
  [x] Package builds without modification
  [x] concavity installs cleanly and runs
  [x] concavity-dbg installs cleanly and runs
  
  *precise:
  [x] Package builds without notification
- [] concavity installs cleanly and runs
- [] concavity-dbg installs cleanly and runs
+ [x] concavity installs cleanly and runs
+ [x] concavity-dbg installs cleanly and runs
  
  No reverse dependencies

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  Please backport concavity 0.1-2 (universe) from raring

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[Bug 1168423] [NEW] Please backport conservation-code 20110309.0-1 (universe) from raring

2013-04-12 Thread melchiaros
Public bug reported:

Please backport conservation-code 20110309.0-1 (universe) from raring to 
precise, quantal.
The builds run with succes, performed by backportpackage over pbuilder. The 
installation of the packages were done in precise and quantal over gdebi with 
success. A function test was performed in precise and quantal with utilisation 
of the score_conservation script which is in conservation_code package. The 
example 1 from

man score_conservation

runned with success.

Reason for the backport:

The package concavity which is bending approval for backporting to quantal and 
precise
is signifiacant enhanced with the capabilities of conservation-code.
concavity uses protein 3D information to calculate ligand binding sides, which 
is the first stage in in silico pharmaceutical resarch(followed by docking e.g 
with autodock-vina).
For enhancing the precision of the ligand binding side calculations concavity 
needs informations about conserved chains in proteins. This calculation are 
done by conservation-code.

Testing:


* precise:
[x] Package builds without modification
[x] conservation-code installs cleanly and runs
* quantal:
[x] Package builds without modification
[x] conservation-code installs cleanly and runs

No reverse dependencies

** Affects: precise-backports
 Importance: Undecided
 Status: Confirmed

** Affects: quantal-backports
 Importance: Undecided
 Status: Confirmed

** Changed in: precise-backports
   Status: New = Confirmed

** Changed in: quantal-backports
   Status: New = Confirmed

** Description changed:

  Please backport conservation-code 20110309.0-1 (universe) from raring to 
precise, quantal.
- The builds run with succes, performed by backportpackage over pbuilder. The 
installation of the packages were done in precise and quantal over gdebi with 
success. A functio test was performed in precise and quantal with utilisation 
of the score_conservation script which is in conservation_code package. The 
example 1 from
+ The builds run with succes, performed by backportpackage over pbuilder. The 
installation of the packages were done in precise and quantal over gdebi with 
success. A function test was performed in precise and quantal with utilisation 
of the score_conservation script which is in conservation_code package. The 
example 1 from
  
  man score_conservation
  
  runned with success.
  
- 
  Reason for the backport:
  
  The package concavity which is bending approval for backporting to quantal 
and precise
  is signifiacant enhanced with the capabilities of conservation-code.
- concavity uses protein 3D information to calculate ligand binding sides, 
which is the first stage in in silico pharmaceutical resarch(followed by 
docking e.g with autodock-vina). 
- For enhancing the precision of the ligand binding side calculations concavity 
needs informations about conserved chains in proteins. This calculation are 
done by conservation-code. 
+ concavity uses protein 3D information to calculate ligand binding sides, 
which is the first stage in in silico pharmaceutical resarch(followed by 
docking e.g with autodock-vina).
+ For enhancing the precision of the ligand binding side calculations concavity 
needs informations about conserved chains in proteins. This calculation are 
done by conservation-code.
  
  Testing:
  
  
  * precise:
  [x] Package builds without modification
  [x] conservation-code installs cleanly and runs
  * quantal:
  [x] Package builds without modification
  [x] conservation-code installs cleanly and runs
  
  No reverse dependencies

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  Please backport conservation-code 20110309.0-1 (universe) from raring

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[Bug 1168423] Re: Please backport conservation-code 20110309.0-1 (universe) from raring

2013-04-12 Thread melchiaros
The backport request for concavity can be found here:

https://bugs.launchpad.net/quantal-backports/+bug/1165011

The debian alioth (tasks) point on the enhancement connection between
concavity and conservation-code.


The manpages of concavity point also to this.

My own experiments gives this too.

Let us belive.

melchiaros

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[Bug 1119581] Re: display divided into 1 - 2 - 3 and showing as 3 - 2- 1

2013-04-11 Thread melchiaros
Pava,

would you please give a good description as requested in comment #2

The status will not change until you have done this. And there will be
no handling without the information requested.

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  display divided into 1 - 2 - 3 and showing as 3 - 2- 1

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[Bug 1094914] Re: nautilus is not able to change owner of a selection of files

2013-04-11 Thread melchiaros
*** This bug is a duplicate of bug 123684 ***
https://bugs.launchpad.net/bugs/123684

** This bug has been marked a duplicate of bug 123684
   can't change owner of multiple files in nautilus

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  nautilus is not able to change owner of a selection of files

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[Bug 123684] Re: can't change owner of multiple files in nautilus

2013-04-11 Thread melchiaros
Still actual for raring.

** Tags added: amd64 raring

** Tags added: hardy

** Tags added: karmic

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[Bug 1165011] Re: Please backport concavity 0.1-2 (universe) from raring

2013-04-11 Thread melchiaros
I have figured out how to handle with backporting script and pbuilder.

The build for quantal and precise run with success to the end.  The
binary packages for Quantal and Precise are now there, and also the -dbg
packages for Quantal and Precise.

A testinstallation on Quantal is already performed and Precise is
pendig, but should be tested until the evening.

I adapt the bug desription to this.

** Description changed:

  Please backport concavity 0.1-2 (universe) from raring to quantal and
  precise.
  
  Reason for the backport:
  
  One of the major issues for drug development in any way is to have a clue 
what kind of substances could bound to a protein.
  For in silico prediction on this(e.g. with AutoDock) it is helpfull to reduce 
the protein surface to just
  that parts where an interaction is possible at all. This are the ligand 
binding sides of a protein.
  That is where concavity fits. It arises a precision up to 80%, which is 
remarkable more that other
  programs/algorithms archive. The most establisched ones are arround 60% 
precision is ligand binding side prediction.
  So, concavity makes a remarkable advance in this area and should be brought 
to those parts of the community who reside on stable release Quantal and LTS 
Precise.
  
  Testing:
  
  Mark off items in the checklist [X] as you test them, but please leave the 
checklist so that backporters can quickly evaluate the state of testing.
  
  You can test-build the backport in your PPA with backportpackage:
  $ backportpackage -u ppa:lp username/ppa name -s raring -d quantal 
concavity
  
  * quantal:
  [x] Package builds without modification
  [x] concavity installs cleanly and runs
- [ ] concavity-dbg installs cleanly and runs
+ [x] concavity-dbg installs cleanly and runs
  
  *precise:
  [x] Package builds without notification
- [x] concavity installs cleanly and runs
- [] concavity-dbg installs cleanly and runs 
+ [] concavity installs cleanly and runs
+ [] concavity-dbg installs cleanly and runs
  
  No reverse dependencies
- 
- 
- Additional:
- 
- This here is not done in the common way.
- 
- I am a little bit overwhelmed by the possibilities of backporting script
- and pbuild.
- 
- I have done both builds in quantal and precise in pbuild and both
- running with success. At the end is a signing error, but that was to
- expect, because I have not provided any key for signing(Sorry, but to
- get this all on at the same time is behond my skills).
- 
- The testinstallation of concavity in quantal and precise was also not
- performed fully correct. I have just done an installation of the
- original raring package trough gdebi.
- 
- Both insatllations are working for the examples in the manpage of
- concavity and produces valid results(.pdb files which are able to be
- visualized in Jmol or RasMol).
- 
- 
- Soory, for the figuring arround, but in near futhur I am not able to provide 
better.

** Changed in: precise-backports
   Status: Confirmed = New

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  Please backport concavity 0.1-2 (universe) from raring

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[Bug 1166048] Re: update error

2013-04-09 Thread melchiaros
In VarLogDistupgradeAptlog.txt:

ERROR:root:failed to mark 'ubuntu-desktop' for install (E:Unable to correct 
problems, you have held broken packages.)
ERROR:root:Dist-upgrade failed: 'The package 'ubuntu-release-upgrader-gtk' is 
marked for rem

** Summary changed:

- update error
+ dist-upgrade12.10 - 13.04 failed on ubuntu-desktop package

** Summary changed:

- dist-upgrade12.10 - 13.04 failed on ubuntu-desktop package
+ dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and 
ubuntu-release-upgrader package itself

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  dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-
  release-upgrader package itself

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[Bug 1166048] Re: dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-release-upgrader package itself

2013-04-09 Thread melchiaros
This here happends with ubuntu-release-upgrader 1:0.190.5.

Actual in quantal-updates is 1:0.190.6

, but refering to the changelog

ubuntu-release-upgrader (1:0.190.6) quantal-proposed; urgency=low

  * Fix a couple path joins and bugs that prevented check-new-release-gtk
from working.  (LP: #1094777)

 -- Michael Terry mte...@ubuntu.com  Tue, 22 Jan 2013 10:21:27 -0500

this should have no effect here.

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  dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-
  release-upgrader package itself

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[Bug 1166048] Re: dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-release-upgrader package itself

2013-04-09 Thread melchiaros
A retest with ubuntu-release-upgrader 1:0.190.6

should be obsolote with refering to the changelog entry.

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  dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-
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[Bug 1166048] Re: dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-release-upgrader package itself

2013-04-09 Thread melchiaros
@Sanan

As I have shown above it is not neccesary to do, but well, it could be
helpul.

Havwe you time to upgrade your system to the latest ubuntu-release
upgrader a retest?

If you want:

Please enable the proposed repositories and run from command lilne

sudo apt-cache update

and after this

sudo apt-get dist-upgrade


With this you will have for sure the latest packages for Quantal.

After this start your system new(recommend, because of kernel upgrades)
and than retry with the distribution upgrade.

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  dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-
  release-upgrader package itself

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[Bug 1166048] Re: dist-upgrade12.10 - 13.04 failed on ubuntu-desktop, and ubuntu-release-upgrader package itself

2013-04-09 Thread melchiaros
I let the status of the report to new.

Expanation above.

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[Bug 1166346] Re: do-release-upgrade 12.04 to 12.10 gives fatal error

2013-04-09 Thread melchiaros
@fisharebest

Hi, thank you for reporting.

One hint to accelerate a handling:

It ishelpfull to set the status of the report back from incomplete if a
requested information is provided.

Oh, well, let me do it for you this time.


greetings

 melchiaros

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = New

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  do-release-upgrade 12.04 to 12.10 gives fatal error

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[Bug 1164955] [NEW] backportpackage crashed with IOError in _download_file(): [Errno 2] No such file or directory: u'/home/user/Downloads/concavity_0.1.orig.tar.xz'

2013-04-05 Thread melchiaros
Public bug reported:

I have called from terminal:

:~/Downloads$ backportpackage -b -s raring -d quantal -w .
concavity_0.1-2.dsc

As can be seen the actual directory is /home/user/Downloads/

The concavity_0.1-2.dsc file from Raring is stored there.



After this the following stacktrace occures:

:~/Downloads$ backportpackage -b -s raring -d quantal -w .  concavity_0.1-2.dsc 
backportpackage: Downloading concavity_0.1.orig.tar.xz from None (0.307 MiB)
Traceback (most recent call last):
  File /usr/bin/backportpackage, line 399, in module
sys.exit(main(sys.argv))
  File /usr/bin/backportpackage, line 377, in main
pkg.pull()
  File /usr/lib/python2.7/dist-packages/ubuntutools/archive.py, line 362, in 
pull
if self._download_file(url, name):
  File /usr/lib/python2.7/dist-packages/ubuntutools/archive.py, line 322, in 
_download_file
in_ = open(parsed.path, 'r')
IOError: [Errno 2] No such file or directory: 
u'/home/user/Downloads/concavity_0.1.orig.tar.xz'


--

This is one of my first experiments with  the  backportpackage script.
So, may be it is a case of user misbehaviour.

-

Steps to reproduce:

1. Downlaod

http://archive.ubuntu.com/ubuntu/pool/universe/c/concavity/concavity_0.1-2.dsc

into your download folder

2. Call a terminal
3. Use the command

cd Downloads

4. Use the command

backportpackage -b -s raring -d quantal -w .  concavity_0.1-2.dsc

5.See the crash

---

Additional:

The are two points I want to bring attention on:

backportpackage is a bit unhappy(with other command) if a package
resides in Universe and not in main security restricted proposed. This
may be one cause.

The second is a special in the .dsc file:

concavity_0.1.orig.tar.xz from None (0.307 MiB)

the number 0.1 for concavity is obfuscating me a little bit. The version
number is more 0.1-2.


Just this two hints. May be it is one of them(I just digging a bit).

ProblemType: Crash
DistroRelease: Ubuntu 12.10
Package: ubuntu-dev-tools 0.143ubuntu0.2
ProcVersionSignature: Ubuntu 3.5.0-27.46-generic 3.5.7.7
Uname: Linux 3.5.0-27-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
Date: Fri Apr  5 13:26:16 2013
ExecutablePath: /usr/bin/backportpackage
ExecutableTimestamp: 1352840357
InstallationDate: Installed on 2013-01-13 (81 days ago)
InstallationMedia: Ubuntu 12.10 Quantal Quetzal - Release amd64 (20121017.5)
InterpreterPath: /usr/bin/python2.7
MarkForUpload: True
PackageArchitecture: all
ProcCmdline: /usr/bin/python /usr/bin/backportpackage -b -s raring -d quantal 
-w . concavity_0.1-2.dsc
ProcCwd: /home/user/Downloads
ProcEnviron:
 TERM=xterm
 SHELL=/bin/bash
 PATH=(custom, no user)
 LANG=de_DE.UTF-8
 XDG_RUNTIME_DIR=set
PythonArgs: ['/usr/bin/backportpackage', '-b', '-s', 'raring', '-d', 'quantal', 
'-w', '.', 'concavity_0.1-2.dsc']
SourcePackage: ubuntu-dev-tools
Title: backportpackage crashed with IOError in _download_file(): [Errno 2] No 
such file or directory: u'/home/user/Downloads/concavity_0.1.orig.tar.xz'
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo

** Affects: ubuntu-dev-tools (Ubuntu)
 Importance: Undecided
 Status: New


** Tags: amd64 apport-crash need-duplicate-check quantal running-unity

** Information type changed from Private to Public

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  such file or directory:
  u'/home/user/Downloads/concavity_0.1.orig.tar.xz'

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[Bug 1164300] Re: Fix a couple path joins and bugs that prevented check-new-release-gtk from working. (LP: #1094777)

2013-04-05 Thread melchiaros
Hi Satya,

Sampo is unfortunately absolut correct.


You have choosen old style reporting. The past has shown that this makes a lot 
of work to both sides. Yours and developers.

Your system is logging the errors for distribution upgrades
automatically.

We need them here.

Please call a terminal and run:

apport-collect 1164300

If it ask for additional libraries than please install them.

Thnak you in advance

melchiaros

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[Bug 1165011] [NEW] Please backport concavity 0.1-2 (universe) from raring

2013-04-05 Thread melchiaros
Public bug reported:

Please backport concavity 0.1-2 (universe) from raring to quantal and
precise.

Reason for the backport:

One of the major issues for drug development in any way is to have a clue what 
kind of substances could bound to a protein.
For in silico prediction on this(e.g. with AutoDock) it is helpfull to reduce 
the protein surface to just
that parts where an interaction is possible at all. This are the ligand binding 
sides of a protein.
That is where concavity fits. It arises a precision up to 80%, which is 
remarkable more that other
programs/algorithms archive. The most establisched ones are arround 60% 
precision is ligand binding side prediction.
So, concavity makes a remarkable advance in this area and should be brought to 
those parts of the community who reside on stable release Quantal and LTS 
Precise.

Testing:

Mark off items in the checklist [X] as you test them, but please leave the 
checklist so that backporters can quickly evaluate the state of testing.

You can test-build the backport in your PPA with backportpackage:
$ backportpackage -u ppa:lp username/ppa name -s raring -d quantal concavity

* quantal:
[x] Package builds without modification
[x] concavity installs cleanly and runs
[ ] concavity-dbg installs cleanly and runs

*precise:
[x] Package builds without notification
[x] concavity installs cleanly and runs
[] concavity-dbg installs cleanly and runs 

No reverse dependencies


Additional:

This here is not done in the common way.

I am a little bit overwhelmed by the possibilities of backporting script
and pbuild.

I have done both builds in quantal and precise in pbuild and both
running with success. At the end is a signing error, but that was to
expect, because I have not provided any key for signing(Sorry, but to
get this all on at the same time is behond my skills).

The testinstallation of concavity in quantal and precise was also not
performed fully correct. I have just done an installation of the
original raring package trough gdebi.

Both insatllations are working for the examples in the manpage of
concavity and produces valid results(.pdb files which are able to be
visualized in Jmol or RasMol).


Soory, for the figuring arround, but in near futhur I am not able to provide 
better.

** Affects: precise-backports
 Importance: Undecided
 Status: Confirmed

** Affects: quantal-backports
 Importance: Undecided
 Status: Confirmed

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[Bug 1165011] Re: Please backport concavity 0.1-2 (universe) from raring

2013-04-05 Thread melchiaros
** Also affects: precise-backports
   Importance: Undecided
   Status: New

** Changed in: precise-backports
   Status: New = Confirmed

** Changed in: quantal-backports
   Status: New = Confirmed

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[Bug 1098732] Re: menu-cached crashed with SIGSEGV in malloc()

2013-04-04 Thread melchiaros
In respect that b00507031 has used a pure Lubuntu, the crash is
definitivly not caused by the Unity desktop system in any way.

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  menu-cached crashed with SIGSEGV in malloc()

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[Bug 1098732] Re: menu-cached crashed with SIGSEGV in malloc()

2013-04-04 Thread melchiaros
It is a little bit evil behave, but for those who comes new here, it
might help more to get to the upstream report at

http://sourceforge.net/tracker/index.php?func=detailaid=3603920group_id=180858atid=894869

and give it a ping or +1 or whatever.

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[Bug 1159492] Re: science PDB file is not processed correctly after extraction

2013-04-01 Thread melchiaros
** Also affects: file-roller
   Importance: Undecided
   Status: New

** Project changed: file-roller = rasmol (Ubuntu)

** Also affects: rasmol
   Importance: Undecided
   Status: New

** Project changed: rasmol = jmol (Ubuntu)

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  science PDB file is not processed correctly after extraction

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[Bug 930598] Re: rasmol-classic command crashes, only gtk version works, is impossibile to use in a real scientific contest

2013-04-01 Thread melchiaros
Reproduced with Ubuntu12.10.

Setting the status of the report to confirmed.

** Changed in: rasmol (Ubuntu)
   Status: New = Confirmed

** Tags added: amd64 quantal

** Tags added: natty

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  rasmol-classic command crashes, only gtk version works, is impossibile
  to use in a real scientific contest

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[Bug 1159502] Re: Not Able to upgrade from 12.10 to 13.04

2013-04-01 Thread melchiaros
Hi Op4Mox,

I have just looked into the logs.

There is documented an error in VarLogDistupgradeMainlog.txt:

2013-03-24 21:32:42,333 ERROR openCache() failed: 'E:Tiedostoa
/var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_quantal-
backports_multiverse_binary-amd64_Packages ei voitu avata -

.
..
... and so on

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  Not Able to upgrade from 12.10 to 13.04

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[Bug 1159502] Re: Not Able to upgrade from 12.10 to 13.04

2013-04-01 Thread melchiaros
Sorry Joeri,

there is no cause to set the status of the report to incomplete.

When there are reasons it is common to write them down, for the next who
comes here.

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = New

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[Bug 1159502] Re: Not Able to upgrade from 12.10 to 13.04

2013-04-01 Thread melchiaros
This closes with:

2013-03-24 21:32:42,333 ERROR self.prepared() failed

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[Bug 1159502] Re: Not Able to upgrade from 12.10 to 13.04

2013-04-01 Thread melchiaros
So, this could be caused by a other application with apt access that
runs at the same time(like automatik security packages installation,
update packes list through update-manager, a other terminal with a
running apt task, something more)

Could you agree with this?

If the written above is correct, than y simple retest would make sense
here.

It is unlikely that a second time a second apt process is runnig while
you start the relase upgrade.

I give it a 99% that it works on a retest.

In meantime I set this back to incomplete. If you have done, please set
the status back to new.

Thank you so far and sorry for the unconvinience.

melchiaros

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: New = Incomplete

** Summary changed:

- Not Able to upgrade from 12.10 to 13.04
+ Not Able to upgrade from 12.10 to 13.04 - cache not open

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[Bug 1155648] Re: update to 12-10 crashes

2013-04-01 Thread melchiaros
o.K here.

You have clearly a traceback of the ubuntu-release upgrader.

And a following one of appor(the crash reporter itself).

Whuu, a double one.


** Summary changed:

- update to 12-10 crashes
+ update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, 
in module

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
I set this back to new for now, bnecause Pierre has provided the logs.


** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = New

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
Pierre,
 I know time is low, but could you attach from your archive the apt and the 
main log seperately?

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
The apt_clone file is in the tar.gz archive, if someone whant to play
arround.

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
(smile)

o.K my fault.

Ment was without compressing.

But it is o.K like it is.

Let it in this style. A little bit more clicking for those who whant to
handle(I am only on preparation).

Thank you for bear on this.

melchiaros

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
Jup, clearly in the main log:

Traceback (most recent call last):

  File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

  File /tmp/update-manager-9JqPjZ/DistUpgrade/DistUpgradeMain.py, line
240, in main

  File /tmp/update-manager-
9JqPjZ/DistUpgrade/DistUpgradeController.py, line 1764, in run

  File /tmp/update-manager-
9JqPjZ/DistUpgrade/DistUpgradeController.py, line 1681, in fullUpgrade

  File /tmp/update-manager-
9JqPjZ/DistUpgrade/DistUpgradeController.py, line 207, in openCache

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
Interestingly there is just before a problem to lock the cache:

2013-03-15 10:45:24,464 DEBUG openCache()
2013-03-15 10:45:24,464 DEBUG failed to SystemUnLock() (E:Not locked) 
2013-03-15 10:45:35,026 DEBUG failed to lock the cache, retrying (1)
2013-03-15 10:45:44,726 DEBUG failed to lock the cache, retrying (2)
.
..
...

and so on.

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 1155648] Re: update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal, line 10, in module

2013-04-01 Thread melchiaros
I have seen just something similiar here:

https://bugs.launchpad.net/ubuntu/+source/ubuntu-release-
upgrader/+bug/1159502

, but this is on quantal to raring and without stacktrace.

** Tags added: dist-upgrade precise precise2quantal

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  update to 12-10 crashes- File /tmp/update-manager-9JqPjZ/quantal,
  line 10, in module

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[Bug 915228] Re: rasmol.32 crashed with SIGSEGV in XCopyArea()

2013-04-01 Thread melchiaros
Seen on quantal. I add the tag for.

** Tags added: quantal

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Title:
  rasmol.32 crashed with SIGSEGV in XCopyArea()

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[Bug 914919] Re: rasmol.32 crashed with SIGSEGV in XCopyArea()

2013-04-01 Thread melchiaros
*** This bug is a duplicate of bug 915228 ***
https://bugs.launchpad.net/bugs/915228

** This bug has been marked a duplicate of bug 915228
   rasmol.32 crashed with SIGSEGV in XCopyArea()

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Title:
  rasmol.32 crashed with SIGSEGV in XCopyArea()

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[Bug 1162850] [NEW] rasmol-gtk crashed with SIGABRT in raise()

2013-04-01 Thread melchiaros
Public bug reported:

Afer loading a .pdb file in RasMol a print attemped failed with this
crash.

The affected .pdb file will be attached.

Steps to reproduce:
1.Open the .pdb file with RasMol gtk
2.Use the menu point File-Print
3.See the crash.

ProblemType: Crash
DistroRelease: Ubuntu 12.10
Package: rasmol 2.7.5.2-1ubuntu1
ProcVersionSignature: Ubuntu 3.5.0-27.46-generic 3.5.7.7
Uname: Linux 3.5.0-27-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
Date: Mon Apr  1 17:12:59 2013
ExecutablePath: /usr/bin/rasmol-gtk
ExecutableTimestamp: 1349103392
InstallationDate: Installed on 2013-01-13 (78 days ago)
InstallationMedia: Ubuntu 12.10 Quantal Quetzal - Release amd64 (20121017.5)
MarkForUpload: True
ProcCmdline: rasmol-gtk /tmp/mustang/1sp1.pdb
ProcCwd: /home/user
ProcEnviron:
 PATH=(custom, no user)
 XDG_RUNTIME_DIR=set
 LANG=de_DE.UTF-8
 SHELL=/bin/bash
Signal: 6
SourcePackage: rasmol
StacktraceTop:
 raise () from /lib/x86_64-linux-gnu/libc.so.6
 abort () from /lib/x86_64-linux-gnu/libc.so.6
 g_assertion_message () from /lib/x86_64-linux-gnu/libglib-2.0.so.0
 g_assertion_message_expr () from /lib/x86_64-linux-gnu/libglib-2.0.so.0
 ?? ()
Title: rasmol-gtk crashed with SIGABRT in raise()
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo

** Affects: rasmol (Ubuntu)
 Importance: Undecided
 Status: New


** Tags: amd64 apport-crash need-amd64-retrace quantal running-unity

** Information type changed from Private to Public

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  rasmol-gtk crashed with SIGABRT in raise()

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[Bug 1162850] Re: rasmol-gtk crashed with SIGABRT in raise()

2013-04-01 Thread melchiaros
** Attachment added: 1sp1.pdb
   
https://bugs.launchpad.net/ubuntu/+source/rasmol/+bug/1162850/+attachment/3612134/+files/1sp1.pdb

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  rasmol-gtk crashed with SIGABRT in raise()

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[Bug 915228] Re: rasmol.32 crashed with SIGSEGV in XCopyArea()

2013-04-01 Thread melchiaros
This also happends with the gtk version

** Also affects: rasmol
   Importance: Undecided
   Status: New

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  rasmol.32 crashed with SIGSEGV in XCopyArea()

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[Bug 915228] Re: rasmol.32 crashed with SIGSEGV in XCopyArea()

2013-04-01 Thread melchiaros
The upstream report could be found at:

https://sourceforge.net/p/openrasmol/bugs/10/

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[Bug 915228] Re: rasmol.32 crashed with SIGSEGV in XCopyArea()

2013-04-01 Thread melchiaros
hjd,

may be it makes sense to leafe a comment on the upstream tracker.

You know more noise generate sometimes more attention(not the nice
style).

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[Bug 975887] Re: gschem initial start brings on malformed information window

2013-03-31 Thread melchiaros
Than please use the also affects me button in the left upper corner.

Also check on which Ubuntu version you are.

If it is quantal please at this tag. If it is raring do the same. If you
also on precise, do nothing on the tags.

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
Encounter this problem on dist-upgrade from Ubuntu12.04 to Ubuntu 12.10.

Tags for this will be added. and logs attached.

** Tags added: dist-upgrade precise2quantal

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: apt.log
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593705/+files/apt.log

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: apt-term.log
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593707/+files/apt-term.log

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: history.log
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593714/+files/history.log

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: lspci.txt
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593715/+files/lspci.txt

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: main.log
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593716/+files/main.log

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1089041] Re: package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess installiertes post-installation-Skript gab den Fehlerwert 1 zurück

2013-03-24 Thread melchiaros
** Attachment added: apt-clone_system_state.tar.gz
   
https://bugs.launchpad.net/ubuntu/+source/emacsen-common/+bug/1089041/+attachment/3593717/+files/apt-clone_system_state.tar.gz

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Title:
  package emacsen-common 2.0.3 failed to install/upgrade: Unterprozess
  installiertes post-installation-Skript gab den Fehlerwert 1 zurück

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[Bug 1069733] Re: Release upgrade 12.10 - kubuntu-netbook could not be installed - Unicode error u'\xbb'

2013-03-24 Thread melchiaros
With respect to the circumstances that 3 people has encounterd the
problem and that we have a stacktrace I set this to confirmed.

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: New = Confirmed

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Title:
  Release upgrade 12.10 - kubuntu-netbook could not be installed -
  Unicode error u'\xbb'

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[Bug 1069733] Re: Release upgrade 12.10 - kubuntu-netbook could not be installed

2013-03-24 Thread melchiaros
In apt.log there is a traceback:

Traceback (most recent call last):
  File /usr/lib/python2.7/logging/__init__.py, line 846, in emit
msg = self.format(record)
  File /usr/lib/python2.7/logging/__init__.py, line 723, in format
return fmt.format(record)
  File /usr/lib/python2.7/logging/__init__.py, line 464, in format
record.message = record.getMessage()
  File /usr/lib/python2.7/logging/__init__.py, line 328, in getMessage
msg = msg % self.args
UnicodeEncodeError: 'ascii' codec can't encode character u'\xbb' in position 
10: ordinal not in range(128)
Logged from file DistUpgradeCache.py, line 715

** Tags added: dist-upgrade precise precise2quantal

** Summary changed:

- Release upgrade 12.10 - kubuntu-netbook could not be installed 
+ Release upgrade 12.10 - kubuntu-netbook could not be installed - Unicode 
error u'\xbb'

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  Release upgrade 12.10 - kubuntu-netbook could not be installed -
  Unicode error u'\xbb'

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[Bug 1159492] Re: science PDB file is not processed correctly after extraction

2013-03-24 Thread melchiaros
** Attachment added: the affected archiv
   
https://bugs.launchpad.net/ubuntu/+source/file-roller/+bug/1159492/+attachment/3594390/+files/pdb163d.ent.gz

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Title:
  science PDB file is not processed correctly after extraction

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[Bug 1159492] [NEW] science PDB file is not processed correctly after extraction

2013-03-24 Thread melchiaros
Public bug reported:

The affected archiv will be attached.

When I open the archiv

pdb163d.ent.gz

with file roller, I get the compressed file shown in file-roller GUI,

When I open it within the file-roller GUI with rasmol or jmol all works
correct and the protein structure is shown.

So, far so good.


When I extract the compressed file to the filesystem, close file-roller, 
because it is no longer needed.

When I ttry then to open the file

pdb163d.ent

with rasmol or jmol it is not possible. The file is not anymore a
appopriate format for those programs.


Steps to reproduce:

1.Install rasmol and jmol (oneof them may be enough)
2.Donwlaod the file

pdb163d.ent.gz

from here,
3.Extract the file to the filesytem with file-roller
4.Try to open the file with right mouse click -  open with... -  choose 
rasmol or jmol as your choice 
5.See only a black visualisation or in jmol an error message(file not found 
exception)

ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: file-roller 3.6.1.1-0ubuntu1.1
ProcVersionSignature: Ubuntu 3.5.0-27.45-generic 3.5.7.7
Uname: Linux 3.5.0-27-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
Date: Sun Mar 24 19:33:18 2013
ExecutablePath: /usr/bin/file-roller
InstallationDate: Installed on 2013-01-13 (70 days ago)
InstallationMedia: Ubuntu 12.10 Quantal Quetzal - Release amd64 (20121017.5)
MarkForUpload: True
ProcEnviron:
 PATH=(custom, no username)
 XDG_RUNTIME_DIR=set
 LANG=de_DE.UTF-8
 SHELL=/bin/bash
SourcePackage: file-roller
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: file-roller (Ubuntu)
 Importance: Undecided
 Status: New


** Tags: amd64 apport-bug quantal running-unity

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[Bug 1069133] Re: Get upgrade error 12.04 - 12.10 Could not determine upgrade - xorg from ppa

2013-03-24 Thread melchiaros
o.K this was just for information.

I see this not as essential to handle this report.

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: Incomplete = New

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Title:
  Get upgrade error 12.04 - 12.10 Could not determine upgrade - xorg
  from ppa

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[Bug 1068297] Re: error when upgrading from 10.04 to 10.10

2013-03-22 Thread melchiaros
Yes, I know.

It was not to expect that you still have the logs.

But I have had to ask.

Sorry,

but bug triaging is mostly community driven(I am not paied by
canonical), so the delays are more often huge than it is good for the
distribution.

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  error when upgrading from 10.04 to 10.10

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[Bug 1068297] Re: error when upgrading from 10.04 to 10.10

2013-03-22 Thread melchiaros
Anyway,

that above where the standard questions.

I would like to invest some of my time to investigate this a bit
further.

Can you try to help me.

What have you done with your system. Are there some specific Software
that you have installed that you expect not to much other users have
too.

So some hints would be enough.

greetings

melchiaros

(Sorry, when I have blamed you)

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[Bug 1078653] Re: upgrade Ubuntu 12.04 - 12.10 has several problems: grub-pc, apport, older linux versions

2013-03-22 Thread melchiaros
** Tags added: dist-upgrade precise precise2quantal

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Title:
  upgrade Ubuntu 12.04 - 12.10 has several problems: grub-pc, apport,
  older linux versions

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What we have learned so far on ubuntu-release upgrader hugday

2013-03-22 Thread melchiaros
We have done the hugday on ubuntu-release-upgrader yesterday and there 
are still tickets open, especially for the triaging step - so you can 
still come up, e.g with recreation with apt-clone.tar.gz in a VM:


http://linuxundich.de/de/ubuntu/mit-apt-clone-die-installation-eines-rechners-auf-andere-ubertragen/

(Sorry, the website is written in german; please use e.g chromium 
translation popup on entering the website)


).

The question arises: What we have seen from the bunch of reports there 
so far?



I start this with one of my observations.

A good part of the problems are caused by ppa's that users have 
nincorporated in their system.


Especially the logs shown often to me xorg problems.

They have ppa's integrated that provides xorg components for resolving 
their graphical problems that they have with xorg from the main repositorie.



So far we could not say that they do nonsense to their system. 
Dysfunctional graphics are good reasons for incroporationg not official 
software.



The problem is that the ubuntu-release-upgrader is able to disable ppa's 
from source.list, but not able to handle the xorg move back to main with 
success.


This makes the upgrade process failing.

Is the user the problem?

Likely not.

I have seen a comment from Sampo555 that points to the policy to 
deactivate xorg ppa's before upgrading(thank you that you give the 
people a workarround Sampo).


Let us switch for the moment the perspective to that of a user(not 
anymore a newbie, but also not down to the shoulders in Ubuntu).


- S/he could not see that policy from the front of the computer. The 
only thing what they see is that without ppa the graphic is a mess. I 
have read cases on Ubuntu question section where the graphical system 
was completely not useable.


It would affect a good part of the release upgrade problems (may be 
arround 20%-30%- just a guess on what I have seen in the logs) when it 
would be possible to teach ubuntu-release-upgrader to handle this.



What do you think about?

greetings

melchiaros

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[Bug 1106081] Re: TypeError from do-release-upgrade when LANG=C

2013-03-21 Thread melchiaros
Hi Martin,

In VarLogDistupgradeMainlog.txt

you have a woanderfull stacktrace:

Traceback (most recent call last):

  File /tmp/ubuntu-release-upgrader-406zz2/raring, line 10, in module
sys.exit(main())

  File /tmp/ubuntu-release-upgrader-406zz2/DistUpgrade/DistUpgradeMain.py, 
line 240, in main
if app.run():

  File 
/tmp/ubuntu-release-upgrader-406zz2/DistUpgrade/DistUpgradeController.py, 
line 1769, in run
return self.fullUpgrade()

  File 
/tmp/ubuntu-release-upgrader-406zz2/DistUpgrade/DistUpgradeController.py, 
line 1668, in fullUpgrade
if not self.updateSourcesList():

  File 
/tmp/ubuntu-release-upgrader-406zz2/DistUpgrade/DistUpgradeController.py, 
line 818, in updateSourcesList
_(Some third party entries in your sources.list 

  File 
/tmp/ubuntu-release-upgrader-406zz2/DistUpgrade/DistUpgradeViewText.py, line 
138, in information
sys.stdin.readline().decode(ENCODING, backslashreplace)

TypeError: decode() argument 1 must be string, not None

** Tags added: quantal2raring

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Title:
  TypeError from do-release-upgrade when LANG=C

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[Bug 1106081] Re: TypeError from do-release-upgrade when LANG=C

2013-03-21 Thread melchiaros
This is properly caused by

_(Some third party entries in your sources.list 

and with this it imay be

http://ppa.launchpad.net/hrw/my-own-packages/ubuntu

your own ppa that makes trouble.

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https://bugs.launchpad.net/bugs/1106081

Title:
  TypeError from do-release-upgrade when LANG=C

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[Bug 1106081] Re: TypeError from do-release-upgrade when LANG=C

2013-03-21 Thread melchiaros
We are glad over every hint what could be improved.

Can you provide a good algorithmic description, that is complete and can
guide a beginner to the point where the problem happends.

(step1,
 step2,
.
.
.
finished)


After that set the status of this report back to new.


Thanks

** Changed in: ubuntu-release-upgrader (Ubuntu)
   Status: New = Incomplete

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Title:
  TypeError from do-release-upgrade when LANG=C

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[Bug 1068297] Re: error when upgrading from 10.04 to 10.10

2013-03-21 Thread melchiaros
Hi turul69,

that are bad news.

The ubuntu-release-upgrader should be one of the most reliable programs
we have here.

Sorry, for the inconvenience.

Could you help us on further handling here.

I am a bit in doubt that this report is on the correct package.

ubuntu-release-upgrader is first indroduced with Ubuntu12.04.

Before that it was just the update-manager that must do all the job.

I changed the package for this.


** Package changed: ubuntu-release-upgrader (Ubuntu) = update-manager (Ubuntu)

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Title:
  error when upgrading from 10.04 to 10.10

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[Bug 1068297] Re: error when upgrading from 10.04 to 10.10

2013-03-21 Thread melchiaros
Mhh, yes

we need some logs here.

Can you provide?

You may want to run

apport-collect 1068297

from termianl(if there are any missed libraries for the process, please
install them).

There should also be a folder

/var/log/dist-upgrade

could you compress that folder and attach it here?

In fact that folder might be more important than the apoort procedure.
You might be forced to call

gksu nautilus

because the folder is owned by root(may be also the same for firefox to
upload).

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Title:
  error when upgrading from 10.04 to 10.10

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[Bug 1068297] Re: error when upgrading from 10.04 to 10.10

2013-03-21 Thread melchiaros
One more step it is there I have to request.

Please give a step by step description like pushing this button,
choosing that, waiting for, and so on). Give a good algorithmic
description, that is complete and can guide a beginner.

(step1,
 step2,
.
.
.
finished)


After that set the status of this report back to new.


Thanks

** Changed in: update-manager (Ubuntu)
   Status: New = Incomplete

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Title:
  error when upgrading from 10.04 to 10.10

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[Bug 1069133] Re: Get upgrade error 12.04 - 12.10 Could not determine upgrade

2013-03-21 Thread melchiaros
Hi npp,

we have today a hugday and we go to all ubuntu-release-upgrader
bugreports we have on launchpad.


Can you give us a answer if the workarround to switch off the ppa for xorg 
files is working(see the comments above)?

We need that info to decide what further on this problem.

** Summary changed:

- Get upgrade error 12.04 - 12.10 Could not determine upgrade
+ Get upgrade error 12.04 - 12.10 Could not determine upgrade - xorg from ppa

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https://bugs.launchpad.net/bugs/1069133

Title:
  Get upgrade error 12.04 - 12.10 Could not determine upgrade - xorg
  from ppa

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