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Question: error in library(clusterProfiler)
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gravatar for nakanomasayuki265
4 months ago by
nakanomasayuki2650 wrote:

 

I would like to execute the clusterProfiler in R package.

But the following error message comes out.

How should I do to solve this problem?

Error: 'GSEA_internal' is not an exported object from 'namespace:DOSE'

Error: package or namespace load failed for ‘clusterProfiler’

R
ADD COMMENTlink modified 29 days ago by ningzhilin0 • written 4 months ago by nakanomasayuki2650

Are your packages from a consistent version of Bioconductor, and up-to-date? Try BiocInstaller::biocValid().

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 20k
0
gravatar for ningzhilin
29 days ago by
ningzhilin0
Shanghai
ningzhilin0 wrote:

I also have this problem!!! Have you solved it?

I use conda to install clusterProfiler after created a new env in python3 version.

When I use it:

(laplace) -bash-4.1$ R

 

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"

Copyright (C) 2016 The R Foundation for Statistical Computing

Platform: x86_64-pc-linux-gnu (64-bit)

 

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

 

  Natural language support but running in an English locale

 

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

 

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

 

> library(DOSE)

 

DOSE v3.2.0  For help: https://guangchuangyu.github.io/DOSE

 

If you use DOSE in published research, please cite:

Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

 

There were 24 warnings (use warnings() to see them)

> library(clusterProfiler)

Error : object ‘GSEA_internal’ is not exported by 'namespace:DOSE'

Error: package or namespace load failed for ‘clusterProfiler’

 

The problem comes

How should I do?

ADD COMMENTlink written 29 days ago by ningzhilin0
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