Question: Pathview error: ran fine yesterday
gravatar for Epic Tinus
2.4 years ago by
Epic Tinus10
Epic Tinus10 wrote:

Hey, earlier today/yesterday pathview code ran fine. Right now getting this error

Error in UseMethod("select_") : 
  no applicable method for 'select_' applied to an object of class "c('OrgDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"
Error in `$<`(`*tmp*`, "labels", value = c("", "", "", "",  : 
  replacement has 105 rows, data has 122

Anyone any clue what this could be? As I said, all the code ran fine yesterday.

pathview • 625 views
ADD COMMENTlink modified 16 months ago by Martin Morgan ♦♦ 23k • written 2.4 years ago by Epic Tinus10

Could you please show us the code that produced this error?  Which version of Pathview do you use ?

ADD REPLYlink written 2.3 years ago by Lluís Revilla Sancho510

You have to make sure that dplyr is not masking the "source_" command.

Simply try this before your command to confirm:

detach("package:pathview", unload=TRUE)
detach("package:dplyr", unload=TRUE)


ADD REPLYlink written 18 months ago by tiroshamit0

Dear tiroshamit,

i cannot unload dplyr as i am using plotly as well. Where in the code is the source_ function defined so i can change its name?

Many thanks!

ADD REPLYlink written 16 months ago by hr2810
Answer: Pathview error: ran fine yesterday
gravatar for Martin Morgan
16 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Probably you have a script that says


and you need to specify that you are using the AnnotationDbi version of select(),


Probably the most robust solution is to adopt this practice for all function calls in packages -- fully specify the location of the function you use.

Another strategy is after loading dplyr etc you write

select <- AnnotationDbi::select

and make no further changes.

Another solution is to not say library(dplyr), but whenever you use a dplyr function say


If you need more help then post at least the command that leads to the error, ideally a fully reproducible example.

ADD COMMENTlink written 16 months ago by Martin Morgan ♦♦ 23k
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