Question: pathview: object 'bods' not found
gravatar for Shi-Xiang Wang
13 months ago by
China/Shanghai/ShanghaiTech. University
Shi-Xiang Wang0 wrote:

I use pathfindR package and find a problem related to pathview package.

Error in pathview::pathview( = genedata, gene.idtype = "SYMBOL",  : 
  object 'bods' not found
In addition: Warning messages:
1: In runpathfindR(RAinput, outputdir = "testdir") :
  There already is a directoy named "testdir". Changing to "testdir(1)" not to overwrite the previous results.
2: In inputprocessing(input, pvalthreshold, pin_path) :
  The gene column was turned into character from factor.
3: In data(bods) : data set ‘bods’ not found

I followed the suggestion by Author of package pathfindR and still cannot fix problem. I think the developer of pathview should fix source code of data() part in all functions.

pathview • 249 views
ADD COMMENTlink modified 3 months ago by anamaria0 • written 13 months ago by Shi-Xiang Wang0

It would be also helpful for the pathview maintainers if you included your sessionInfo() so they are aware what os system, version of R, and version of the package you are using.

ADD REPLYlink modified 13 months ago • written 13 months ago by shepherl ♦♦ 1.6k
Answer: pathview: object 'bods' not found
gravatar for anamaria
3 months ago by
London, United Kingdom
anamaria0 wrote:

As per here, this is a common issue and usually can be solved by unloading and loading the package:

detach("package:pathfindR", unload=TRUE)
detach("package:pathview", unload=TRUE)
ADD COMMENTlink written 3 months ago by anamaria0
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