Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

2024-05-13 Thread Thorn, Dr. Andrea 
Renato and Stuart McNicholls wrote exactly the right thing: deleting this file 
resolved the issue. Thank you very much!

-Original Message-
From: CCP4 bulletin board  On Behalf Of Renato Weiße
Sent: 08 May 2024 16:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Hi Andrea,

concerning Log #1: there is a log file 
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is 
probably empty. If it is, then deleting it should resolve the error. I have 
seen this problem from time to time on students laptops, but could not figure 
out, for what reason it occurs.

Cheers,
Renato


Zitat von "Thorn, Dr. Andrea" <d000cdf57279-dmarc-requ...@jiscmail.ac.uk>:

> Dear all,
> My ccp4i2 installation stopped working - it does not start up  
> properly anymore (see Log #1 below for the output).
> I started ccp4i which brought up the update manager and ran  
> outstanding updates. This did not fix the issue. I also sourced the  
> source file manually, just to make sure.
> Then I ran ./find-missing-libs.sh and fixed some issues, but got  
> stuck (see Log #2 below).
> Deleting the ccp4 folder and re-install also did not help.
> The system is Ubuntu in a virtual box.
> I would be grateful for any advice.
> Best wishes,
>
> Andrea.
>
> __
>
> LOG #1:
>
> Running CCP4i2 browser from:  
> /opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
> Python 3.7.12 (default, Jan  6 2022, 21:30:12)
> [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
> Qt version 5.15.2
>
> Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use  
> QT_QPA_PLATFORM=wayland to run on Wayland anyway.
> Sandboxing disabled by user.
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.browser.py'
> [0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> ccp4i2 version 1.1.0
> ccp4i2 source revision 6539
> CPrintHandler saving print output to directory:  
> /home/athorn/.CCP4I2/logs/started_1715177113
> None
> None
> Starting Project Manager
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> Starting Project Manager - DONE
> Starting Job Controller
> Starting Job Controller - DONE
> 
> isDarkMode? False
> 
> Starting   0.00048089027404785156
> StyleSheet screen size: 1920 1089
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> CCP4i2 starting HTTP server on 127.0.0.1 port 43434
>
> Retrieving status  
> file:/

Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

2024-05-08 Thread Renato Weiße 

Hi Andrea,

concerning Log #1: there is a log file  
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which  
is probably empty. If it is, then deleting it should resolve the  
error. I have seen this problem from time to time on students laptops,  
but could not figure out, for what reason it occurs.


Cheers,
Renato


Zitat von "Thorn, Dr. Andrea" :


Dear all,
My ccp4i2 installation stopped working - it does not start up  
properly anymore (see Log #1 below for the output).
I started ccp4i which brought up the update manager and ran  
outstanding updates. This did not fix the issue. I also sourced the  
source file manually, just to make sure.
Then I ran ./find-missing-libs.sh and fixed some issues, but got  
stuck (see Log #2 below).

Deleting the ccp4 folder and re-install also did not help.
The system is Ubuntu in a virtual box.
I would be grateful for any advice.
Best wishes,

Andrea.

__

LOG #1:

Running CCP4i2 browser from:  
/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2

Python 3.7.12 (default, Jan  6 2022, 21:30:12)
[GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
Qt version 5.15.2

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use  
QT_QPA_PLATFORM=wayland to run on Wayland anyway.

Sandboxing disabled by user.
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.browser.py'
[0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
[0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale

ccp4i2 version 1.1.0
ccp4i2 source revision 6539
CPrintHandler saving print output to directory:  
/home/athorn/.CCP4I2/logs/started_1715177113

None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
Starting Job Controller
Starting Job Controller - DONE

isDarkMode? False

Starting   0.00048089027404785156
StyleSheet screen size: 1920 1089
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
CCP4i2 starting HTTP server on 127.0.0.1 port 43434

Retrieving status  
file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml

Traceback (most recent call last):
  File  
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",  
line 266, in openFileToEtree

tree = parse_from_unicode(s,useLXML=useLXML)
  File  
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",  
line 255, in parse_from_unicode

return etree.fromstring(s, parser=utf8_parser)
  File "src/lxml/etree.pyx", line 3211, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
  File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
  File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc
  File "src/lxml/parser.pxi", line 601, in

[ccp4bb] ccp4i2 stopped working (no startup) - advice?

2024-05-08 Thread Thorn, Dr. Andrea 
Dear all,
My ccp4i2 installation stopped working - it does not start up properly anymore 
(see Log #1 below for the output).
I started ccp4i which brought up the update manager and ran outstanding 
updates. This did not fix the issue. I also sourced the source file manually, 
just to make sure.
Then I ran ./find-missing-libs.sh and fixed some issues, but got stuck (see Log 
#2 below).
Deleting the ccp4 folder and re-install also did not help.
The system is Ubuntu in a virtual box.
I would be grateful for any advice.
Best wishes,

Andrea.

__

LOG #1:

Running CCP4i2 browser from: 
/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
Python 3.7.12 (default, Jan  6 2022, 21:30:12)
[GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
Qt version 5.15.2

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use 
QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Sandboxing disabled by user.
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path '/home/athorn/.browser.py'
[0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
[0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
CPrintHandler saving print output to directory: 
/home/athorn/.CCP4I2/logs/started_1715177113
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
Starting Job Controller
Starting Job Controller - DONE

isDarkMode? False

Starting   0.00048089027404785156
StyleSheet screen size: 1920 1089
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
CCP4i2 starting HTTP server on 127.0.0.1 port 43434

Retrieving status 
file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
Traceback (most recent call last):
  File 
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line 
266, in openFileToEtree
tree = parse_from_unicode(s,useLXML=useLXML)
  File 
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line 
255, in parse_from_unicode
return etree.fromstring(s, parser=utf8_parser)
  File "src/lxml/etree.pyx", line 3211, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
  File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
  File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc
  File "src/lxml/parser.pxi", line 601, in 
lxml.etree._ParserContext._handleParseResultDoc
  File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
  File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
  File "", line 1
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File 
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py", line 
1263, in getEtreeRoot