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cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
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mergeNetworks: Error: $ operator is invalid for atomic vectors #179

Closed veroniquevoisin closed 1 year ago

veroniquevoisin commented 2 years ago

Hi, I was using the mergeNetworks function and an error was thrown :Error: $ operator is invalid for atomic vectors However the merged network is created with no apparent issue. I'm just reporting it in case this feedback is helpful.

RCy3::mergeNetworks(c("mir20CBAML_1", "genemania"), "mir20CBAML", nodeKeys=c("name","query term")) Error: $ operator is invalid for atomic vectors

AlexanderPico commented 2 years ago

Thanks for reporting this, @veroniquevoisin!

yihangx commented 2 years ago

@AlexanderPico As Barry mentioned, this is related to https://cytoscape.atlassian.net/browse/CSD-668.

AlexanderPico commented 2 years ago

@yihangx Are you saying this is a cyrest issue that will be fixed when cyrest is updated? Or it is an RCy3 issue that is related to the other issue, but requires a fix to RCy3 code as well?

yihangx commented 2 years ago

@AlexanderPico I coordinated with Mike, and he said this is a cyrest issue. It will be fixed when cyrest is updated.

AlexanderPico commented 2 years ago

Great! We'll leave this open until we can confirm, but in the meantime, there isn't anything we can do in RCy3 to fix this.

melissaszy commented 1 year ago

Hello. I am currently facing this issue:

mergeNetworks(c("network1.sif", "network2.sif"), "merged_network") Error in res.data$SUID : $ operator is invalid for atomic vectors

Am I right to say that the merged_network is accurate and can be used despite the error message?

Cheers!

yihangx commented 1 year ago

@melissaszy If the merged network result is correct, then you do not need to worry.

melissaszy commented 1 year ago

@yihangx thank you for your help. the number of nodes and edges are correct, so I shall proceed and use the merged network. Thanks again!