| Linux version bugs [message #1461] |
Fri, 07 January 2022 07:42  |
zhentg
Messages: 25
Registered: March 2020
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Junior Member |
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Hi Thomas,
I used to run Datawarrior on my Linux box smoothly.
I updated the files by unzip the downloaded dw550x.zip(2022/1/6 nightly build).
Then I got the following error and DataWarrior exit. Could you help to check?
Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: com.actelion.research.datawarrior.DEMainPane.addDividerChang eLister(Lcom/actelion/research/gui/dock/DividerChangeListene r;)V
at com.actelion.research.datawarrior.DEParentPane.<init>(DEParentPane.java:60)
at com.actelion.research.datawarrior.DEFrame.<init>(DEFrame.java:65)
at com.actelion.research.datawarrior.DataWarrior.createNewFrame (DataWarrior.java:692)
at com.actelion.research.datawarrior.DataWarrior.<init>(DataWarrior.java:208)
at com.actelion.research.datawarrior.DataWarriorLinux.<init>(DataWarriorLinux.java:29)
at com.actelion.research.datawarrior.DataWarriorLinux.lambda$ma in$3(DataWarriorLinux.java:161)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java :311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doInte rsectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis patchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat chThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis patchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread. java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread. java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82 )
Datawarrior is a good tool
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| Re: Linux version bugs [message #1462 is a reply to message #1461] |
Tue, 11 January 2022 06:44  |
nbehrnd
Messages: 227
Registered: June 2019
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Senior Member |
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Dear zhentg,
departing from default native Linux installation running in Linux Debian 12/bookworm (branch testing), which I previously was updated (December 8th, 2021), I unzipped the currently available dw550x.zip (md5sum 780819003b519e34586c0d32678b2f27) you mention. After copy-paste of the three files extracted (cp -arvx * /opt/datawarrior/), I was able to start DataWarrior as usual. A few functions tested (e.g., compute smiles for a structure, search in Google Patents) work as anticipated.
Norwid
[Updated on: Tue, 11 January 2022 06:45] Report message to a moderator |
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| Re: Linux version bugs [message #1472 is a reply to message #1468] |
Fri, 14 January 2022 10:37 |
nbehrnd
Messages: 227
Registered: June 2019
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Senior Member |
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Dear zhentg,
attempting the export of a .dwar file as a .sdf with DataWarrior, I received an error as shown in the attachment below for the Linux version of DW. It may be replicated by
+ running the native Linux installer in Debian 12 (datawarrior550.tar_gz, md5sum 1feb7bff2ad7129ac677973186436ee8), followed by
+ running the nightly update, apparently packaged on December 8th, 2021 (md5sum d4b262e803117dbbb3bc4dfb5c4d8bf1), followed by
+ running the nightly update, apparently packaged on January 6th, 2022 (md5sum 780819003b519e34586c0d32678b2f27).
This pattern is an update on top of an other/others already existing.
The export I aimed for was however possible again by starting from scratch. Let me suggest the following:
+ remove DW. The bash script unistall.sh is is provided in /opt/datawarrior as well in the .tar_gz of the installation archive. This is followed by
+ pristine installation of DW 5.5.0/April 2021, followed by
+ direct installation of the nightly update packaged by January 6th, 20222.
Without analysis of the updates provided by December 2021 and January 2022, it would be speculation where/why the two differ. As long as there is no major release update of DW (as pointed out in the right hand side column «recent changes»[1]), it appears safest to i) download once the installer archive, and ii) archives of the nightly updates separately in a local backup prior to an update of the local installation. To retain the archives doesn't cost much space either (as archives, the updates are about a seventh of the volume of the installer).
Norwid
[1] https://openmolecules.org/
[Updated on: Fri, 14 January 2022 10:37] Report message to a moderator |
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| Re: Linux version bugs [message #1477 is a reply to message #1475] |
Mon, 24 January 2022 09:48 |
nbehrnd
Messages: 227
Registered: June 2019
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Senior Member |
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Dear Thomas,
the problem exporting the .sdf was noticed (yet not reported) because it still was possible to assign SMILES to the structures then exported in a text file. After accessing the column in question (via awk), OpenBabel provided external regeneration of the .sdf.
Norwid
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