Question

Pathview error: ran fine yesterday

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Epic Tinus ▴ 10

@epic-tinus-12731

Last seen 7.5 years ago

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 `$<-.data.frame`(`*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 • 1.8k views

ADD COMMENT • link updated 6.6 years ago by Martin Morgan 25k • written 7.5 years ago by Epic Tinus ▴ 10

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

ADD REPLY • link 7.5 years ago Lluís Revilla Sancho ▴ 760

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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)
library(pathview)

ADD REPLY • link 6.7 years ago tiroshamit • 0

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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 REPLY • link 6.6 years ago hr281 • 0

score 0 · Answer 1 · 2018-06-01

Probably you have a script that says

select(...)

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

AnnotationDbi::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

dplyr::select(...)

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