Cytoscape 3.8.0启动时出现错误，R包RCy3无法与其配合使用

Question

当我启动Cytoscape 3.8.0时，我看到以下错误消息

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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，Cytoscape3.7.x可以顺利启动，RCy3::cytoscapePing()会生成[1] "You are connected to Cytoscape!"。RCy3版本为2.4.6。在我看来，这看起来像是一个java错误，因为Cytoscape 3.8.0使用的是java11，Cytoscape 3.7.x使用的是java 1.8。如何修复此错误？

whereis -b java生成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显然在前进的道路上。

update-alternatives --config java显示该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

Answer 1

正如错误消息中所述，当该对话框弹出时，您需要重新启动Cytoscape。在此之前，Cytoscape将不会侦听端口1234。一旦您重新启动，并且该对话框不再弹出，事情就会好起来。