Hello everyone,
I installed and used KNIME for a long time until I had to download and install some KNIME plugins (done through the program) a couple of months ago. I updated KNIME through Add/Remove software and now I cannot start KNIME from the menu, I get error message stating “An error has occurred. See the log file null”. I can start it from command line if I do sudo, so I assumed it was permission issue and changed permissions for /usr/share/java/knime-desktop but it did not help. I do not know what is that log file null is, all knime log files I could find on the system are related to previous installation (that I removed but I guess it was not a clean removal). If you could point me to the right direction what to do I would greatly appreciate it.
Hi vshimano,
You are correct, that does indeed sound like permissions. Please provide all output in the terminal emulator if you run it without sudo.
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This will just cause it to be rendered like this:
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@Mirdarthos thank you! Here is the output:
knime-desktop
java.lang.IllegalStateException: Error initializing storage for Equinox container.
at org.eclipse.osgi.internal.framework.EquinoxContainer.<init>(EquinoxContainer.java:110)
at org.eclipse.osgi.launch.Equinox.<init>(Equinox.java:53)
at org.eclipse.osgi.launch.Equinox.<init>(Equinox.java:46)
at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:342)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:267)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
at org.eclipse.equinox.launcher.Main.main(Main.java:1432)
Caused by: java.io.FileNotFoundException: /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/.fileTableLock (Permission denied)
at java.base/java.io.RandomAccessFile.open0(Native Method)
at java.base/java.io.RandomAccessFile.open(Unknown Source)
at java.base/java.io.RandomAccessFile.<init>(Unknown Source)
at java.base/java.io.RandomAccessFile.<init>(Unknown Source)
at org.eclipse.osgi.internal.location.Locker_JavaNio.lock(Locker_JavaNio.java:40)
at org.eclipse.osgi.storagemanager.StorageManager.lock(StorageManager.java:403)
at org.eclipse.osgi.storagemanager.StorageManager.open(StorageManager.java:715)
at org.eclipse.osgi.storage.Storage.getChildStorageManager(Storage.java:2290)
at org.eclipse.osgi.storage.Storage.getInfoInputStream(Storage.java:2308)
at org.eclipse.osgi.storage.Storage.<init>(Storage.java:267)
at org.eclipse.osgi.storage.Storage.createStorage(Storage.java:186)
at org.eclipse.osgi.internal.framework.EquinoxContainer.<init>(EquinoxContainer.java:108)
... 12 more
What the 12 more are - I don’t know.
I see it’s an AUR package, so have you tried rebuilding it:
pamac build knime-desktop
AUR packages should be rebuilt after updates, especially if there are any problems.
I was assuming (maybe wrongly) that if I install/update packages through Add/Remove software it is building/re-building packages for me.
I just rebuilt the package from command line as you suggested, then tried starting KNIME from menu and then from command line with the same result as before.
Looking through comments at the knime-desktop AUR page, I see some permission issues mentioned sometime last month.
I suggest contacting the knime-desktop maintainer, and working with them to solve your issue, might be the best path toward a solution.
A reminder that the AUR is not officially supported by Manjaro, and the Unstable branch is generally suggested for those who insist on building AUR packages.
Regards.
@soundofthunder Thank you for suggestion, I will do that.
Most welcome.
You will need to create an account to post comments at AUR, if you don’t already have one.
Regards.
Did you see this line from your post ?
@Denis_Pom Yes, I did but I don’t know what to do with it. I thought that my issue was something permission related, so I changed permissions recursively for /usr/share/java/knime-desktop/ but apparently it changed only for the first level of files/directories. I just changed permissions for that particular file and that didn’t help
Never edit or change anything under the /usr hierarchy, unless you absolutely know what you’re doing.
Besides, you did not say what the permissions were, nor what you changed them into.
They were -rw-r–r-- owner and group is root
That’s how it should be.
But that’s what causes issues when KNIME is started not by root. I’m not sure what to do besides always starting KNIME using sudo
Please provide the output of:
ls -laH /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/
I just built & successfully opened knime-desktop as a non-privileged user on my system. This is the output I got for the above command:
ls -laH /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/
total 16
drwxr-xr-x 2 root root 4096 Jun 12 09:58 .
drwxr-xr-x 8 root root 4096 Jun 12 09:58 ..
-rw-r--r-- 1 root root 76 Jun 12 09:56 .fileTable.1
-rw-r--r-- 1 root root 76 Jun 12 09:56 .fileTable.2
-rw-r--r-- 1 root root 0 Jun 12 09:56 .fileTableLock
As you can see, the files are all owned by root.
The error message you are receiving seems to indicate that either the /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/.fileTableLock lockfile is missing, or it cannot be accessed due to incorrect permissions.
As those files are included with the knime-desktop package:
pamac list -f knime-desktop | grep -e 'org.eclipse.osgi/.manager'
/usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/.fileTable.1
/usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/.fileTable.2
/usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/.fileTableLock
the simplest solution may be to just uninstall knime-desktop, clean the build files, and then rebuild it:
pamac remove knime-desktop && pamac clean --build-files && pamac build knime-desktop
@scotty65
Here is the output (as I said before I changed the permissions)
ls -laH /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/
total 24
drwxr-xr-x 2 root root 4096 Jun 11 12:03 .
drwxrwxrwx 44 root root 4096 Jun 11 12:03 ..
-rwxrwxrwx 1 root root 76 Jun 11 12:01 .fileTable.1
-rwxrwxrwx 1 root root 76 Jun 11 12:01 .fileTable.2
-rwxrwxrwx 1 root root 75 Jun 11 09:22 .fileTable.8
-rwxrwxrwx 1 root root 75 Jun 11 10:25 .fileTable.9
-rwxrwxrwx 1 root root 0 Jun 11 12:01 .fileTableLock
As you suggested I removed knime and cleaned the build files, then reinstalled knime, it did not help, same error. While I was reinstalling knime I encountered some problems although the transaction completed successfully. Here is the part of the output that indicated an issue, maybe that will shed some light:
Password:
==== AUTHENTICATION COMPLETE ====
cp: cannot access '/var/lib/pacman/sync/download-Yc4fX4': Permission denied
Building knime-desktop...
==> Making package: knime-desktop 5.4.4-2 (Wed 11 Jun 2025 10:05:32 PM EDT)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
-> Downloading knime_5.4.4.linux.gtk.x86_64.tar.gz...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 717M 100 717M 0 0 28.5M 0 0:00:25 0:00:25 --:--:-- 33.2M
-> Found knime.sh
-> Found knime-desktop.desktop
-> Found LICENSE
==> Validating source files with sha256sums...
knime_5.4.4.linux.gtk.x86_64.tar.gz ... Passed
knime.sh ... Passed
knime-desktop.desktop ... Passed
LICENSE ... Passed
==> Removing existing $srcdir/ directory...
==> Extracting sources...
-> Extracting knime_5.4.4.linux.gtk.x86_64.tar.gz with bsdtar
==> Entering fakeroot environment...
==> Starting package()...
WARNING: The convert command is deprecated in IMv7, use "magick" instead of "convert" or "magick convert"
==> Tidying install...
-> Removing empty directories...
-> Removing libtool files...
-> Purging unwanted files...
-> Removing static library files...
-> Stripping unneeded symbols from binaries and libraries...
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-aarch64/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-arm/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-armel/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-loongarch64/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-mips64el/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-ppc/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-ppc64le/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-riscv64/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/linux-s390x/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/sunos-sparc/libjnidispatch.so'
strip: Unable to recognise the format of the input file `./usr/share/java/knime-desktop/plugins/com.sun.jna_5.14.0.v20231211-1200/com/sun/jna/sunos-sparcv9/libjnidispatch.so'
-> Compressing man and info pages...
==> Checking for packaging issues...
==> Creating package "knime-desktop"...
-> Generating .PKGINFO file...
-> Generating .BUILDINFO file...
-> Adding changelog file...
-> Generating .MTREE file...
-> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: knime-desktop 5.4.4-2 (Wed 11 Jun 2025 10:06:51 PM EDT)
==> Cleaning up...
Checking keyring... [1/1]
Checking integrity... [1/1]
Loading packages files... [1/1]
Checking file conflicts... [1/1]
Checking available disk space... [1/1]
Installing knime-desktop (5.4.4-2)... [1/1]
Running post-transaction hooks...
Arming ConditionNeedsUpdate... [1/2]
Updating the desktop file MIME type cache... [2/2]
Transaction successfully finished.
@scotty65 I forgot to include output of ln after I reinstalled knime:
ls -laH /usr/share/java/knime-desktop/configuration/org.eclipse.osgi/.manager/
total 24
drwxr-xr-x 2 root root 4096 Jun 11 22:06 .
drwxrwxrwx 44 root root 4096 Jun 11 22:06 ..
-rw-r--r-- 1 root root 76 Jun 11 22:05 .fileTable.1
-rw-r--r-- 1 root root 76 Jun 11 22:05 .fileTable.2
-rwxrwxrwx 1 root root 75 Jun 11 09:22 .fileTable.8
-rwxrwxrwx 1 root root 75 Jun 11 10:25 .fileTable.9
-rw-r--r-- 1 root root 0 Jun 11 22:05 .fileTableLock
You can get rid of that message by running:
sudo rm -fr /var/lib/pacman/sync/download-*
Regarding the knime-desktop issue,
Looks like the changing of permissions you did earlier might be the cause of the problem. Try this:
pamac remove -on knime-desktop
Then remove any remnants that were not removed by Pamac:
sudo rm -fr /usr/share/java/knime-desktop/
Then build knime-desktop again:
pamac build knime-desktop
That will recreate the /usr/share/java/knime-desktop/ directory & subdirectories with the correct files and permissions. And a reminder: make sure you do not use sudo when running the pamac commands, as that can mess up permissions.
@scotty65 Thank you very much! It helped!
I think there were two problems - one is that I did not clean up after removing knime, and the second one I ran pamac with sudo. I usually install and remove programs with Add/Remove software, I will make sure from now on to clean from command line after a package removal.
Thank you again!
The pamac clean --build-files command just empties out the directory where AUR packages are downloaded and built, so rebuilding will ensure the latest source files are downloaded.
You can see what packages are in your build directory by running the following command:
ls -laH /var/tmp/pamac-build-${USER}
or, to list everything including subdirectories:
ls -laHR /var/tmp/pamac-build-${USER}
The tree command (tree may need installing) is also useful:
tree /var/tmp/pamac-build-${USER}
/var/tmp/pamac-build-scotty
└── knime-desktop
├── ChangeLog
├── knime_5.4.4.linux.gtk.x86_64.tar.gz
├── knime-desktop.desktop
├── knime.sh
├── LICENSE
└── PKGBUILD
or
tree -a /var/tmp/pamac-build-${USER}
to list everything including subdirectories:
Output of tree -a /var/tmp/pamac-build-${USER}
tree -a /var/tmp/pamac-build-${USER}
/var/tmp/pamac-build-scotty
└── knime-desktop
├── ChangeLog
├── .git
│ ├── config
│ ├── description
│ ├── FETCH_HEAD
│ ├── HEAD
│ ├── hooks
│ │ ├── applypatch-msg.sample
│ │ ├── commit-msg.sample
│ │ ├── fsmonitor-watchman.sample
│ │ ├── post-update.sample
│ │ ├── pre-applypatch.sample
│ │ ├── pre-commit.sample
│ │ ├── pre-merge-commit.sample
│ │ ├── prepare-commit-msg.sample
│ │ ├── pre-push.sample
│ │ ├── pre-rebase.sample
│ │ ├── pre-receive.sample
│ │ ├── push-to-checkout.sample
│ │ ├── sendemail-validate.sample
│ │ └── update.sample
│ ├── index
│ ├── info
│ │ └── exclude
│ ├── logs
│ │ ├── HEAD
│ │ └── refs
│ │ ├── heads
│ │ │ └── master
│ │ └── remotes
│ │ └── origin
│ │ └── HEAD
│ ├── objects
│ │ ├── info
│ │ └── pack
│ │ ├── pack-a085bf2fb4b5fdc080579df685645e1f596fe72f.idx
│ │ ├── pack-a085bf2fb4b5fdc080579df685645e1f596fe72f.pack
│ │ └── pack-a085bf2fb4b5fdc080579df685645e1f596fe72f.rev
│ ├── ORIG_HEAD
│ ├── packed-refs
│ ├── refs
│ │ ├── heads
│ │ │ └── master
│ │ ├── remotes
│ │ │ └── origin
│ │ │ └── HEAD
│ │ └── tags
│ └── shallow
├── .gitignore
├── knime_5.4.4.linux.gtk.x86_64.tar.gz
├── knime-desktop.desktop
├── knime.sh
├── LICENSE
├── PKGBUILD
└── .SRCINFO
18 directories, 39 files