系统检查器在MacOS大Sur上“无法访问”时失败

Question

我在MacOS Big上运行Cytoscapa3.9.1有困难。系统检查器在下列情况下失败：

############# Cytoscape System Requirements Checker for Mac ##############
Target Cytoscape version: 3.9.0
Your shell is bash
Compatible OS version found: 11.6
 - Pass: OS Version = 11.6.1
 - Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk-11.0.5.jdk
Fail: Java is not reachable.
Try re-installing Java 11.

我在输出中显示的位置安装了Java 11，它似乎很好：

$ /Library/Java/JavaVirtualMachines/jdk-11.0.5.jdk/Contents/Home/bin/java -version
java version "11.0.5" 2019-10-15 LTS
Java(TM) SE Runtime Environment 18.9 (build 11.0.5+10-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.5+10-LTS, mixed mode)

权限看起来是对的(这些权限在目录层次结构上都是一样的)：

$ ls -lh /Library/Java/JavaVirtualMachines/jdk-11.0.5.jdk/Contents/Home/bin/
total 6672
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jaotc
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jar
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jarsigner
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 java
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 javac
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 javadoc
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 javap
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jcmd
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jconsole
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jdb
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jdeprscan
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jdeps
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jhsdb
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jimage
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jinfo
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jjs
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jlink
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jmap
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jmod
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jps
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jrunscript
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jshell
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jstack
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jstat
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 jstatd
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 keytool
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 pack200
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 rmic
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 rmid
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 rmiregistry
-rwxr-xr-x  1 root  wheel   101K Oct  6  2019 serialver
-rwxr-xr-x  1 root  wheel   110K Oct  6  2019 unpack200

我还安装了几个最新的Java版本(我不确定这些版本是否导致了问题)：

$ ls /Library/Java/JavaVirtualMachines/
jdk-10.0.2.jdk      jdk-12.0.2.jdk      jdk-14.0.1.jdk      jdk1.8.0_181.jdk
jdk-11.0.5.jdk      jdk-13.0.2.jdk      jdk-17.0.1.jdk

默认情况是JDK17：

$ java -version
java version "17.0.1" 2021-10-19 LTS
Java(TM) SE Runtime Environment (build 17.0.1+12-LTS-39)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.1+12-LTS-39, mixed mode, sharing)

如果我直接从命令行调用cytoscape.sh，那么它似乎是试图在Java 8下运行：

$ ./cytoscape.sh 
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/cytoscape/launcher/internal/Launcher has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:495)

Answer 1

JAVA_HOME 3.9.1不会在JDK 17上运行。您需要设置您的以指向JDK 11的安装，并且应该可以正常工作。

-滑板车

Answer 2

我对Java也有类似的问题。如果其他人和我有同样的问题，我会在这里给出答案。我第一次来到这里是为了找出"How to set or change the default Java (JDK) version on macOS?“

在那里，您应该能够找到您想要使用的Java版本。然后设置JAVA_HOME变量

使用bash或zsh，可以设置JAVA_HOME环境变量，如下所示：

巴什实例

echo export "JAVA_HOME=\$(/usr/libexec/java_home -v 11.0.7)" >> ~/.bash_profile

或者在Zsh

echo export "JAVA_HOME=\$(/usr/libexec/java_home -v 11.0.7)" >> ~/.zshrc

在此之后重启终端。

您可以检查您的shell配置文件，并看到这一行已经添加到配置文件的末尾：

nano ~/.bash_profile

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.7.jdk/Contents/Home

在默认情况下，您还可以检查java是否映射到所需的Java版本：

java -version

在Mac上运行System脚本现在应该可以识别Java是正确安装的

./mac.sh

现在应该通过单击cytoscape.sh脚本来运行Cytoscape