java Cytoscape 3.8.0启动时出现错误,R包RCy3无法使用

2nc8po8w  于 2023-05-12  发布在  Java
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当我启动Cytoscape 3.8.0时,我看到以下错误消息

然后我查看了任务历史记录,发现了许多错误,如下所示:

 couldn't find resource 'groupSettings.props' in jar.
 couldn't find resource 'layout.grid.props' in jar.
 couldn't find resource 'layout.hierarchical.props' in jar.
 couldn't find resource 'layout.circular.props' in jar.
 couldn't find resource 'layout.stacked-node-layout.props' in jar.
 couldn't find resource 'layout.attribute-circle.props' in jar.
 couldn't find resource 'layout.degree-circle.props' in jar.
 couldn't find resource 'layout.attributes-layout.props' in jar.
 couldn't find resource 'layout.kamada-kawai.props' in jar.
 couldn't find resource 'layout.fruchterman-rheingold.props' in jar.
 couldn't find resource 'layout.cose.props' in jar.
 couldn't find resource 'layout.isom.props' in jar.
 couldn't find resource 'layout.force-directed.props' in jar.
 couldn't find resource 'stringApp.props' in jar.
 couldn't find resource 'enrichmentmap.props' in jar.
 couldn't find resource 'layout.genemania-force-directed.props' in jar.

当我在R控制台中运行RCy3::cytoscapePing()时,我看到以下错误

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failed to connect to localhost port 1234: Connection refused

但是,Cytoscape 3.7.x顺利启动,RCy3::cytoscapePing()生成[1] "You are connected to Cytoscape!"。RCy3版本为2.4.6。对我来说,它看起来像一个java错误,因为Cytoscape 3.8.0使用java11,Cytoscape 3.7.x使用java 1.8。如何修复此错误?
whereis -b java产生java: /usr/bin/java /etc/java /usr/share/java /opt/jdk1.8.0_73/bin/java /usr/lib/jvm/java-8-oracle/bin/java /usr/lib/jvm/java-8-oracle/jre/bin/java /usr/lib/jvm/jdk-11.0.8/bin/java。java11显然是在这条路上。
update-alternatives --config java显示java11被选为默认Java。

Selection        Path                                     Priority   Status
  -------------------------------------------------------------------------------
     0            /usr/lib/jvm/java-8-oracle/jre/bin/java    1081      auto mode
     1            /usr/lib/jvm/java-8-oracle/jre/bin/java    1081      manual mode
   * 2            /usr/lib/jvm/jdk-11.0.8/bin/java           1         manual mode
vc9ivgsu

vc9ivgsu1#

如错误消息中所述,当弹出该对话框时,您需要重新启动Cytoscape。在此之前,Cytoscape不会监听端口1234。一旦你重新启动,对话框不再弹出,事情应该是好的。

mjqavswn

mjqavswn2#

打开Cytoscape应用程序,重新启动R,加载库(RCy 3)并添加options("cyRestApi"="http://localhost:1234"),并检查cytoscapePing ()是否正确,输出将是 * 您已连接到Cytoscape!*

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