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
2条答案
按热度按时间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。
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!*