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JRE Load Error on MacOS
Hi all,
I just downloaded the Protege app for Mac. When I try to start it, I get a "JRE Load Error"
java -version returns java version "11.0.11" 2021-04-20 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.11+9-LTS-194) Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.11+9-LTS-194, mixed mode)
OS is macOS 11.4
Has anyone else seen this? All suggestions/ideas welcome
Howard
This problem has been reported many times and isn't new. There's some problem with the used Java-Version (see this: https://github.com/protegeproject/protege/pull/846). But since the last release of Protege was in 2019, I don't think the developers are paying attention to issues and I wouldn't hope a fix soon. :/
My solution for now is to download the platform independent version of Protege and run it using the terminal (just run this script "/Protege-5.5.0/run.sh" inside the downloaded package)
@HowardLander do you by chance have an M1 mac? On my (intel) MacBook Pro with the latest macOS it works without problems. Protege uses its own (bundled) JRE so the version of Java that is installed on the system is irrelevant.
No, I have an intel mac, so I don't think that is the difference. I will probably try the solution suggested by @AneesHl
@HowardLander to get a little bit more info, could you try to launch the Protege app from the terminal. For this, just open the terminal, navigate to the Protege app folder (e.g., cd /Applications/Protégé.app) and run:
./Contents/MacOS/JavaAppLauncher
Do you see any output?
You can also test if the JRE bundled with Protege works:
./Contents/Plugins/JRE/Contents/Home/jre/bin/java -version
Hi Yevgeny
I did this
cd /Applications/Protege-5.5.0/Protégé.app
./Contents/MacOS/JavaAppLauncher
No output on the command line and this on the screen
[cid:b9551000-f6c9-44ba-84f9-f2f1fceb1b45]
I found the bundled JRE here:
/Applications/Protege-5.5.0/Protégé.app/Contents/Plugins/JRE/Contents/Home/jre/bin
The output was
java -version java version "11.0.11" 2021-04-20 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.11+9-LTS-194) Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.11+9-LTS-194, mixed mode)
which looks OK.
Hope this is helpful
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 5:09 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander to get a little bit more info, could you try to launch the Protege app from the terminal. For this, just open the terminal, navigate to the Protege app folder (e.g., cd /Applications/Protégé.app) and run:
./Contents/MacOS/JavaAppLauncher
Do you see any output?
You can also test if the JRE bundled with Protege works:
./Plugins/JRE/Contents/Home/jre/bin/java -version
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@HowardLander
java -version java version "11.0.11" 2021-04-20 LTS …
Looks like you run the java installed on the system, not the one from the JRE folder. You need to run:
./java -version
This is what I get:
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
Sorry about that:
./java -version java version "1.8.0_121" Java(TM) SE Runtime Environment (build 1.8.0_121-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 9:47 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander
java -version java version "11.0.11" 2021-04-20 LTS …
Looks like you run the java installed on the system, not the one from the JRE folder. You need to run:
./java -version
This is what I get:
ava version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/protegeproject/protege/issues/1027#issuecomment-931338571, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAJUNLJSYKGMYZNVM6GQKJDUERS57ANCNFSM5DCJYOPQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
OK, looks good!
Now from the /Contents/Java subfolder try to run the following command (just copy & paste in the terminal):
../Plugins/JRE/Contents/Home/jre/bin/java \
-classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
org.protege.osgi.framework.Launcher
I tried the command and it started Protege up just fine.
[cid:49cc2d53-8a02-4d11-83ff-fb0f6ef1c799]
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 10:01 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
OK, looks good! Now from the /Contents/Java subfolder try to run the following command (just copy & paste in the terminal):
../Plugins/JRE/Contents/Home/jre/bin/java
-classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar
org.protege.osgi.framework.Launcher
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Great!
So it looks like the app somehow does not find the JRE within the subfolder.
Just to double check, can you paste the content of the file ./Contents/Info.plist.
Oh, b.t.w., you screenshots are not attached in your messages (probably email replies with attachments do not work).
Sure, here it is. Hope I got it right. I would have attached the file, but I didn't know it that would work
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 11:02 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
Great! So it looks like the app somehow does not find the JRE within the subfolder. Just to double check, can you paste the content of the file ./Contents/Info.plist. Oh, b.t.w., you screenshots are not attached in your messages (probably email replies with attachments do not work).
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The file seems right.
Try installing Oracle JRE 1.8 and removing these two lines from ./Contents/Info.plist:
<key>JVMRuntime</key>
<string>JRE</string>
Then Protege should pick up the system java instead of the bundled one (just tried on my mac). Or maybe something was missing and it even stats working without modifying this file.
Hi Yevgeny,
The only problem with this idea is that I do have software on my machine that requires Java 11. Seems like the real problem is that the package isn't using the bundled JRE. Can we fix that somehow?
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 11:54 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
Try installing Oracle JRE 1.8https://www.java.com/en/download/manual.jsp and removing these two lines from ./Contents/Info.plist:
Then Protege should pick up the system java instead of the bundled one (just tried on my mac). Or maybe something was missing and it even stats working without modifying this file.
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@HowardLander
You can install several versions of java on your mac and easily switch between them by setting JAVA_HOME to whatever you need. See for example here.
I cannot reproduce your problem, so we need to diagnose it on your machine. ;-)
The next step (if the installed JRE works but the bundled still does not) would be to copy the installed JRE 1.8 to the Protege app and see if that would work.
Ok, I'll do it in the morning
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 6:22 PM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander You can install several versions of java on your mac and easily switch between them by setting JAVA_HOME to whatever you need. See for example herehttps://stackoverflow.com/a/24657630. I cannot reproduce your problem, so we need to diagnose it on your machine. ;-)
The next step (if the installed JRE works but the bundled still does not) would be to copy the installed JRE 1.8 to the Protege app and see if that would work.
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Hi Yevgeny,
I did install Java 1.8. I had to change the PATH variable as well as change JAVA_HOME, but when I took out the 2 lines in the plist Protege started as expected. Just to test, I put the 2 lines back into the plist and the original error resurfaced.
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, September 30, 2021 6:22 PM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander You can install several versions of java on your mac and easily switch between them by setting JAVA_HOME to whatever you need. See for example herehttps://stackoverflow.com/a/24657630. I cannot reproduce your problem, so we need to diagnose it on your machine. ;-)
The next step (if the installed JRE works but the bundled still does not) would be to copy the installed JRE 1.8 to the Protege app and see if that would work.
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I had to change the PATH variable as well as change JAVA_HOME
Hmm.. normally you do not need to change the path. The java executable in /usr/bin/java executes the version of java based on JAVA_HOME. Check the output of:
/usr/bin/java -version
Then set a different value for JAVA_HOME like in the link above
export JAVA_HOME=`/usr/libexec/java_home -v 1.8`
or
export JAVA_HOME=`/usr/libexec/java_home -v 11`
and try /usr/bin/java -version again. It should display the corresponding java version.
You should then remove the additional entries from PATH.
Now you can test if copying the installed Oracle JRE 1.8 to the Protege folder works. Please do:
mkdir -p /Applications/Protege-5.5.0/Protégé.app/Contents/Plugins/JRE18/Contents/Home/
cp -R /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home /Applications/Protege-5.5.0/Protégé.app/Contents/Plugins/JRE18/Contents/Home/jre
Then change the lines in Contents/Info.plist
<key>JVMRuntime</key>
<string>JRE</string>
to
<key>JVMRuntime</key>
<string>JRE18</string>
Protege should then pick up the JRE18 from the subfolder. If it starts then it means that the JRE provided in Protege was somehow broken. If not, then the JavaAppLauncher for some reasone does not pick up the JRE bundled with Protege.
@ykazakov Copying Java from MacOS into the Protété.app didn't fix the Problem. I'm still getting the same Error.
If on the other hand, I run the following as you suggested before (from inside /Contents/Java subfolder):
../Plugins/JRE/Contents/Home/jre/bin/java \ -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \ org.protege.osgi.framework.Launcher
Protégé starts normally using the newly copied Java.
Well, looks like JavaAppLauncher (or whatever it is using) is broken after all.
B.t.w., in your last command, you did not use the new JRE. With the new JRE it should start with ../Plugins/JRE18/.... I suppose it works as well as it does not involve JavaAppLauncher.
Perhaps the last attempt (in case something is wrong with paths or settings): can you create a new user in MacOS, switch to this user, download Protege, and try to run it there. I think the chances are slim because the system is the same, but who knows...
B.t.w., you wrote your MacOS version is 11.4. I assume it was the version when you opened the ticket because mine is 11.6. If not, maybe updating helps?
Copying Java from MacOS into the Protété.app didn't fix the Problem. I'm still getting the same Error.
Just to confirm: you also changed the lines in Info.plist right?
@ykazakov thanks for your replies.
I did use the new JRE because I just emptied the old JRE folder with copied into it the Java from MacOS and adjusted the command accordingly.
I created a new user now and installed Protégé but it still doesn't work.
I'm on macOS 11.6 now.
Yes tried both options for Info.plist, aka <key>JVMRuntime</key> <string>JRE18</string> and <key>JVMRuntime</key> <string>JRE</string>
running /usr/libexec/java_home -Voutputs:
Matching Java Virtual Machines (1): 1.8.0_302 (x86_64) "UNDEFINED" - "OpenJDK 8" /usr/local/Cellar/openjdk@8/1.8.0+302/libexec/openjdk.jdk/Contents/Home /usr/local/Cellar/openjdk@8/1.8.0+302/libexec/openjdk.jdk/Contents/Home
Running cat $JAVA_HOME outputs:
cat: /Library/Java/JavaVirtualMachines/jdk-16.0.1.jdk/Contents/Home: No such file or directory
@AneesHl @HowardLander are you talking about the same machine? ;-)
It is strange that /usr/libexec/java_home -V does not find the installed JDKs, in particular those in /Library/Java/JavaVirtualMachine/.
This is what I have got:
% /usr/libexec/java_home -V
Matching Java Virtual Machines (7):
17 (x86_64) "Azul Systems, Inc." - "Zulu 17.28.13" /Library/Java/JavaVirtualMachines/zulu-17.jdk/Contents/Home
16.0.1 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 16" /Library/Java/JavaVirtualMachines/adoptopenjdk-16.jdk/Contents/Home
11.0.12 (x86_64) "GraalVM Community" - "GraalVM CE 21.2.0" /Library/Java/JavaVirtualMachines/graalvm-ce-java11-21.2.0/Contents/Home
11.0.11 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 11" /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home
1.8.301.09 (x86_64) "Oracle Corporation" - "Java" /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
1.8.0_292 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 8" /Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home
1.8.0_282+07 (x86_64) "GraalVM Community" - "GraalVM CE 21.0.0.2" /Library/Java/JavaVirtualMachines/graalvm-ce-java8-21.0.0.2/Contents/Home
/Library/Java/JavaVirtualMachines/zulu-17.jdk/Contents/Home
Most JVMs that I use are installed by homebrew, but they are still placed for me in /LibraryJava/JavaVirtualMachines/. Maybe something is wrong in the way how java installations are discovered by the system? This could explain why the JRE located in Protege.app not found.
I would suggest to reinstall all Java versions and making sure that /usr/libexec/java_home -V prints the correct locations.
No we are not. I actually do not know @AneesHl. I think they are just another person having the same problem.
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, October 7, 2021 5:29 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@AneesHlhttps://github.com/AneesHl @HowardLanderhttps://github.com/HowardLander are you talking about the same machine? ;-)
It is strange that /usr/libexec/java_home -V does not find the installed JDKs, in particular those in /Library/Java/JavaVirtualMachine/. This is what I have got:
% /usr/libexec/java_home -V Matching Java Virtual Machines (7): 17 (x86_64) "Azul Systems, Inc." - "Zulu 17.28.13" /Library/Java/JavaVirtualMachines/zulu-17.jdk/Contents/Home 16.0.1 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 16" /Library/Java/JavaVirtualMachines/adoptopenjdk-16.jdk/Contents/Home 11.0.12 (x86_64) "GraalVM Community" - "GraalVM CE 21.2.0" /Library/Java/JavaVirtualMachines/graalvm-ce-java11-21.2.0/Contents/Home 11.0.11 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 11" /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home 1.8.301.09 (x86_64) "Oracle Corporation" - "Java" /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home 1.8.0_292 (x86_64) "AdoptOpenJDK" - "AdoptOpenJDK 8" /Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home 1.8.0_282+07 (x86_64) "GraalVM Community" - "GraalVM CE 21.0.0.2" /Library/Java/JavaVirtualMachines/graalvm-ce-java8-21.0.0.2/Contents/Home /Library/Java/JavaVirtualMachines/zulu-17.jdk/Contents/Home
Most JVMs that I use are installed by homebrew, but they are still placed for me in /LibraryJava/JavaVirtualMachines/. Maybe something is wrong in the way how java installations are discovered by the system? This could explain why the JRE located in Protege.app not found.
I would suggest to reinstall all Java versions and making sure that /usr/libexec/java_home -V prints the correct locations.
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No we are not. I actually do not know @AneesHl. I think they are just another person having the same problem. Howard …
Exactly, I've had the same problem for a while.
@HowardLander @AneesHl I see. At some point that became quite confusing as I did not check who is replying. ;-)
@HowardLander can you show us your output of /usr/libexec/java_home -V. Does it find all java versions installed on the system?
Hi Yevgeny,
Here is what I get:
(base) beast:~$ /usr/libexec/java_home -V Matching Java Virtual Machines (3): 11.0.11 (x86_64) "Oracle Corporation" - "Java SE 11.0.11" /Library/Java/JavaVirtualMachines/jdk-11.0.11.jdk/Contents/Home 1.8.301.09 (x86_64) "Oracle Corporation" - "Java" /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home 1.8.0_05 (x86_64) "Oracle Corporation" - "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home /Library/Java/JavaVirtualMachines/jdk-11.0.11.jdk/Contents/Home
Howard
From: Yevgeny Kazakov @.> Sent: Thursday, October 7, 2021 10:45 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander @AneesHlhttps://github.com/AneesHl I see. At some point that became quite confusing as I did not check who is replying. ;-)
@HowardLanderhttps://github.com/HowardLander can you show us your output of ,. Does it find all java versions installed on the system?
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@HowardLander Thanks! Looks good. Did you try to run Protege from another user?
@AneesHl Can you confirm that Protege starts fine (by double clicking on the Protege.app) if you remove the lines
<key>JVMRuntime</key>
<string>JRE</string>
from Contents/Info.plist?
I guess, currently this is the best workaround.
Nope, I haven't tried that. I'm at a conference today and tomorrow, maybe can try that Monday
From: Yevgeny Kazakov @.> Sent: Thursday, October 7, 2021 10:57 AM To: protegeproject/protege @.> Cc: Lander, Howard Michael @.>; Mention @.> Subject: Re: [protegeproject/protege] JRE Load Error on MacOS (#1027)
@HowardLanderhttps://github.com/HowardLander Thanks! Looks good. Did you try to run Protege from another user?
@AneesHlhttps://github.com/AneesHl Can you confirm that Protege starts fine (by double clicking on the Protege.app) if you remove the lines
from Contents/Info.plist?
I guess, currently this is the best workaround.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/protegeproject/protege/issues/1027#issuecomment-937874845, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAJUNLKXQFOE7GJKJZMNBMTUFWYPDANCNFSM5DCJYOPQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
@HowardLander Thanks! Looks good. Did you try to run Protege from another user?
@AneesHl Can you confirm that Protege starts fine (by double clicking on the Protege.app) if you remove the lines
<key>JVMRuntime</key> <string>JRE</string>from
Contents/Info.plist?I guess, currently this is the best workaround.
No this doesn't help, at least not on my machine. :(
@AneesHl did you also install Oracle JRE 1.8? https://github.com/protegeproject/protege/issues/1027#issuecomment-931449695