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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
24 stars 11 forks source link

java issue #68

Closed samoudj closed 5 years ago

samoudj commented 5 years ago

Hello, I got an error while executing the command:

java -jar aptasuite-0.9.4.jar

the error is Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.privateGetMethodRecursive(Class.java:3048) at java.lang.Class.getMethod0(Class.java:3018) at java.lang.Class.getMethod(Class.java:1784) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 7 more

thank you for your answers

drivenbyentropy commented 5 years ago

Hi, thank you for reporting this.

What Java version do you have? I cannot reproduce this error locally. Please make sure you adhere to the system requirement outlined here..

Please let me know if this does not solve your issue. Thanks!

samoudj commented 5 years ago

hi, thank you for your answer , theversion of java I am using is

openjdk version "1.8.0_191" OpenJDK Runtime Environment (build 1.8.0_191-8u191-b12-2ubuntu0.16.04.1-b12) OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode)

Le lun. 8 avr. 2019 à 23:19, drivenbyentropy notifications@github.com a écrit :

Hi, thank you for reporting this.

What Java version do you have? I cannot reproduce this error locally. Please make sure you adhere to the system requirement outlined here. https://github.com/drivenbyentropy/aptasuite/wiki/System-requirements.

Please let me know if this does not solve your issue. Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/drivenbyentropy/aptasuite/issues/68#issuecomment-481086279, or mute the thread https://github.com/notifications/unsubscribe-auth/AVoqAP1EuG9Tj1zhdznR7EivHz9I5QvAks5vfAbagaJpZM4cjfz8 .

drivenbyentropy commented 5 years ago

From what I can tell, this appears to be a local issue with your Java installation.

I just ran aptasuite-0.9.4 (downloaded precompiled from the release page) and it works just fine.

The best I can do is to recommend reinstalling/updating Java and see if this fixes the issue.

samoudj commented 5 years ago

Hello, can you please help a little more, I really installed everything but still the same error

Le mar. 9 avr. 2019 à 10:27, drivenbyentropy notifications@github.com a écrit :

From what I can tell, this appears to be a local issue with your Java installation.

I just ran aptasuite-0.9.4 (downloaded precompiled from the release page) and it works just fine.

The best I can do is to recommend reinstalling/updating Java and see if this fixes the issue.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/drivenbyentropy/aptasuite/issues/68#issuecomment-481275256, or mute the thread https://github.com/notifications/unsubscribe-auth/AVoqACod4B78VTZL0xnVN7W7rDo6CXVgks5vfKNGgaJpZM4cjfz8 .

drivenbyentropy commented 5 years ago

Can you run the following command and paste the output?

java -verbose:class -jar aptasuite-0.9.4.jar | grep commons-cli

Thanks!

samoudj commented 5 years ago

same error

Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.privateGetMethodRecursive(Class.java:3048) at java.lang.Class.getMethod0(Class.java:3018) at java.lang.Class.getMethod(Class.java:1784) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 7 more

Le mar. 9 avr. 2019 à 22:39, drivenbyentropy notifications@github.com a écrit :

Can you run the following command and paste the output?

java -verbose:class -jar aptasuite-0.9.4.jar | grep commons-cli

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/drivenbyentropy/aptasuite/issues/68#issuecomment-481510894, or mute the thread https://github.com/notifications/unsubscribe-auth/AVoqAD-0OH2K-woqTa_5Q21IIHQx6NG8ks5vfU7NgaJpZM4cjfz8 .

drivenbyentropy commented 5 years ago

I am not sure how to proceed from here as I cannot reproduce this issue on any of my development machines. Do you have a secondary computer you could try this on? Again, this issue points to a faulty Java installation which is out of the scope of this project.

One thing I noticed, is that you are running OpenJDK. You could try to install Oracles Java implementation. There are many howtos online on how to do this for Ubuntu.

I hope this helps.

samoudj commented 5 years ago

i installed oracle-java8-installer maven 3.3.9 openjfx

But still have the same error, could at list give what i have to install with the good order

Le mer. 10 avr. 2019 à 10:42, drivenbyentropy notifications@github.com a écrit :

I am not sure how to proceed from here as I cannot reproduce this issue on any of my development machines. Do you have a secondary computer you could try this on? Again, this issue points to a faulty Java installation which is out of the scope of this project.

One thing I noticed, is that you are running OpenJDK. You could try to install Oracles Java implementation. There are many howtos online on how to do this for Ubuntu.

I hope this helps.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/drivenbyentropy/aptasuite/issues/68#issuecomment-481720323, or mute the thread https://github.com/notifications/unsubscribe-auth/AVoqAHZLIwAu9UVOEryAspQEbaVIKdNRks5vffhygaJpZM4cjfz8 .

drivenbyentropy commented 5 years ago

Given that you mention Maven, are you trying to compile the project from source? If so, I would recommend against this as we provide precompiled versions of AptaSuite on the release page.

You should only require to extract the archive and run it, the prerequisites of which are either Oracles Java 1.8 or higher (which ships JavaFX) or openJDK + openJFX.

samoudj commented 5 years ago

Excellent!! it finally worked, I think the problem was with the compilation, thank you very very much

Le mer. 10 avr. 2019 à 13:18, drivenbyentropy notifications@github.com a écrit :

Given that you mention Maven, are you trying to compile the project from source? If so, I would recommend against this as we provide precompiled versions of AptaSuite on the release page https://github.com/drivenbyentropy/aptasuite/releases/download/v0.9.4/aptasuite-0.9.4.zip .

You should only require to extract the archive and run it, the prerequisites of which are either Oracles Java 1.8 or higher (which ships JavaFX) or openJDK + openJFX.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/drivenbyentropy/aptasuite/issues/68#issuecomment-481781957, or mute the thread https://github.com/notifications/unsubscribe-auth/AVoqAJR0EzyYEANzXbRshXDIiPqk0Zktks5vfhzggaJpZM4cjfz8 .

drivenbyentropy commented 5 years ago

Glad to hear!