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Kernel 5.1 & imagej-package & scilab-package

jarkky

Mon Jun 10, 2019 4:35:04 am

Installation of imagej goes well:
jari@jari-PC:~$ sudo apt install imagej

but when I try use it fails as:
jari@jari-PC:~$ imagej
Open other images in this ImageJ panel as follows:
imagej -p 1 <image1> [<image2> ... <imageN>]

Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.



Also it looks like the OS15 does not follow the latest kernel versions like 5.1.6
-> This however was not found to be a problem though.


Also a program 'scilab' was installed with the 'apt' -command, but it seems to give a lot of warnings (even it eventually starts):
jari@jari-PC:~$ scilab
Picked up _JAVA_OPTIONS: -Djava.class.path=/usr/share/java/flexdock.jar:/usr/share/java/skinlf.jar:/usr/share/java/looks.jar:/usr/share/java/commons-logging.jar:/usr/share/java/jhall.jar:/usr/share/java/lucene-core-4.10.4.jar:/usr/share/java/lucene-analyzers-common-4.10.4.jar:/usr/share/java/lucene-queryparser-4.10.4.jar:/usr/share/maven-repo/org/freehep/freehep-util/debian/freehep-util-debian.jar:/usr/share/maven-repo/org/freehep/freehep-io/debian/freehep-io-debian.jar:/usr/share/maven-repo/org/freehep/freehep-graphicsio/debian/freehep-graphicsio-debian.jar:/usr/share/java/freehep-graphicsio-emf-2.1.jar:/usr/share/java/freehep-graphics2d-2.1.1.jar:/usr/share/java/jrosetta-API.jar:/usr/share/java/jrosetta-engine-1.0.4.jar:/usr/share/java/jgraphx.jar:/usr/share/java/jogl2.jar:/usr/share/java/gluegen2-rt.jar:/usr/share/java/jeuclid-core.jar:/usr/share/java/jlatexmath-fop-1.0.7.jar:/usr/share/java/fop.jar:/usr/share/java/saxon.jar:/usr/share/java/batik.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/commons-io.jar:/usr/share/java/xmlgraphics-commons.jar:/usr/share/java/avalon-framework.jar:/usr/share/java/jlatexmath-1.0.7.jar:/usr/share/java/ecj.jar:/usr/share/java/javax.activation.jar:/usr/share/java/jaxb-runtime.jar:/usr/share/scilab/modules/graphic_export/jar/org.scilab.modules.graphic_export.jar:/usr/share/scilab/modules/scirenderer/jar/scirenderer.jar:/usr/share/scilab/modules/commons/jar/org.scilab.modules.commons.jar:/usr/share/scilab/modules/history_browser/jar/org.scilab.modules.history_browser.jar:/usr/share/scilab/modules/preferences/jar/org.scilab.modules.preferences.jar:/usr/share/scilab/modules/renderer/jar/org.scilab.modules.renderer.jar:/usr/share/scilab/modules/localization/jar/org.scilab.modules.localization.jar:/usr/share/scilab/modules/graph/jar/org.scilab.modules.graph.jar:/usr/share/scilab/modules/ui_data/jar/org.scilab.modules.ui_data.jar:/usr/share/scilab/modules/types/jar/org.scilab.modules.types.jar:/usr/share/scilab/modules/history_manager/jar/org.scilab.modules.history_manager.jar:/usr/share/scilab/modules/helptools/jar/scilab_images.jar:/usr/share/scilab/modules/helptools/jar/scilab_ru_RU_help.jar:/usr/share/scilab/modules/helptools/jar/org.scilab.modules.helptools.jar:/usr/share/scilab/modules/helptools/jar/scilab_en_US_help.jar:/usr/share/scilab/modules/javasci/jar/org.scilab.modules.javasci.jar:/usr/share/scilab/modules/completion/jar/org.scilab.modules.completion.jar:/usr/share/scilab/modules/console/jar/org.scilab.modules.console.jar:/usr/share/scilab/modules/xcos/jar/org.scilab.modules.xcos.jar:/usr/share/scilab/modules/graphic_objects/jar/org.scilab.modules.graphic_objects.jar:/usr/share/scilab/modules/jvm/jar/org.scilab.modules.jvm.jar:/usr/share/scilab/modules/action_binding/jar/org.scilab.modules.action_binding.jar:/usr/share/scilab/modules/core/jar/org.scilab.modules.core.jar:/usr/share/scilab/modules/scinotes/jar/org.scilab.modules.scinotes.jar:/usr/share/scilab/modules/gui/jar/org.scilab.modules.gui.jar:/usr/share/scilab/modules/external_objects_java/jar/org.scilab.modules.external_objects_java.jar:
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.scilab.modules.jvm.LibraryPath (file:/usr/share/scilab/modules/jvm/jar/org.scilab.modules.jvm.jar) to field java.lang.ClassLoader.sys_paths
WARNING: Please consider reporting this to the maintainers of org.scilab.modules.jvm.LibraryPath
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
commons module not found.
graphic_objects module not found.
ui_data module not found.
graph module not found.
history_browser module not found.
slint module not found.
coverage module not found.

The scilab package also seems to be missing for some help pages.
This could be better to be reported to the 'scilab' -maintainers, but it is not certain, why the warnings appear.
If I used in the Fedora30 there was less warnings.
I used this ZorinOS for a very small time yet only. But it looks stable in other ways and firefox installation
seems work better so that netflix movies work with this ZorinOS unlike with Fedora30.

Swarfendor437

Mon Jun 10, 2019 12:17:25 pm

When Zorin release a final image they do so balancing kernel with apps that will work with that kernel - if they go for newer apps that might not run smoothly, it wouldn't look good would it? ;) :D

jarkky

Mon Jun 10, 2019 12:32:04 pm

Swarfendor437 wrote:When Zorin release a final image they do so balancing kernel with apps that will work with that kernel - if they go for newer apps that might not run smoothly, it wouldn't look good would it? ;) :D


Yes. That is a good point of view...
But what is problems with imagej then?
It seems not running in this environment / kernel.

Swarfendor437

Mon Jun 10, 2019 4:03:30 pm

Use the one in the software channel instead:

imagej.jpg

jarkky

Tue Jun 11, 2019 5:44:02 am

Swarfendor437 wrote:Use the one in the software channel instead:

imagej.jpg



That's probably the solution. Which channel you refer?
I don't know why 'sudo apt' gives wrong installation.

Swarfendor437

Tue Jun 11, 2019 12:29:14 pm

It's just the Software channel in the Menu. ;) :D

jarkky

Thu Jun 13, 2019 12:27:30 pm

Swarfendor437 wrote:It's just the Software channel in the Menu. ;) :D

It shows just 'imagej' installed. Maybe I try unistall and then install again.
Screenshot from 2019-06-13 20-25-17.png
install

Result is same:
"Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit."

Are you using the same OS-release:
NAME="Zorin OS"
VERSION="15"
?

System logs seem to have report of some issues, but that is quite incomprehensible to be understood:
Screenshot from 2019-06-13 21-44-08.png
systemlogs

Swarfendor437

Thu Jun 13, 2019 5:35:38 pm

Just found this article:

https://jtdcftul.blogspot.com/2019/03/i ... yland.html

When you login are you logging in to default desktop or Wayland?

Swarfendor437

Thu Jun 13, 2019 5:51:15 pm

I can't get it to run at all - could you try the solution here to enable a java virtual machine to run?:

https://forums.linuxmint.com/viewtopic.php?t=225474

Swarfendor437

Thu Jun 13, 2019 5:57:49 pm

jarkky

Fri Jun 14, 2019 11:11:24 am

Swarfendor437 wrote:OK, you need Fiji:

https://imagej.net/Fiji#Downloads

The attachment Fiji.jpg is no longer available


I try check this... But looks complicated if need be used with LinuxMint packages etc.

Also someapp like "whatsdesk" has issue to install into this system;
Screenshot from 2019-06-14 19-08-26.png

Swarfendor437

Fri Jun 14, 2019 12:07:51 pm

I thought it was going to be complicated to - just download the package, extract and run it from within the extracted folder. ;) :D

Can you please start a new thread for the other app - this thread is for imageJ not all apps. Thanks.