英文:
Trouble installing Cytoscape for Ubuntu
问题
我正在尝试在我的Ubuntu系统（22.04）上安装Cytoscape 3.9。我已经通过OpenJDK和Adoptium链接安装了Java 17，但都没有成功。当我安装Cytoscape时，没有出现错误，并且顺利完成了向导。以下是运行系统要求检查器时的输出：
##### Cytoscape System Requirements Checker for Linux #####
- 目标Cytoscape版本：3.9.0
- 您的Shell：bash
===== 检查发行版 =====
- Linux发行版：Ubuntu
- 版本：22.04
- 目标平台：x86_64
- 通过：发行版 = Ubuntu
失败：不支持此Ubuntu版本：22.04
支持的版本包括：
- 14.04
- 14.10
- 15.04
- 15.10
- 16.04
- 16.10
- 17 04
- 17 10
- 18.04
- 18.10
- 20.04
- 21.04
===== 检查Java版本 =====
错误：“java”命令不可用
您需要设置PATH到$JAVA_HOME/bin。
您当前的$PATH：
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-openjdk/bin:/usr/lib/jvm/java-11-openjdk/bin:/usr/lib/jvm/java-17-openjdk/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin/java/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin
===== 检查$JAVA_HOME =====
- 通过：找到JAVA_HOME：/usr/lib/jvm/java-17-openjdk-amd64
===== 检查连接到Cytoscape App Store =====
- 检查连接到Cytoscape App Store...
apps.cytoscape.org具有地址xx.xx.xxx.xxx
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 50642 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
- 结果：200
- 成功！
----------------------------------------
您的系统仍然存在一些问题。
请修复这些问题，然后再次运行此脚本。
当我尝试运行Cytoscape时，桌面应用程序没有任何反应。当我尝试通过终端运行时，输出如下：
Unrecognized option: -Xdock:icon=./framework/cytoscape_logo_512.png
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
系统要求检查器说明我的Ubuntu版本不兼容，但我正在使用Cytoscape 3.10.0，而版本检查器是针对版本3.9.0的，这应该解释了这个问题。
编辑：运行java -version会给出正确的输出，所以我知道Java已经正确安装。
英文:
I am trying to install Cytoscape 3.9 for my Ubuntu system (22.04). I have installed Java 17 through OpenJDK as well as through the Adoptium link given on the installation page. Neither works. When I installed Cytoscape, I had no errors and went through the wizard without any issues. Here is the output I get when I run the system requirements checker:
##### Cytoscape System Requirements Checker for Linux #####
- Target Cytoscape version: 3.9.0
- Your Shell: bash
===== Checking Distribution =====
- Linux Distribution: Ubuntu
- Version: 22.04
- Target Platform: x86_64
- Pass: Distribution = Ubuntu
Fail: This Ubuntu version is not supported: 22.04
Supported versions are:
- 14.04
- 14.10
- 15.04
- 15.10
- 16.04
- 16.10
- 17 04
- 17 10
- 18.04
- 18.10
- 20.04
- 21.04
===== Checking Java Version =====
Error: "java" command is not available
You need to set PATH to $JAVA_HOME/bin.
Your current $PATH:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-openjdk/bin:/usr/lib/jvm/java-11-openjdk/bin:/usr/lib/jvm/java-17-openjdk/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin/java/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin
===== Checking $JAVA_HOME =====
- Pass: JAVA_HOME found: /usr/lib/jvm/java-17-openjdk-amd64
===== Checking Connection to Cytoscape App Store =====
- Checking connection to Cytoscape App Store...
apps.cytoscape.org has address xx.xx.xxx.xxx
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 50642 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
- Result: 200
- Success!
----------------------------------------
Your system still has some issues.
Please fix those and re-run this script again.
When I try to run Cytoscape, the desktop application does nothing. When I try to run through terminal, this is the output:
Unrecognized option: -Xdock:icon=./framework/cytoscape_logo_512.png
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
The requirements checker states that my Ubuntu version isn't compatible, however, I'm using Cytoscape 3.10.0 and the version checker is for version 3.9.0, which should explain this.
Edit: running java -version gives me the correct output. So I know java is installed correctly.
答案1
得分: 0
无论我如何将Java与Cytoscape组合使用，似乎都无法解决这个问题。对我来说，解决方案最终是我需要降级到Cytoscape 3.9.1和Java 11。这个版本的应用程序运行完美。
英文:
No matter what combination of Java I used with Cytoscape, nothing seemed to fix this issue. The solution for me ended up being that I needed to downgrade to Cytoscape 3.9.1 with Java 11. This version of the application runs perfectly.
答案2
得分: 0
你应该在终端中运行的是cytoscape.sh。对于3.10版本，你确实需要Java 17。-Xdock的问题将在3.10.1中修复。
-- scooter
英文:
What you run through the terminal, you should use cytoscape.sh. You do need Java 17 for 3.10. The -Xdock stuff will be fixed in 3.10.1.
-- scooter
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