Linux JabRef does not start at all #7367

ilippert · 2021-01-19T08:07:34Z

I am using
jabref-5.3.85-1.x86_64, downloaded morning of 19th Jan GMT with bellsoft-java15.x86_64 on Fedora 33.

JabRef does not start.

Happy to provide details if you tell me which commands to run in the shell ;)

ilippert · 2021-01-19T18:23:10Z

@systemoperator sorry to bother, does the latest master run on your Linux machine?

Siedlerchr · 2021-01-19T18:41:37Z

Can you try to start it from the script under runtime/bin/JabRef ?

ilippert · 2021-01-19T18:46:46Z

I get this result

Log File

ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
%d [%thread] %-5level %logger - %msg%n java.lang.IllegalArgumentException: key
  at com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey(Unknown Source) ~[org.jabref.merged.module:?]
  at org.jabref.gui.Globals.startTelemetryClient(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.Globals.startBackgroundTasks(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.JabRefMain.start(Unknown Source) ~[org.jabref:?]
  at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) ~[org.jabref.merged.module:?]
  at java.security.AccessController.doPrivileged(Unknown Source) ~[?:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) ~[org.jabref.merged.module:?]
  at java.lang.Thread.run(Unknown Source) [?:?]

Siedlerchr · 2021-01-19T19:01:14Z

Hm, this is odd. Seems like somehow the data from our build info are not passed down... As far as I know, nothing to that has changed. I will try something and prepare a new branch build.

sambo57u · 2021-01-19T19:09:08Z

I just tried this on the same configuration and it worked. I put an alias in /etc/bashrc

alias jabref="/opt/jabref/bin/JabRef 2>/dev/null"

after this open a new window and it should work. The logger errors are always there. This is using the rpm version of Jabref
5.3.85

systemoperator · 2021-01-19T21:00:07Z

@ilippert I can confirm your stated issue with your mentioned master build on Ubuntu 16.04, using OpenJDK 15.

The problem is that Globals.BUILD_INFO.azureInstrumentationKey is empty (""), which throws an exception in com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey() when called in

jabref/src/main/java/org/jabref/gui/Globals.java

Line 122 in ee2e2db

    
           telemetryConfiguration.setInstrumentationKey(Globals.BUILD_INFO.azureInstrumentationKey);

because it requires that the key is non-empty and non-null.

Forcing a non-empty value for testing purposes starts the application properly.

Siedlerchr · 2021-01-19T21:21:44Z

The build info key should be set by the CI and gradle
Hmm, as far as I know nobody changed it (at least I guess).

ilippert · 2021-01-20T07:27:06Z

Hi @sambo57u with the proposed alias I get this result

Log File

jabref 
%d [%thread] %-5level %logger - %msg%n java.lang.IllegalArgumentException: key
  at com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey(Unknown Source) ~[org.jabref.merged.module:?]
  at org.jabref.gui.Globals.startTelemetryClient(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.Globals.startBackgroundTasks(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.JabRefMain.start(Unknown Source) ~[org.jabref:?]
  at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) ~[org.jabref.merged.module:?]
  at java.security.AccessController.doPrivileged(Unknown Source) ~[?:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) ~[org.jabref.merged.module:?]
  at java.lang.Thread.run(Unknown Source) [?:?]

sambo57u · 2021-01-20T15:19:50Z

Hmmm.....why do you say bellsoft java? jabref has its own java...perhaps some path is set that interferes with it. I only have openjdk java's from Fedora repository. You get a bunch of logger messages but jabref starts.

ilippert · 2021-01-20T16:57:46Z

Hmmm.....why do you say bellsoft java? jabref has its own java...perhaps some path is set that interferes with it. I only have openjdk java's from Fedora repository. You get a bunch of logger messages but jabref starts.

Since #6559 I have been only working with bellsoft.

Siedlerchr · 2021-01-20T17:59:43Z

The java version doesn't matter. JabRef ships with a custom runtime. Can you try to add the -d all commandline parameter when starting? Maybye your prefs are corrupt

ilippert · 2021-01-20T18:28:31Z

this gets me

Log File

# alias jabref="/opt/jabref/bin/JabRef -d all 2>/dev/null"
# jabref 
%d [%thread] %-5level %logger - %msg%n java.lang.IllegalArgumentException: key
  at com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey(Unknown Source) ~[org.jabref.merged.module:?]
  at org.jabref.gui.Globals.startTelemetryClient(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.Globals.startBackgroundTasks(Unknown Source) ~[org.jabref:?]
  at org.jabref.gui.JabRefMain.start(Unknown Source) ~[org.jabref:?]
  at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) ~[org.jabref.merged.module:?]
  at java.security.AccessController.doPrivileged(Unknown Source) ~[?:?]
  at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[org.jabref.merged.module:?]
  at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) ~[org.jabref.merged.module:?]
  at java.lang.Thread.run(Unknown Source) [?:?]

wujastyk · 2021-01-20T20:07:30Z

same problem here.

Siedlerchr · 2021-01-20T21:08:44Z

Can you test the version from here https://builds.jabref.org/pull/7371/merge/ ?

wujastyk · 2021-01-20T22:20:08Z

On linux mint 20.1 Cinnamon 4.8.

Installed from that deb and got the same-looking startup errors:

/opt/jabref/bin$ ./JabRef 
ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
%d [%thread] %-5level %logger - %msg%n java.lang.IllegalArgumentException: key
	at com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey(Unknown Source) ~[org.jabref.merged.module:?]
	at org.jabref.gui.Globals.startTelemetryClient(Unknown Source) ~[org.jabref:?]
	at org.jabref.gui.Globals.startBackgroundTasks(Unknown Source) ~[org.jabref:?]
	at org.jabref.gui.JabRefMain.start(Unknown Source) ~[org.jabref:?]
	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source) ~[org.jabref.merged.module:?]
	at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) ~[org.jabref.merged.module:?]
	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) ~[org.jabref.merged.module:?]
	at java.security.AccessController.doPrivileged(Unknown Source) ~[?:?]
	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) ~[org.jabref.merged.module:?]
	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source) ~[org.jabref.merged.module:?]
	at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[org.jabref.merged.module:?]
	at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) ~[org.jabref.merged.module:?]
	at java.lang.Thread.run(Unknown Source) [?:?]

koppor · 2021-01-20T22:53:44Z

It could be too late here, but I hink, the solution is simple. I do not find the setting AzureInstrumentationKey (read by gradle), APPLICATION_INSIGHTS_IKEY (read by the code), or APPINSIGHTS_INSTRUMENTATIONKEY (read by the code) in our build secrets (https://github.com/JabRef/jabref/settings/secrets/actions accessible for maintainers only).

The workround is to set the environment variable APPINSIGHTS_INSTRUMENTATIONKEY to x (or any other string).

sambo57u · 2021-01-20T23:47:33Z

This is very puzzling. Why is mine working. I am on Fedora 33 x86_64 too and have done nothing special.

ilippert · 2021-01-21T07:39:38Z

Can you test the version from here https://builds.jabref.org/pull/7371/merge/ ?

The link directed me to the master.

it still gives me the result

Log File

Paste an excerpt of your log file here

# jabref %d [%thread] %-5level %logger - %msg%n java.lang.IllegalArgumentException: key at com.microsoft.applicationinsights.TelemetryConfiguration.setInstrumentationKey(Unknown Source) ~[org.jabref.merged.module:?] at org.jabref.gui.Globals.startTelemetryClient(Unknown Source) ~[org.jabref:?] at org.jabref.gui.Globals.startBackgroundTasks(Unknown Source) ~[org.jabref:?] at org.jabref.gui.JabRefMain.start(Unknown Source) ~[org.jabref:?] at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source) ~[org.jabref.merged.module:?] at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) ~[org.jabref.merged.module:?] at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) ~[org.jabref.merged.module:?] at java.security.AccessController.doPrivileged(Unknown Source) ~[?:?] at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) ~[org.jabref.merged.module:?] at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source) ~[org.jabref.merged.module:?] at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[org.jabref.merged.module:?] at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) ~[org.jabref.merged.module:?] at java.lang.Thread.run(Unknown Source) [?:?]

Siedlerchr · 2021-01-21T11:08:30Z

Can you please try again with the latest master? Newest build contains a workaround

ilippert · 2021-01-21T11:21:05Z

JabRef 5.3--2021-01-21--1be95fc
Linux 5.10.7-200.fc33.x86_64 amd64
Java 15.0.1
JavaFX 15.0.1+1

works!
thanks!

wujastyk · 2021-01-22T01:19:35Z

JabRef 5.3--2021-01-21--94f4c1e
Linux 5.4.0-62-generic amd64
Java 15.0.1
JavaFX 15.0.1+1

Also good. Thank you!

koppor · 2021-01-22T06:03:25Z

Thank you all for the patience 🎉

Siedlerchr mentioned this issue Jan 19, 2021

[WIP] Downgrade jlinkplugin #7369

Closed

5 tasks

Siedlerchr added platform: linux dev: build-system labels Jan 20, 2021

koppor mentioned this issue Jan 20, 2021

Fix Exception if no AzureInstrumentationKey is available #7373

Merged

5 tasks

koppor mentioned this issue Jan 20, 2021

Try if linux works again #7371

Closed

5 tasks

koppor closed this as completed Jan 22, 2021

Siedlerchr mentioned this issue Feb 23, 2021

Telemetry makes JabRef crash on start #7456

Closed

1 task

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Linux JabRef does not start at all #7367

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ilippert commented Jan 19, 2021

ilippert commented Jan 19, 2021

Siedlerchr commented Jan 19, 2021

ilippert commented Jan 19, 2021

Siedlerchr commented Jan 19, 2021

sambo57u commented Jan 19, 2021

systemoperator commented Jan 19, 2021

Siedlerchr commented Jan 19, 2021

ilippert commented Jan 20, 2021

sambo57u commented Jan 20, 2021

ilippert commented Jan 20, 2021

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ilippert commented Jan 20, 2021

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koppor commented Jan 20, 2021

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ilippert commented Jan 21, 2021

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ilippert commented Jan 21, 2021

wujastyk commented Jan 22, 2021

koppor commented Jan 22, 2021

Linux JabRef does not start at all #7367

Linux JabRef does not start at all #7367

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ilippert commented Jan 19, 2021

ilippert commented Jan 19, 2021

Siedlerchr commented Jan 19, 2021

ilippert commented Jan 19, 2021

Siedlerchr commented Jan 19, 2021

sambo57u commented Jan 19, 2021

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