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 <CCP4BB@JISCMAIL.AC.UK> 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" <0000d000cdf57279-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 <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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--
Dr. Renato H. Weiße
Biotechnologisch-Biomedizinisches Zentrum
Institut für Bioanalytische Chemie
Strukturanalytik von Biopolymeren
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Mail renato.wei...@bbz.uni-leipzig.de
Tel. +49 341 97 31316
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