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#1 2019-09-15 09:25:37

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
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My issues with Buster

I am recovering from the self inflicted problems reported here:
https://forums.bunsenlabs.org/viewtopic.php?id=6061
I opted to migrate to Buster aka Debian 10 a la:
https://forums.bunsenlabs.org/viewtopic.php?id=6077

I start this as I face some unexpected issues with Buster. I have elected to start a new subject rather than appending further posts to the old ones mentioned above as I think it will be easier to find for later adopters if we manage to resolve these issues.

First off, Buster is great for the most part. Some programs even exceed my expectations.

Now to my issues so far (early days!):

1) Missing programs:
   - Veusz, a scientific plotting program I use from time to time is not in Buster's repos.
   - Gnome-commander is also missing. I am trying out alternatives but find issues: (Double-commander is bloated and buggy, Tux-commander is nice but still a little buggy, mc is mostly OK...)
   - A number of emacs add-ons are listed as incompatible by the emacs package tool.

2) Problems running these:
   - Wikidpad is a personal wiki tool written in Python. I have used it for many years on different systems both at home and at work. On Buster it does not start. There seems to be an issue when Python calls in GTK but I find no difference in installed libraries between a working system and this one. This is a bummer as Wikidpad is where I have my notes for setting up some of the less intuitive programs I use...
   - Docear is a brilliant tool for academics plowing through scientific literature. I started using it in earnest at work (Ubuntu 16.04) late last year after having tested a little at home (Helium on Debian 9). Now (Helium on Debian 10) it does not start. Java something?? Again, comparing with a system on which Docear works I fail to find differences. This is less of a bummer as I only run Docear here for testing/practicing.
   - Jupyter notebook does not fire up a session in Firefox automatically. I found out late yesterday so I have not had time to investigate yet.

/Martin

Last edited by Martin (2019-09-15 10:22:23)


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#2 2019-09-15 10:02:19

damo
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Registered: 2015-08-20
Posts: 5,197

Re: My issues with Buster

Martin wrote:

...
1) Missing programs:
   - Veusz, a scientific plotting program I use from time to time is not in Buster's repos.
   - Gnome-commander is also missing. I am trying out alternatives but find issues: (Double-commander is bloated and buggy, Tux-commander is nice but still a little buggy, mc is mostly OK...)

You can get a lot of information from Debian - Search package directories. Both packages are available in sid, so you could try backporting them yourself: Backport a Debian sid package to BunsenLabs (quick method)

2) Problems running these:
   - Wikidpad is a personal wiki tool written in Python. I have used it for many years on different systems both at home and at work. On Buster it does not start. There seems to be an issue when Python calls in GTK but I find no difference in installed libraries between a working system and this one. This is a bummer as Wikidpad is where I have my notes for setting up some of the less intuitive programs I use...
...

Check your python environment, and the shebang at the start of your script. You may need to run it in a python virtual environment?


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#3 2019-09-16 19:38:50

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
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Re: My issues with Buster

There seems to be a general problem with things combining Python and GTK and/or WX. Playonlinux is also misbehaving but in a somewhat different fashion. Trying to install wxPython in a user-specific way using pip3 I fail completely and only get a very long error message. At first it only looked like pathlib2 was missing but installing that only solved that problem. Installing pathlib2 system-wide helped the system-wide installation of wxPython some but not Playonlinux or Wikidpad.

pathlib2 is not needed in the older, working system.

Scratching my head...

/Martin

Last edited by Martin (2019-09-16 20:28:34)


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#4 2019-09-16 20:27:18

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
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Re: My issues with Buster

Veusz was easy to get working. I simply downloaded the latest Linux binary from here. I then created a simple shell script in $HOME/bin pointing to where the veusz binary ended up and made the script executable and, viola, I can start veusz using dmenu.

/Martin


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#5 2019-09-18 02:58:24

DeepDayze
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From: In Linux Land
Registered: 2017-05-28
Posts: 759

Re: My issues with Buster

Martin wrote:

Veusz was easy to get working. I simply downloaded the latest Linux binary from here. I then created a simple shell script in $HOME/bin pointing to where the veusz binary ended up and made the script executable and, viola, I can start veusz using dmenu.

/Martin

You could do that for many of the programs you mentioned so maybe wrapping them in a script may help. Have you tried executing any of those programs in a terminal to see the output or error message?


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#6 2019-09-20 21:14:37

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

DeepDayze wrote:
Martin wrote:

Veusz was easy to get working. I simply downloaded the latest Linux binary from here. I then created a simple shell script in $HOME/bin pointing to where the veusz binary ended up and made the script executable and, viola, I can start veusz using dmenu.

/Martin

You could do that for many of the programs you mentioned so maybe wrapping them in a script may help. Have you tried executing any of those programs in a terminal to see the output or error message?

I have spent some time trying to figure out why WikidPad will not work after the upgrade to Buster by looking at the error messages and discussing it on alt.os.debian -- to no avail so far. There seems be some issue with gtk or rather wxPython but all looks the same as on my Debian 9 machine where WikidPad works just fine.

/Martin

Last edited by Martin (2019-09-20 21:21:14)


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#7 2019-09-20 21:20:44

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
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Re: My issues with Buster

Martin wrote:

   - Jupyter notebook does not fire up a session in Firefox automatically. I found out late yesterday so I have not had time to investigate yet.

/Martin

This one turned out to be caused by me doing the mistake of specifying a non-standard directory for doing

pip3 install --user

I soon realized this was just silly and re-did it with the standard location $HOME/.local and now my Jupyter notebooks show up in Firefox automagically.

/Martin


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prove their worth by hitting back."
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#8 2019-09-21 01:03:50

DeepDayze
Member
From: In Linux Land
Registered: 2017-05-28
Posts: 759

Re: My issues with Buster

Martin wrote:
DeepDayze wrote:
Martin wrote:

Veusz was easy to get working. I simply downloaded the latest Linux binary from here. I then created a simple shell script in $HOME/bin pointing to where the veusz binary ended up and made the script executable and, viola, I can start veusz using dmenu.

/Martin

You could do that for many of the programs you mentioned so maybe wrapping them in a script may help. Have you tried executing any of those programs in a terminal to see the output or error message?

I have spent some time trying to figure out why WikidPad will not work after the upgrade to Buster by looking at the error messages and discussing it on alt.os.debian -- to no avail so far. There seems be some issue with gtk or rather wxPython but all looks the same as on my Debian 9 machine where WikidPad works just fine.

/Martin

Why not reach out to the developer of WikidPad and maybe the issue can be spotted and fixed. I suspect there may have been a change within some libraries that could cause bugs.

If there's a new update why not try it?

EDIT: In reviewing the application site, it seems this is a very old application that's not really maintained. As python has evolved programs written for older python versions may not work properly on newer python versions.

Last edited by DeepDayze (2019-09-21 01:06:54)


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#9 2019-09-21 10:02:26

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

DeepDayze wrote:

Why not reach out to the developer of WikidPad and maybe the issue can be spotted and fixed. I suspect there may have been a change within some libraries that could cause bugs.

If there's a new update why not try it?

EDIT: In reviewing the application site, it seems this is a very old application that's not really maintained. As python has evolved programs written for older python versions may not work properly on newer python versions.

WikidPad being old -- yes that's a thought. I am using the latest, stable version. There is a later release candidate for version 2.3. Maybe I should give that a spin.

And, since I have the source code, I could try to fix it myself despite lacking skill and time :-)

But if this is about the age of WikidPad, why do PlayOnLinux also act up?

/Martin


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prove their worth by hitting back."
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#10 2019-09-21 11:19:23

twoion
ほやほや
Registered: 2015-08-10
Posts: 2,541

Re: My issues with Buster

Docear launches on latest Arch Linux, so it should launch on Debian...How do you launch it? I just downloaded and launched using the docear.sh script in the console, and it prints a lot of debug information, so perhaps if you try launching it and post the log, if any, somebody could comment on it.


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#11 2019-09-21 12:37:30

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

Martin wrote:

WikidPad being old -- yes that's a thought. I am using the latest, stable version. There is a later release candidate for version 2.3. Maybe I should give that a spin.

WikidPad 2.3 rc02 fires up OK. Not much testing yet.

/Martin


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prove their worth by hitting back."
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#12 2019-09-21 18:57:46

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

twoion wrote:

Docear launches on latest Arch Linux, so it should launch on Debian...How do you launch it? I just downloaded and launched using the docear.sh script in the console, and it prints a lot of debug information, so perhaps if you try launching it and post the log, if any, somebody could comment on it.

When I try to launch Docear there is a ton of things printed. Here are just the error messages:

STDERR: java.lang.NoClassDefFoundError: org/omg/CORBA/portable/UnknownException
STDERR: 	at org.docear.plugin.services.features.user.DocearUserController.<init>(DocearUserController.java:42)
STDERR: 	at org.docear.plugin.services.ServiceController.initialize(ServiceController.java:86)
STDERR: 	at org.docear.plugin.services.Activator.startService(Activator.java:29)
STDERR: 	at org.docear.plugin.core.Activator.startPluginServices(Activator.java:67)
STDERR: 	at org.docear.plugin.core.Activator.startPlugin(Activator.java:35)
STDERR: 	at org.freeplane.plugin.workspace.Activator.startPluginServices(Activator.java:83)
STDERR: 	at org.freeplane.plugin.workspace.Activator$2.installExtension(Activator.java:45)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.startFramework(ActivatorImpl.java:208)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.start(ActivatorImpl.java:79)
STDERR: 	at org.freeplane.main.osgi.Activator.start(Activator.java:36)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start0(BundleImpl.java:374)
STDERR: 	at org.knopflerfish.framework.PermissionOps.callStart0(PermissionOps.java:215)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start(BundleImpl.java:321)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.increaseStartLevel(StartLevelImpl.java:285)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl$1.run(StartLevelImpl.java:217)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.run(StartLevelImpl.java:178)
STDERR: 	at java.base/java.lang.Thread.run(Thread.java:834)
STDERR: Caused by: java.lang.ClassNotFoundException: org.omg.CORBA.portable.UnknownException
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.findClass(BundleClassLoader.java:339)
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.loadClass(BundleClassLoader.java:438)
STDERR: 	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
STDERR: 	... 17 more
STDOUT: ## DEBUG: errors - FrameworkErrorEvent bundle #1
STDOUT: ## DEBUG: errors - FrameworkErrorEvent throwable: 
STDERR: org.osgi.framework.BundleException: BundleActivator start failed
STDERR: 	at org.knopflerfish.framework.BundleImpl.start0(BundleImpl.java:419)
STDERR: 	at org.knopflerfish.framework.PermissionOps.callStart0(PermissionOps.java:215)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start(BundleImpl.java:321)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.increaseStartLevel(StartLevelImpl.java:285)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl$1.run(StartLevelImpl.java:217)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.run(StartLevelImpl.java:178)
STDERR: 	at java.base/java.lang.Thread.run(Thread.java:834)
STDERR: Caused by: java.lang.NoClassDefFoundError: org/omg/CORBA/portable/UnknownException
STDERR: 	at org.docear.plugin.services.features.user.DocearUserController.<init>(DocearUserController.java:42)
STDERR: 	at org.docear.plugin.services.ServiceController.initialize(ServiceController.java:86)
STDERR: 	at org.docear.plugin.services.Activator.startService(Activator.java:29)
STDERR: 	at org.docear.plugin.core.Activator.startPluginServices(Activator.java:67)
STDERR: 	at org.docear.plugin.core.Activator.startPlugin(Activator.java:35)
STDERR: 	at org.freeplane.plugin.workspace.Activator.startPluginServices(Activator.java:83)
STDERR: 	at org.freeplane.plugin.workspace.Activator$2.installExtension(Activator.java:45)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.startFramework(ActivatorImpl.java:208)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.start(ActivatorImpl.java:79)
STDERR: 	at org.freeplane.main.osgi.Activator.start(Activator.java:36)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start0(BundleImpl.java:374)
STDERR: 	... 6 more
STDERR: Caused by: java.lang.ClassNotFoundException: org.omg.CORBA.portable.UnknownException
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.findClass(BundleClassLoader.java:339)
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.loadClass(BundleClassLoader.java:438)
STDERR: 	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
STDERR: 	... 17 more
STDOUT: Nested bundle exception:
STDERR: java.lang.NoClassDefFoundError: org/omg/CORBA/portable/UnknownException
STDERR: 	at org.docear.plugin.services.features.user.DocearUserController.<init>(DocearUserController.java:42)
STDERR: 	at org.docear.plugin.services.ServiceController.initialize(ServiceController.java:86)
STDERR: 	at org.docear.plugin.services.Activator.startService(Activator.java:29)
STDERR: 	at org.docear.plugin.core.Activator.startPluginServices(Activator.java:67)
STDERR: 	at org.docear.plugin.core.Activator.startPlugin(Activator.java:35)
STDERR: 	at org.freeplane.plugin.workspace.Activator.startPluginServices(Activator.java:83)
STDERR: 	at org.freeplane.plugin.workspace.Activator$2.installExtension(Activator.java:45)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.startFramework(ActivatorImpl.java:208)
STDERR: 	at org.freeplane.main.osgi.ActivatorImpl.start(ActivatorImpl.java:79)
STDERR: 	at org.freeplane.main.osgi.Activator.start(Activator.java:36)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start0(BundleImpl.java:374)
STDERR: 	at org.knopflerfish.framework.PermissionOps.callStart0(PermissionOps.java:215)
STDERR: 	at org.knopflerfish.framework.BundleImpl.start(BundleImpl.java:321)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.increaseStartLevel(StartLevelImpl.java:285)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl$1.run(StartLevelImpl.java:217)
STDERR: 	at org.knopflerfish.framework.StartLevelImpl.run(StartLevelImpl.java:178)
STDERR: 	at java.base/java.lang.Thread.run(Thread.java:834)
STDERR: Caused by: java.lang.ClassNotFoundException: org.omg.CORBA.portable.UnknownException
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.findClass(BundleClassLoader.java:339)
STDERR: 	at org.knopflerfish.framework.BundleClassLoader.loadClass(BundleClassLoader.java:438)
STDERR: 	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
STDERR: 	... 17 more
STDOUT: Framework launched

/Martin


"Problems worthy of attack
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#13 2019-09-21 19:02:04

Martin
Member
From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

I just found this which is hinting at the possibility that this is another example of Buster being too modern for the program I want to use.

/Martin


"Problems worthy of attack
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#14 2019-09-25 18:38:01

Martin
Member
From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

So Docear needs Oracle-JDK-8 to work. This is OK with my Ubuntu 16.04 at work and my old Debian 9 based Helium but not the current Debian 10 based Helium. Browsing around I find various instructions for how to install Oracle-JDK-8 on Debian 10 but is it a good idea? (Apart from  making Docear work, that is.)

In the Debian 10 repo I find nvidia-openjdk-8-jre. Would that work?

/Martin


"Problems worthy of attack
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#15 2019-10-04 06:12:08

Martin
Member
From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

Gnome-commander depends on old libraries that have been ditched in Debian 10. For now I will have to make do with MC.

/Martin


"Problems worthy of attack
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#16 2019-10-04 09:16:47

rbh
Member
From: Sweden/Vasterbotten/Rusfors
Registered: 2016-08-11
Posts: 67

Re: My issues with Buster

Martin wrote:

For now I will have to make do with MC.

Other possible graphical twin panel file manager in buster repo is doublecmd tuxcmd.
If you have other kde-libraries krusader is a very good choise

Last edited by rbh (2019-10-04 09:17:07)


// Regards rbh

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#17 2019-10-04 17:55:48

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 366
Website

Re: My issues with Buster

rbh wrote:
Martin wrote:

For now I will have to make do with MC.

Other possible graphical twin panel file manager in buster repo is doublecmd tuxcmd.
If you have other kde-libraries krusader is a very good choise

I have tried both doublecmd and tuxcmd. The latter was kind of nice but I found both too buggy.

Krusader wants to install a never ending list of dependencies. I don't have much K-stuff on my machine right now I guess.

/Martin


"Problems worthy of attack
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#18 2019-10-04 22:33:45

DeepDayze
Member
From: In Linux Land
Registered: 2017-05-28
Posts: 759

Re: My issues with Buster

Martin wrote:
DeepDayze wrote:

Why not reach out to the developer of WikidPad and maybe the issue can be spotted and fixed. I suspect there may have been a change within some libraries that could cause bugs.

If there's a new update why not try it?

EDIT: In reviewing the application site, it seems this is a very old application that's not really maintained. As python has evolved programs written for older python versions may not work properly on newer python versions.

WikidPad being old -- yes that's a thought. I am using the latest, stable version. There is a later release candidate for version 2.3. Maybe I should give that a spin.

And, since I have the source code, I could try to fix it myself despite lacking skill and time :-)

But if this is about the age of WikidPad, why do PlayOnLinux also act up?

/Martin

Maybe some python gurus could help you with any python coding stuff to get that app working :-)


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