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 <class 'core.CCP4DataManager.CDataManager'> 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 "<string>", 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
root = CCP4Utils.openFileToEtree(fileName,useLXML=useLXML)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",
line 268, in openFileToEtree
raise CException(CUtils, 104, fileName)
core.CCP4ErrorHandling.CException: None -ERROR-
CUtils:104 Failed parsing file
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
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/bin/browser.py", line
109, in <module>
startBrowser(sys.argv[1:], app=app, splash=splash)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/utils/startup.py",
line 306, in startBrowser
CCP4WebBrowser.restoreStatus()
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/qtgui/CCP4WebBrowser.py", line 215, in
restoreStatus
statusEtree = retrieveStatus()
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/qtgui/CCP4WebBrowser.py", line 347, in
retrieveStatus
f = CCP4File.CI2XmlDataFile(statusFileList[-1])
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 1236, in __init__
CXmlDataFile.__init__(self, value=value, qualifiers=qualifiers,
parent=parent, name=name, fullPath=fullPath, keywords=keywords, **kw)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 477, in __init__
self.setFullPath(fPath, checkDb=checkDb)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 567, in setFullPath
self.updateData()
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 1241, in updateData
self.loadFile()
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 1248, in loadFile
root = self.getEtreeRoot(fileName)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py",
line 1267, in getEtreeRoot
raise CException(self.__class__, 1001, fileName + ' : ' +
str(e), name=self.objectPath())
core.CCP4ErrorHandling.CException: -ERROR-
CI2XmlDataFile:1001 : Unknown error reading XML file
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml :
None -ERROR- CUtils:104 Failed parsing file
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
CDbThread shut down
Restoring stdout
No need to push back local db file.
Backed up list of projects to /home/athorn/.CCP4I2/projectList-backup.xml
______________________________________________________
LOG #2:
Searching for ELF-files in:
/opt/xtal/ccp4-8.0
found 6135 executable and library files
found 2345 ELF-files
Excluding:
/coot_py2/lib/libgfortran.so.3.0.0
/coot_py2/lib/libopenblas-r0.3.3.so
/lib-dynload/
/lib/python3.7/site-packages/ccp4mg/cpptable.so
/lib/python3.7/site-packages/ccp4mg/mgglframebufferobject.so
/lib/python3.7/site-packages/ccp4mg/mgradialgradient.so
/lib/python3.7/site-packages/ccp4mg/PdbView.so
/lib/python3.7/site-packages/PySide2/designer
/lib/python3.7/site-packages/PySide2/pyside2-lupdate
/lib/python3.7/site-packages/PySide2/uic
/shiboken2_generator/shiboken2
/webkit2gtk-4.0/
Running ldd on 2195 ELF-files
/opt/xtal/ccp4-8.0/bin/ipmosflm:
libncurses.so.5 => not found
libtinfo.so.5 => not found
/opt/xtal/ccp4-8.0/coot_py2/lib/libguilereadline-v-17.so.17.0.3:
libncurses.so.5 => not found
libtinfo.so.5 => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libawt_headless.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libawt.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libawt_xawt.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libfontmanager.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libjavajpeg.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libjava.so:
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libjawt.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libjimage.so:
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libjsound.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/liblcms.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libmlib_image.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libnet.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libnio.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libprefs.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libsplashscreen.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libverify.so:
libjvm.so => not found
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/libzip.so:
libjvm.so => not found
libjvm.so => not found
libjvm.so => not found
not found:
libjvm.so
libncurses.so.5
libtinfo.so.5
run patch_rpaths.sh to fix these:
/opt/xtal/ccp4-8.0/libexec/desktop.jre/lib/server/libjvm.so
Running apt-file -l on missing libaries, this may take a while
See:
https://www.ccp4.ac.uk/download/doc/known_issues_linux.html
./patch-rpaths.sh just gives "done" as output.
__
Dr. Andrea Thorn | group leader
andrea.th...@uni-hamburg.de<mailto:andrea.th...@uni-hamburg.de>
Institute for Nanostructure and Solid State Physics, Universität Hamburg
Luruper Chaussee 149 / Bldg. 610 (HARBOR) | 22761 Hamburg | Germany
Tel. +49 (0)40 42838 3651
www.thorn-lab.de<http://www.thorn-lab.de/> |
www.insidecorona.net<http://www.insidecorona.net/>
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