Re: [ccp4bb] ccp4 installation problem
Hi Robert,
On Fri, Sep 16, 2022 at 4:11 PM Kay Diederichs
wrote:
> Your real problem seems to be the Qt installation; I think that the error
> message
> qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though
> it was found.
> This application failed to start because no Qt platform plugin could be
> initialized. Reinstalling the application may fix this problem.
> prevents the graphics of the CCP4 programs from working properly.
This is my thinking too - the OS seems to be missing libxcb QT plugins.
You can get better debug info from QT by setting the QT_DEBUG_PLUGINS
variable ("export QT_DEBUG_PLUGINS=1" for bash or zsh, "setenv
QT_DEBUG_PLUGINS 1" for tcsh). Then when you launch the application
you should get a much more informative message. Perhaps too
informative.
Usually the error in this case is a missing xcb library or two,
something like libxcb-icccm.so.4 No such file or directory. You
should be able to add these with your package manager.
Best,
Jason
--
Jason Key, PhD
SBGrid Consortium, Harvard Medical School
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Re: [ccp4bb] ccp4 installation problem
Hi Kay Thanks again and for more insight and feedback on the Qt installation. Reply in blue text below. Take care, Rob -Original Message- From: Kay Diederichs Sent: Friday, September 16, 2022 4:11 PM To: CCP4BB@JISCMAIL.AC.UK; Robert Gampe Subject: Re: ccp4 installation problem ALERT! Outside Org Hi Robert, you are welcome. It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You should revert the ownerships in /software/ccp4-8.0 from root.root with sudo chown -R rgampe.rgampe /software/ccp4-8.0 so that in the future you don't need sudo for updates. The above fix is along the lines Andrey provided on Aug 30. As for your installation. ccp4um switches to admin mode if it finds any single file inside ccp4 that does not belong to you. In the admin mode, it check if all files belong to the same user as the top ccp4-8.0 directory and changes ownership of all files that belong to different user. If ccp4 originally belonged to your account, not to root account, you can repair installation from command line using sudo chown -R : ccp4-8.0 arpwarp_8.0. Your real problem seems to be the Qt installation; I think that the error message qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. prevents the graphics of the CCP4 programs from working properly. I have no idea, though, if your Qt is too new or too old or somehow corrupted. I've never heard of POP_OS or the like so maybe it's just not compatible with CCP4. I will definitely have to learn more on what the Qt is and how to fix or update GOOGLE: Qt Creator is a cross-platform integrated development environment (IDE) built for the maximum developer experience.. The POP_OS! system 76 is built upon Ubuntu and comes with a ready to use desktop. https://pop.system76.com/ Pop!_OS is an operating system for STEM and creative professionals who use their computer as a tool to discover and create. HTH, Kay This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ccp4 installation problem
Hi Robert, you are welcome. It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You should revert the ownerships in /software/ccp4-8.0 from root.root with sudo chown -R rgampe.rgampe /software/ccp4-8.0 so that in the future you don't need sudo for updates. Your real problem seems to be the Qt installation; I think that the error message qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. prevents the graphics of the CCP4 programs from working properly. I have no idea, though, if your Qt is too new or too old or somehow corrupted. I've never heard of POP_OS or the like so maybe it's just not compatible with CCP4. HTH, Kay To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ccp4 installation problem
Hi Robert, hmm, more ideas: a) check if CCP4 directory is writable, and who the owner is: mount | grep software sudo touch /software/ccp4-8.0/deleteme ls -ld /software/ccp4-8.0 ls -l /software/ccp4-8.0/deleteme sudo rm /software/ccp4-8.0/deleteme b) try sudo su ccp4um c) try sudo -i ccp4um d) also try "ccp4um -auto" - I think this does not require the graphics e) try which ccp4um HTH, Kay To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ccp4 installation problem
Hi Robert, two points - a) before you tried to update, did you source /where/ever/ccp4/bin/ccp4.setup-sh ? The above applies to bash; for (t)csh you need to source /where/ever/ccp4/bin/ccp4.setup-csh That sets the PATH environment variable such that you don't always have to specify the absolute path when you want to run a CCP4 program, AND it also makes sure that CCP4 programs such as ccp4um find other CCP4 binaries that they need. Without that "sourcing" I can imagine that an update is not possible. b) since ccp4i seems to start: did you tick the box(es) that specify the available update(s)? You have to do this before clicking "Proceed". HTH, Kay To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ccp4 installation problem
Hi Robert, Concerning PROBLEM 1: have you tried sudo ccp4um or sudo ccp4i ? HTH, Kay P.S. didn't find Andrey Lebedev's reply on August 30 that you refer to On Fri, 16 Sep 2022 14:11:34 +, Robert Gampe wrote: >Hello Marcin Pedro and the CCP4 community, > > > >PROBLEM 1: I have the same still unresolved problem when trying to install the >recent CCP-8.0 updates on a POP_OS!/Ubuntu box. > > > >The updater will not accept my SUDO password and returns to the linux prompt. > > > >Using sudo -l reports I am a sudo user for ALL commands and my sudo password >has worked for other sudo required actions. > > > >I also tried using sudo and root to run CCP4-8.0, but that too failed. > > > >Without the updates installed, the acedrg program does NOT start up for me, >but other programs, eg REFMAC, seem to start up but I have not run since I >need acedrg cif files. > > > >See Andrey Lebedev reply on August 30 in reply to my original post and CCP4's >use of ccp4um and pkexec. > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ccp4 installation problem
Hi Marcin, If you are not logged on as root I think you need to run the installer with sudo Hope this helps, Pedro Matias Em 06/09/2022 13:33, Marcin Jaciuk escreveu: Dear All, After upgrading to newest Ubuntu 22.04 I am trying to install ccp4 via Package Manager with /opt directory as installation destination. When installer asks me for super user password (which I am) it rejects it, see below: AUTHENTICATING FOR org.freedesktop.policykit.exec === Authentication is needed to run `/tmp/ccp4sm/install_all.sh' as the super user Authenticating as: Marcin Jaciuk (mjaciuk) Password: AUTHENTICATION FAILED === Did anyone encounter this problem before and/or know the solution to it? Regards, Marcin Jaciuk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] CCP4 installation problem
Appu, You will have to edit your .tcshrc (startup) file to point to the correct setup script with a line like this: source /usr/local/xtal/ccp4-6.5/ccp4.setup-csh If you are using a different shell, e.g. bash, you will have to edit the appropriate startup file, e.g. .bashrc. You will likely find the offending line pointing to the old installation in your run command (startup) file and can edit it. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 6/16/2015 11:13 AM, Appu kumar wrote: Hello, I have downloaded 'ccp4-6.5 and deleted the older version of ccp4 installed. After installing the new version, it is giving the following problem on executing the ccp4i command. Error in startup script: couldn't read file /usr/local/xtal/ccp4-6.2.0/share/dbccp4i/ClientAPI/dbClientAPI.tcl: no such file or directory while executing source [FileJoin [GetEnvPath DBCCP4I_TOP] ClientAPI dbClientAPI.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/src/projectdirs.tcl line 23) invoked from within source [SearchPath TOP src projectdirs.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/src/system.tcl line 3379) invoked from within source [file join $env(CCP4I_TOP) src system.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/bin/ccp4i.tcl line 79) invoked from within source [file join $env(CCP4I_TOP) bin ccp4i.tcl] (file /home/appu/software/destination/ccp4-6.5/bin/ccp4i line 12) I have deleted ccp4-6.2.0 version. Somehow ccp4-6.5 is looking for the older version upon execution. I will be thankful your your advice. Appu
Re: [ccp4bb] CCP4 installation problem
Hello, I have already edited my .cshrc file where i removed the line which was pointing to older version and sourced the newer version ccp4-6.5/ccp4.setup-csh but problem still exist. Thank you Appu On 16 June 2015 at 09:25, Roger Rowlett rrowl...@colgate.edu wrote: Appu, You will have to edit your .tcshrc (startup) file to point to the correct setup script with a line like this: source /usr/local/xtal/ccp4-6.5/ccp4.setup-csh If you are using a different shell, e.g. bash, you will have to edit the appropriate startup file, e.g. .bashrc. You will likely find the offending line pointing to the old installation in your run command (startup) file and can edit it. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 6/16/2015 11:13 AM, Appu kumar wrote: Hello, I have downloaded 'ccp4-6.5 and deleted the older version of ccp4 installed. After installing the new version, it is giving the following problem on executing the ccp4i command. Error in startup script: couldn't read file /usr/local/xtal/ccp4-6.2.0/share/dbccp4i/ClientAPI/dbClientAPI.tcl: no such file or directory while executing source [FileJoin [GetEnvPath DBCCP4I_TOP] ClientAPI dbClientAPI.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/src/projectdirs.tcl line 23) invoked from within source [SearchPath TOP src projectdirs.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/src/system.tcl line 3379) invoked from within source [file join $env(CCP4I_TOP) src system.tcl] (file /home/appu/software/destination/ccp4-6.5/share/ccp4i/bin/ccp4i.tcl line 79) invoked from within source [file join $env(CCP4I_TOP) bin ccp4i.tcl] (file /home/appu/software/destination/ccp4-6.5/bin/ccp4i line 12) I have deleted ccp4-6.2.0 version. Somehow ccp4-6.5 is looking for the older version upon execution. I will be thankful your your advice. Appu
Re: [ccp4bb] CCP4 installation problem in Mac OS 10.10
Hi, See this post which should sort your problem: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1410L=ccp4bbP=R1184621=ccp4bb9=AJ=ond=No+Match%3BMatch%3BMatchesz=4 Jonathan Quoting anil kumar anilkumar...@yahoo.co.in: Hello, I recently updated my OS which had a fine running CCP4 package. After the update, the new installation look fine. But it do not open the interface at all.I am attaching the error messages. May be someone might have faced similar issue and can help. With best regards,Anil
