Failed to load class "org.slf4j.impl.StaticLoggerBinder" message on MacOS when GUI crashes.
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Visvaldas Kairys
Jul 11, 2019, 9:21:22 AM7/11/19
to cytoscape-helpdesk
Hi all,
I was trying this for several hours. On My MacOS Cytoscape versions 3.7.1 to 3.4.0 crash. The GUI shows up fpr a brief moment but then disappears.
What is frustrating and strange, two days ago Cytosccape 3.6.1 ran fine (!?), so I had to uninstall 3.7.1 and run 3.6.1, but today it started crashing again.
The output of cytoscape.sh:
karaf.base: /Applications/Cytoscape_v3.7.1/Cytoscape.app/../framework
JAVA_HOME: null
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
{visvaldas}/Applications/Cytoscape_v3.7.1% sh cytoscape.sh
karaf.base: /Applications/Cytoscape_v3.7.1/framework
JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home
_
___ _ _| |_ ___ ___ ___ __ _ _ __ ___
/ __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
| (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/
\___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
|___/ |_|
Cytoscape 3.7.1
Hit '<tab>' for a list of available commands
and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.
karaf@Cytoscape 3.7.1()> SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
JAVA_HOME: null
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
{visvaldas}/Applications/Cytoscape_v3.7.1% sh cytoscape.sh
karaf.base: /Applications/Cytoscape_v3.7.1/framework
JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home
_
___ _ _| |_ ___ ___ ___ __ _ _ __ ___
/ __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
| (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/
\___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
|___/ |_|
Cytoscape 3.7.1
Hit '<tab>' for a list of available commands
and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.
karaf@Cytoscape 3.7.1()> SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
The output of system checker script:
############# Cytoscape System Requirements Checker for Mac ##############
Target Cytoscape version: 3.7.1
Your shell is tcsh
Compatible OS version found: 10.13
- Pass: OS Version = 10.13.6
- Pass: Following Oracle JDK found:
/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk
/Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk
/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk
- Pass: Current Java Version = 1.8.0_181
- Pass: JAVA_HOME found: /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home
Checking connection to Cytoscape App Store...
5 packets transmitted, 5 packets received, 0.0% packet loss
Done! You are ready to run Cytoscape 3.7.1
Target Cytoscape version: 3.7.1
Your shell is tcsh
Compatible OS version found: 10.13
- Pass: OS Version = 10.13.6
- Pass: Following Oracle JDK found:
/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk
/Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk
/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk
- Pass: Current Java Version = 1.8.0_181
- Pass: JAVA_HOME found: /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home
Checking connection to Cytoscape App Store...
5 packets transmitted, 5 packets received, 0.0% packet loss
Done! You are ready to run Cytoscape 3.7.1
I am running MacOS High Sierra 10.13.6
java version output is:
java version "1.8.0_181"
Java(TM) SE Runtime Environment (build 1.8.0_181-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.181-b13, mixed mode)
Java(TM) SE Runtime Environment (build 1.8.0_181-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.181-b13, mixed mode)
(I downloaded JDK version 211 and set JAVA_HOME to it; I am not sure why java -version does not show it; but back when JAVA_HOME pointed to version 181, the result was exactly the same anyway).
Best regards,
Visvaldas
David Otasek
Jul 11, 2019, 12:26:33 PM7/11/19
to cytoscape-helpdesk
It does look like you've done everything correctly, and thank you for reporting your error so thoroughly.
We might be able to get more information from checking the framework log, which is located in the CytoscapeConfiguration directory. Normally, this is ~\CytoscapeConfiguration\3\framework-cytoscape.log or C:\Users\YourUserName\CytoscapeConfiguration\3\framework-cytoscape.log
If you could share the contents of that file, it could be very useful.
If you could share the contents of that file, it could be very useful.
David Otasek
Jul 11, 2019, 6:45:29 PM7/11/19
to cytoscape-helpdesk
Thank you. Unfortunately, what I see isn't explaining the behaviour. It gets as far as loading all the apps, and then it appears to perform a clean exit without any errors. This is very odd.
There's one more possibility. In your Cytoscape install directory, there might be some localized logs or Java memory dumps. If you could share a listing of that directory, that could point us to more information.
Mine, for example, looks like this:
drwxrwxrwx 2 user1 user1 12288 Jun 10 11:46 apps
-rwxr-xr-x 1 user1 user1 14333 Jan 3 2019 Cytoscape
-rwxr-xr-x 1 user1 user1 213 Feb 19 15:55 Cytoscape.desktop
-rw-rw-r-- 1 user1 user1 57 Feb 19 15:55 Cytoscape.installoptions
-rwxr-xr-x 1 user1 user1 2646 Jan 3 2019 cytoscape.sh
-rw-rw-r-- 1 user1 user1 21 Feb 19 15:55 Cytoscape.vmoptions
-rw-rw-r-- 1 user1 user1 0 May 3 15:02 derby.log
drwxrwxrwx 8 user1 user1 4096 Jun 7 17:01 framework
-rwxr-xr-x 1 user1 user1 1474 Jan 3 2019 gen_vmoptions.sh
-rw-rw-r-- 1 user1 user1 17524 Jun 28 14:52 output.log
drwxrwxrwx 3 user1 user1 4096 Feb 19 15:55 sampleData
-rwx------ 1 user1 user1 13768 Jan 3 2019 uninstall
There's one more possibility. In your Cytoscape install directory, there might be some localized logs or Java memory dumps. If you could share a listing of that directory, that could point us to more information.
Mine, for example, looks like this:
drwxrwxrwx 2 user1 user1 12288 Jun 10 11:46 apps
-rwxr-xr-x 1 user1 user1 14333 Jan 3 2019 Cytoscape
-rwxr-xr-x 1 user1 user1 213 Feb 19 15:55 Cytoscape.desktop
-rw-rw-r-- 1 user1 user1 57 Feb 19 15:55 Cytoscape.installoptions
-rwxr-xr-x 1 user1 user1 2646 Jan 3 2019 cytoscape.sh
-rw-rw-r-- 1 user1 user1 21 Feb 19 15:55 Cytoscape.vmoptions
-rw-rw-r-- 1 user1 user1 0 May 3 15:02 derby.log
drwxrwxrwx 8 user1 user1 4096 Jun 7 17:01 framework
-rwxr-xr-x 1 user1 user1 1474 Jan 3 2019 gen_vmoptions.sh
-rw-rw-r-- 1 user1 user1 17524 Jun 28 14:52 output.log
drwxrwxrwx 3 user1 user1 4096 Feb 19 15:55 sampleData
-rwx------ 1 user1 user1 13768 Jan 3 2019 uninstall
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Visvaldas Kairys
Jul 12, 2019, 3:35:45 AM7/12/19
to cytoscape...@googlegroups.com
Ok, I think there is not much meat there, but here it is:
{visvaldas}/Applications/Cytoscape_v3.7.1% ls -l
total 40
drwxr-xr-x 3 visvaldas admin 102 Jul 11 13:31 Cytoscape Uninstaller.app
drwxr-xr-x 3 visvaldas admin 102 Jan 3 2019 Cytoscape.app
-rw-r--r-- 1 visvaldas admin 57 Jul 11 13:31 Cytoscape.installoptions
-rw-r--r-- 1 visvaldas admin 20 Jul 11 13:32 Cytoscape.vmoptions
drwxrwxrwx 21 visvaldas admin 714 Jul 11 13:31 apps
-rwxr-xr-x 1 visvaldas admin 2646 Jan 3 2019 cytoscape.sh
drwxrwxrwx 10 visvaldas admin 340 Jul 11 13:32 framework
-rwxr-xr-x 1 visvaldas admin 1474 Jan 3 2019 gen_vmoptions.sh
-rw-r--r-- 1 visvaldas admin 296 Jul 11 14:01 output.log
drwxrwxrwx 22 visvaldas admin 748 Jul 11 13:31 sampleData
total 40
drwxr-xr-x 3 visvaldas admin 102 Jul 11 13:31 Cytoscape Uninstaller.app
drwxr-xr-x 3 visvaldas admin 102 Jan 3 2019 Cytoscape.app
-rw-r--r-- 1 visvaldas admin 57 Jul 11 13:31 Cytoscape.installoptions
-rw-r--r-- 1 visvaldas admin 20 Jul 11 13:32 Cytoscape.vmoptions
drwxrwxrwx 21 visvaldas admin 714 Jul 11 13:31 apps
-rwxr-xr-x 1 visvaldas admin 2646 Jan 3 2019 cytoscape.sh
drwxrwxrwx 10 visvaldas admin 340 Jul 11 13:32 framework
-rwxr-xr-x 1 visvaldas admin 1474 Jan 3 2019 gen_vmoptions.sh
-rw-r--r-- 1 visvaldas admin 296 Jul 11 14:01 output.log
drwxrwxrwx 22 visvaldas admin 748 Jul 11 13:31 sampleData
I re-ran (re-crashed:-) the program right now, and only output.log data changed:
-rw-r--r-- 1 visvaldas admin 296 Jul 12 08:02 output.log
drwxrwxrwx 10 visvaldas admin 340 Jul 11 13:32 framework/
-rw-r--r-- 1 visvaldas admin 20 Jul 11 13:32 Cytoscape.vmoptions
-rw-r--r-- 1 visvaldas admin 57 Jul 11 13:31 Cytoscape.installoptions
drwxrwxrwx 22 visvaldas admin 748 Jul 11 13:31 sampleData/
drwxr-xr-x 3 visvaldas admin 102 Jul 11 13:31 Cytoscape Uninstaller.app/
drwxrwxrwx 21 visvaldas admin 714 Jul 11 13:31 apps/
drwxr-xr-x 3 visvaldas admin 102 Jan 3 2019 Cytoscape.app/
-rwxr-xr-x 1 visvaldas admin 2646 Jan 3 2019 cytoscape.sh*
-rwxr-xr-x 1 visvaldas admin 1474 Jan 3 2019 gen_vmoptions.sh*
drwxrwxrwx 10 visvaldas admin 340 Jul 11 13:32 framework/
-rw-r--r-- 1 visvaldas admin 20 Jul 11 13:32 Cytoscape.vmoptions
-rw-r--r-- 1 visvaldas admin 57 Jul 11 13:31 Cytoscape.installoptions
drwxrwxrwx 22 visvaldas admin 748 Jul 11 13:31 sampleData/
drwxr-xr-x 3 visvaldas admin 102 Jul 11 13:31 Cytoscape Uninstaller.app/
drwxrwxrwx 21 visvaldas admin 714 Jul 11 13:31 apps/
drwxr-xr-x 3 visvaldas admin 102 Jan 3 2019 Cytoscape.app/
-rwxr-xr-x 1 visvaldas admin 2646 Jan 3 2019 cytoscape.sh*
-rwxr-xr-x 1 visvaldas admin 1474 Jan 3 2019 gen_vmoptions.sh*
and the contents of output.log file is the same:
karaf.base: /Applications/Cytoscape_v3.7.1/Cytoscape.app/../framework
JAVA_HOME: null
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
JAVA_HOME: null
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Meanwhile, I tried to list all files modified at the crash time (8:02):
{visvaldas}/Applications/Cytoscape_v3.7.1% ls-recent.sh . -50
2019-07-12 08:02:19.000000000 +0100 ./output.log
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/profile.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.ops4j.pax.url.mvn.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.ops4j.pax.logging.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.cytoscape.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.shell.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.management.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.log.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.kar.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.jaas.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.features.repos.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.features.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.system.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.shell.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.scope_bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.kar.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.jaas.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.feature.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.config.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.felix.eventadmin.impl.EventAdmin.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.osgi.compendium.cm.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.security.jmx.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.config.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.java.lang.Memory.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.cfg
2019-07-12 08:02:00.000000000 +0100 ./framework/instances/instance.properties
2019-07-12 08:02:19.000000000 +0100 ./output.log
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/profile.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.ops4j.pax.url.mvn.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.ops4j.pax.logging.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.cytoscape.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.shell.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.management.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.log.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.kar.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.jaas.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.features.repos.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.features.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.system.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.shell.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.scope_bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.kar.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.jaas.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.feature.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.config.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.karaf.command.acl.bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/org.apache.felix.eventadmin.impl.EventAdmin.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.osgi.compendium.cm.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.security.jmx.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.config.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.org.apache.karaf.bundle.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.java.lang.Memory.cfg
2019-07-12 08:02:01.000000000 +0100 ./framework/etc/jmx.acl.cfg
2019-07-12 08:02:00.000000000 +0100 ./framework/instances/instance.properties
Note that Cytoscape is still running (after the GUI crash that is), it’s just the graphics window is missing. If I try to create empty new network, nothing happens, and no new log file is written in the app directory.
When I start the program empty GUI window appeared seemingly okay
and it suddenly disappeared, it seems this happened after or before it started filling with the sample data.
I was wondering if there is an option to start Cytoscape with just the empty Window, without the demo data.
I hope this will be helpful.
Visvaldas
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CAGXvV6RFhJ6j3DJJGDbc0h87hv38eEYRdfkpU-6wd9Pb9qprfw%40mail.gmail.com.
Visvaldas Kairys
Jul 12, 2019, 3:57:26 AM7/12/19
to cytoscape-helpdesk
I am not not sure how useful this will be, but I dived into Console.app looking for clues, and found a JavaApplicationStub_2019-07-09-092441_Humuhumunukunukuapuaa.cpu_resource.diag for cytoscape 3.6.1 apparently from the time I was able to run it successfully without crashes. Funnily, I had JAVA_HOME pointing to /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home. In order to fix crashes I pointed it to the /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home (as well as version 181), to no avail. When I return JAVA_HOME to JavaAppletPlugin, the same problem persists and nothing changes anyway.
Date/Time: 2019-07-09 09:22:49.604345 +0100
OS Version: Mac OS X 10.13.6 (Build 17G7024)
Architecture: x86_64
Report Version: 19
Command: JavaApplicationStub
Path: /Applications/Cytoscape_v3.6.1/Cytoscape.app/Contents/MacOS/JavaApplicationStub
Version: 3.6.1 (3.6.1)
Parent: launchd [1]
PID: 17948
Event: cpu usage
Action taken: none
CPU: 90 seconds cpu time over 102 seconds (88% cpu average), exceeding limit of 50% cpu over 180 seconds
CPU limit: 90s
Limit duration: 180s
CPU used: 90s
Duration: 102.07s
Steps: 60
Hardware model: MacBookPro9,2
Active cpus: 4
Fan speed: 2291 rpm
Powerstats for: JavaApplicationS [17948]
UUID: 24EBE302-01AB-3854-B9AD-92C10C2965FD
Start time: 2019-07-09 09:22:55 +0100
End time: 2019-07-09 09:24:31 +0100
Parent: launchd
Microstackshots: 60 samples (100%)
Primary state: 30 samples Frontmost App, User mode, Effective Thread QoS Default, Requested Thread QoS Default, Override Thread QoS Unspecified
User Activity: 0 samples Idle, 60 samples Active
Power Source: 60 samples on Battery, 0 samples on AC
13 ??? [0xda00be55f80062fd]
3 ??? [0x10c19bbc8]
2 ??? [0x10c427564]
2 ??? [0x10c19c5df]
1 <Kernel mode>
2 ??? [0x10c19bbdd]
1 ??? [0x10c19c5da]
1 <Kernel mode>
1 ??? [0x10c19c5d7]
1 <Non-Frontmost App>
1 ??? [0x10c19bc80]
1 <Kernel mode>
1 ??? [0x10b4e4563]
12 thread_start + 13 (libsystem_pthread.dylib) [0x7fff7812abf9]
12 _pthread_start + 377 (libsystem_pthread.dylib) [0x7fff7812b50d]
12 _pthread_body + 340 (libsystem_pthread.dylib) [0x7fff7812b661]
12 java_start(Thread*) + 246 (libjvm.dylib) [0x104c8f30a]
9 JavaThread::run() + 450 (libjvm.dylib) [0x104d7228e]
9 JavaThread::thread_main_inner() + 155 (libjvm.dylib) [0x104d70b93]
5 thread_entry(JavaThread*, Thread*) + 124 (libjvm.dylib) [0x104b4bf5d]
5 JavaCalls::call_virtual(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Thread*) + 74 (libjvm.dylib) [0x104af166e]
5 JavaCalls::call_virtual(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*) + 356 (libjvm.dylib) [0x104af14c2]
5 JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) + 1710 (libjvm.dylib) [0x104af0d1e]
5 ??? [0x10a5577a7]
2 ??? [0x10a55f302]
1 ??? [0x10a55f040]
1 ??? [0x10b483164]
1 ??? [0x10b1747aa]
1 Unsafe_Park + 126 (libjvm.dylib) [0x104d871e3]
1 Parker::park(bool, long) + 527 (libjvm.dylib) [0x104c8bd01]
1 __psynch_cvwait + 10 (libsystem_kernel.dylib) [0x7fff77f63a16]
1 <Non-Frontmost App, Kernel mode>
1 ??? [0x10a55f2bd]
1 ??? [0x10c1a74cc]
1 ??? [0x10b1747aa]
1 Unsafe_Park + 126 (libjvm.dylib) [0x104d871e3]
1 Parker::park(bool, long) + 527 (libjvm.dylib) [0x104c8bd01]
1 _pthread_cond_wait + 866 (libsystem_pthread.dylib) [0x7fff7812c60f]
1 _pthread_cond_updateval + 40 (libsystem_pthread.dylib) [0x7fff7812cb12]
1 <Non-Frontmost App>
2 ??? [0x10c2b22fc]
2 ??? [0x10b93b0aa]
1 Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer + 674 (libawt_lwawt.dylib) [0x1084eb1fa]
1 OGLTR_DrawGlyphList + 698 (libawt_lwawt.dylib) [0x1084ee5ae]
1 Java_sun_java2d_opengl_OGLSurfaceData_initFlipBackbuffer + 145 (libawt_lwawt.dylib) [0x1084edd8d]
1 <Kernel mode>
1 OGLSD_Flush + 109 (libawt_lwawt.dylib) [0x1084c9b5c]
1 -[NSObject(NSThreadPerformAdditions) performSelectorOnMainThread:withObject:waitUntilDone:modes:] + 87 (Foundation) [0x7fff52014bce]
1 -[NSObject(NSThreadPerformAdditions) performSelector:onThread:withObject:waitUntilDone:modes:] + 865 (Foundation) [0x7fff51f703ee]
1 -[NSThread _nq:] + 781 (Foundation) [0x7fff51f70840]
1 CFRunLoopWakeUp + 363 (CoreFoundation) [0x7fff4fe3925b]
1 _pthread_mutex_unlock_slow + 459 (libsystem_pthread.dylib) [0x7fff78129917]
1 __psynch_mutexdrop + 10 (libsystem_kernel.dylib) [0x7fff77f63a2e]
1 <Non-Frontmost App, Kernel mode>
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1 os::sleep(Thread*, long, bool) + 239 (libjvm.dylib) [0x104c8ed6f]
1 os::PlatformEvent::park(long) + 404 (libjvm.dylib) [0x104c8bf22]
1 __psynch_cvwait + 10 (libsystem_kernel.dylib) [0x7fff77f63a16]
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4 CompileBroker::invoke_compiler_on_method(CompileTask*) + 1458 (libjvm.dylib) [0x1049b8376]
4 C2Compiler::compile_method(ciEnv*, ciMethod*, int) + 178 (libjvm.dylib) [0x1049511fe]
3 Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool, bool) + 2445 (libjvm.dylib) [0x1049b4cd9]
3 Compile::Code_Gen() + 334 (libjvm.dylib) [0x1049b0adc]
1 PhaseChaitin::Register_Allocate() + 1557 (libjvm.dylib) [0x104961fdd]
1 PhaseIFG::SquareUp() + 90 (libjvm.dylib) [0x104ab21a8]
1 IndexSetIterator::advance_and_next() + 163 (libjvm.dylib) [0x104ab6671]
1 PhaseChaitin::Register_Allocate() + 1309 (libjvm.dylib) [0x104961ee5]
1 PhaseChaitin::Split(unsigned int, ResourceArea*) + 2472 (libjvm.dylib) [0x104cd991c]
1 PhaseChaitin::Register_Allocate() + 1617 (libjvm.dylib) [0x104962019]
1 PhaseChaitin::Select() + 507 (libjvm.dylib) [0x104960ccb]
1 PhaseChaitin::bias_color(LRG&, int) + 602 (libjvm.dylib) [0x104960a70]
1 RegMask::find_first_elem() const + 165 (libjvm.dylib) [0x10484a86b]
1 Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool, bool) + 2284 (libjvm.dylib) [0x1049b4c38]
1 Compile::Optimize() + 175 (libjvm.dylib) [0x1049b1579]
1 PhaseIterGVN::optimize() + 53 (libjvm.dylib) [0x104cb996f]
1 PhaseIterGVN::transform_old(Node*) + 58 (libjvm.dylib) [0x104cb9e34]
1 RegionNode::Ideal(PhaseGVN*, bool) + 941 (libjvm.dylib) [0x10495e567]
1 RegionNode::is_unreachable_region(PhaseGVN*) const + 369 (libjvm.dylib) [0x10495dcaf]
3 GCTaskThread::run() + 417 (libjvm.dylib) [0x104a7949b]
2 OldToYoungRootsTask::do_it(GCTaskManager*, unsigned int) + 75 (libjvm.dylib) [0x104ccf5df]
2 CardTableExtension::scavenge_contents_parallel(ObjectStartArray*, MutableSpace*, HeapWord*, PSPromotionManager*, unsigned int, unsigned int) + 896 (libjvm.dylib) [0x104957e3a]
2 PSPromotionManager::drain_stacks_depth(bool) + 279 (libjvm.dylib) [0x104ccba9f]
2 PSPromotionManager::process_popped_location_depth(StarTask) + 115 (libjvm.dylib) [0x104ccca7f]
2 oopDesc* PSPromotionManager::copy_to_survivor_space<false>(oopDesc*) + 556 (libjvm.dylib) [0x104ccc760]
2 Copy::pd_disjoint_words(HeapWord*, HeapWord*, unsigned long) + 108 (libjvm.dylib) [0x10499d870]
2 _platform_memmove$VARIANT$Nehalem + 224 (libsystem_platform.dylib) [0x7fff781214e0]
2 <Non-Frontmost App, Kernel mode>
1 StealTask::do_it(GCTaskManager*, unsigned int) + 45 (libjvm.dylib) [0x104ccf6b9]
1 PSPromotionManager::drain_stacks_depth(bool) + 138 (libjvm.dylib) [0x104ccba12]
1 PSPromotionManager::process_popped_location_depth(StarTask) + 115 (libjvm.dylib) [0x104ccca7f]
1 oopDesc* PSPromotionManager::copy_to_survivor_space<false>(oopDesc*) + 556 (libjvm.dylib) [0x104ccc760]
1 Copy::pd_disjoint_words(HeapWord*, HeapWord*, unsigned long) + 108 (libjvm.dylib) [0x10499d870]
1 _platform_memmove$VARIANT$Nehalem + 235 (libsystem_platform.dylib) [0x7fff781214eb]
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2 <Non-Frontmost App>
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2 ??? [0x10b1747aa]
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0x7fff78120000 - 0x7fff78127ff7 libsystem_platform.dylib (161.50.1) <6355EE2D-5456-3CA8-A227-B96E8F1E2AF8> /usr/lib/system/libsystem_platform.dylib
0x7fff78128000 - 0x7fff78133fff libsystem_pthread.dylib (301.50.1) <0E51CCBA-91F2-34E1-BF2A-FEEFD3D321E4> /usr/lib/system/libsystem_pthread.dylib
OS Version: Mac OS X 10.13.6 (Build 17G7024)
Architecture: x86_64
Report Version: 19
Command: JavaApplicationStub
Path: /Applications/Cytoscape_v3.6.1/Cytoscape.app/Contents/MacOS/JavaApplicationStub
Version: 3.6.1 (3.6.1)
Parent: launchd [1]
PID: 17948
Event: cpu usage
Action taken: none
CPU: 90 seconds cpu time over 102 seconds (88% cpu average), exceeding limit of 50% cpu over 180 seconds
CPU limit: 90s
Limit duration: 180s
CPU used: 90s
Duration: 102.07s
Steps: 60
Hardware model: MacBookPro9,2
Active cpus: 4
Fan speed: 2291 rpm
Powerstats for: JavaApplicationS [17948]
UUID: 24EBE302-01AB-3854-B9AD-92C10C2965FD
Start time: 2019-07-09 09:22:55 +0100
End time: 2019-07-09 09:24:31 +0100
Parent: launchd
Microstackshots: 60 samples (100%)
Primary state: 30 samples Frontmost App, User mode, Effective Thread QoS Default, Requested Thread QoS Default, Override Thread QoS Unspecified
User Activity: 0 samples Idle, 60 samples Active
Power Source: 60 samples on Battery, 0 samples on AC
13 ??? [0xda00be55f80062fd]
3 ??? [0x10c19bbc8]
2 ??? [0x10c427564]
2 ??? [0x10c19c5df]
1 <Kernel mode>
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1 ??? [0x10c19c5da]
1 <Kernel mode>
1 ??? [0x10c19c5d7]
1 <Non-Frontmost App>
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1 <Kernel mode>
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9 JavaThread::thread_main_inner() + 155 (libjvm.dylib) [0x104d70b93]
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5 JavaCalls::call_virtual(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Thread*) + 74 (libjvm.dylib) [0x104af166e]
5 JavaCalls::call_virtual(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*) + 356 (libjvm.dylib) [0x104af14c2]
5 JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) + 1710 (libjvm.dylib) [0x104af0d1e]
5 ??? [0x10a5577a7]
2 ??? [0x10a55f302]
1 ??? [0x10a55f040]
1 ??? [0x10b483164]
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1 Unsafe_Park + 126 (libjvm.dylib) [0x104d871e3]
1 Parker::park(bool, long) + 527 (libjvm.dylib) [0x104c8bd01]
1 __psynch_cvwait + 10 (libsystem_kernel.dylib) [0x7fff77f63a16]
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1 ??? [0x10c1a74cc]
1 ??? [0x10b1747aa]
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1 Parker::park(bool, long) + 527 (libjvm.dylib) [0x104c8bd01]
1 _pthread_cond_wait + 866 (libsystem_pthread.dylib) [0x7fff7812c60f]
1 _pthread_cond_updateval + 40 (libsystem_pthread.dylib) [0x7fff7812cb12]
1 <Non-Frontmost App>
2 ??? [0x10c2b22fc]
2 ??? [0x10b93b0aa]
1 Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer + 674 (libawt_lwawt.dylib) [0x1084eb1fa]
1 OGLTR_DrawGlyphList + 698 (libawt_lwawt.dylib) [0x1084ee5ae]
1 Java_sun_java2d_opengl_OGLSurfaceData_initFlipBackbuffer + 145 (libawt_lwawt.dylib) [0x1084edd8d]
1 <Kernel mode>
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1 -[NSObject(NSThreadPerformAdditions) performSelectorOnMainThread:withObject:waitUntilDone:modes:] + 87 (Foundation) [0x7fff52014bce]
1 -[NSObject(NSThreadPerformAdditions) performSelector:onThread:withObject:waitUntilDone:modes:] + 865 (Foundation) [0x7fff51f703ee]
1 -[NSThread _nq:] + 781 (Foundation) [0x7fff51f70840]
1 CFRunLoopWakeUp + 363 (CoreFoundation) [0x7fff4fe3925b]
1 _pthread_mutex_unlock_slow + 459 (libsystem_pthread.dylib) [0x7fff78129917]
1 __psynch_mutexdrop + 10 (libsystem_kernel.dylib) [0x7fff77f63a2e]
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1 ??? [0x10a55f2bd]
1 ??? [0x10a55f2bd]
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1 __psynch_cvwait + 10 (libsystem_kernel.dylib) [0x7fff77f63a16]
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4 CompileBroker::compiler_thread_loop() + 657 (libjvm.dylib) [0x1049ba8bd]
4 CompileBroker::invoke_compiler_on_method(CompileTask*) + 1458 (libjvm.dylib) [0x1049b8376]
4 C2Compiler::compile_method(ciEnv*, ciMethod*, int) + 178 (libjvm.dylib) [0x1049511fe]
3 Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool, bool) + 2445 (libjvm.dylib) [0x1049b4cd9]
3 Compile::Code_Gen() + 334 (libjvm.dylib) [0x1049b0adc]
1 PhaseChaitin::Register_Allocate() + 1557 (libjvm.dylib) [0x104961fdd]
1 PhaseIFG::SquareUp() + 90 (libjvm.dylib) [0x104ab21a8]
1 IndexSetIterator::advance_and_next() + 163 (libjvm.dylib) [0x104ab6671]
1 PhaseChaitin::Register_Allocate() + 1309 (libjvm.dylib) [0x104961ee5]
1 PhaseChaitin::Split(unsigned int, ResourceArea*) + 2472 (libjvm.dylib) [0x104cd991c]
1 PhaseChaitin::Register_Allocate() + 1617 (libjvm.dylib) [0x104962019]
1 PhaseChaitin::Select() + 507 (libjvm.dylib) [0x104960ccb]
1 PhaseChaitin::bias_color(LRG&, int) + 602 (libjvm.dylib) [0x104960a70]
1 RegMask::find_first_elem() const + 165 (libjvm.dylib) [0x10484a86b]
1 Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool, bool) + 2284 (libjvm.dylib) [0x1049b4c38]
1 Compile::Optimize() + 175 (libjvm.dylib) [0x1049b1579]
1 PhaseIterGVN::optimize() + 53 (libjvm.dylib) [0x104cb996f]
1 PhaseIterGVN::transform_old(Node*) + 58 (libjvm.dylib) [0x104cb9e34]
1 RegionNode::Ideal(PhaseGVN*, bool) + 941 (libjvm.dylib) [0x10495e567]
1 RegionNode::is_unreachable_region(PhaseGVN*) const + 369 (libjvm.dylib) [0x10495dcaf]
3 GCTaskThread::run() + 417 (libjvm.dylib) [0x104a7949b]
2 OldToYoungRootsTask::do_it(GCTaskManager*, unsigned int) + 75 (libjvm.dylib) [0x104ccf5df]
2 CardTableExtension::scavenge_contents_parallel(ObjectStartArray*, MutableSpace*, HeapWord*, PSPromotionManager*, unsigned int, unsigned int) + 896 (libjvm.dylib) [0x104957e3a]
2 PSPromotionManager::drain_stacks_depth(bool) + 279 (libjvm.dylib) [0x104ccba9f]
2 PSPromotionManager::process_popped_location_depth(StarTask) + 115 (libjvm.dylib) [0x104ccca7f]
2 oopDesc* PSPromotionManager::copy_to_survivor_space<false>(oopDesc*) + 556 (libjvm.dylib) [0x104ccc760]
2 Copy::pd_disjoint_words(HeapWord*, HeapWord*, unsigned long) + 108 (libjvm.dylib) [0x10499d870]
2 _platform_memmove$VARIANT$Nehalem + 224 (libsystem_platform.dylib) [0x7fff781214e0]
2 <Non-Frontmost App, Kernel mode>
1 StealTask::do_it(GCTaskManager*, unsigned int) + 45 (libjvm.dylib) [0x104ccf6b9]
1 PSPromotionManager::drain_stacks_depth(bool) + 138 (libjvm.dylib) [0x104ccba12]
1 PSPromotionManager::process_popped_location_depth(StarTask) + 115 (libjvm.dylib) [0x104ccca7f]
1 oopDesc* PSPromotionManager::copy_to_survivor_space<false>(oopDesc*) + 556 (libjvm.dylib) [0x104ccc760]
1 Copy::pd_disjoint_words(HeapWord*, HeapWord*, unsigned long) + 108 (libjvm.dylib) [0x10499d870]
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1 <Kernel mode>
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2 Parker::park(bool, long) + 527 (libjvm.dylib) [0x104c8bd01]
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0x104800000 - 0x105016fef libjvm.dylib (1) <231D7825-F196-31D5-846D-5F71C71A24FB> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server/libjvm.dylib
0x1084ad000 - 0x108522ff7 libawt_lwawt.dylib (1) <69A7B6E0-185C-377D-B81C-5015C7FDBD6C> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/libawt_lwawt.dylib
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0x7fff51f42000 - 0x7fff52308ff3 com.apple.Foundation 6.9 (1454.96) <0DD43942-B183-3A39-BCDE-E3CCA0E4DE59> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
0x7fff77f47000 - 0x7fff77f6dff7 libsystem_kernel.dylib (4570.71.45) <939FEA3D-15A3-33E5-9476-789AF120C330> /usr/lib/system/libsystem_kernel.dylib
0x7fff78120000 - 0x7fff78127ff7 libsystem_platform.dylib (161.50.1) <6355EE2D-5456-3CA8-A227-B96E8F1E2AF8> /usr/lib/system/libsystem_platform.dylib
0x7fff78128000 - 0x7fff78133fff libsystem_pthread.dylib (301.50.1) <0E51CCBA-91F2-34E1-BF2A-FEEFD3D321E4> /usr/lib/system/libsystem_pthread.dylib
Visvaldas Kairys
Jul 15, 2019, 5:03:43 AM7/15/19
to cytoscape-helpdesk
This is just to say, I upgraded High Sierra to Mojave; Cytoscape3.7.1 still didn't work. Then I uninstalled 3.7.1 and installed 3.6.1. It seems to work... for now.
Best regards,
Visvaldas
Visvaldas Kairys
Jul 15, 2019, 5:06:23 AM7/15/19
to cytoscape-helpdesk
Oops, that was too hasty.
After I quit working Cytoscape 3.6.1, then started again, and the GUI crashed again! Back to the same problem then...
Visvaldas
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