Question

Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'

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R user Muuchi • 0

@e41f4f96

Last seen 3.1 years ago

United States

Hi, the following problem happens when using clusterProfiler in R.

I don't know how to solve it.

Can someone please tell me how to do this? Does the update of "rvcheck' affect the operation?

Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'

get_fun_from_pkg clusterProfiler rvcheck • 9.8k views

ADD COMMENT • link updated 2.9 years ago by Samanwoy • 0 • written 3.1 years ago by R user Muuchi • 0

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Hi!

Same error for me.

Error: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck' Execution halted ERROR: lazy loading failed for package ‘clusterProfiler’

My R version is 4.0.3

Thanks!

ADD REPLY • link 3.1 years ago mjlopez • 0

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You can install an old version of "rvcheck", then the problem will be solved. My R version is also 4.0.3, and I installed version 0.1.3("rvcehck")

ADD REPLY • link 3.1 years ago yinliangying • 0

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Hi, I'm having a same problem with the 4.0.3 version of R. How did you download the older version 0.1.3 of rvcheck? I tried multiple ways.

ADD REPLY • link 3.0 years ago Chan • 0

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This works for me.


packageurl <- "https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
remove.packages("clusterProfiler")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("clusterProfiler")

ADD REPLY • link 3.0 years ago Vince Schulz ▴ 160

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It works! Thank you ~

ADD REPLY • link 3.0 years ago JunWang • 0

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Hi, Vince thank you so much, I was able to install clusterProfiler_3.14.3 with the method you provided for my

R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

ADD REPLY • link 2.9 years ago Samanwoy • 0

score 1 · Answer 1 · 2021-09-29

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Mike Smith ★ 6.6k

@mike-smith

Last seen 20 minutes ago

EMBL Heidelberg

I think this is probably the same problem seen in ggtree install The solution there was to update the version of R to use a more up-to-date set of Bioconductor packages.

For more details on why it's happening I'll quote my answer to that question, which relates to a slightly different combinations of packages and functions, but the sentiment is the same.

The reason you're running into this error is because the latest version of rvcheck (0.2.0) has removed the get_aes_var function. The current ggtree version (3.0.4) is aware of this change, and doesn't look for it. However, because you're using an old version of R, you're using also using an old version of both Bioconductor and subsequently the ggtree package. This older version still thinks get_aes_var should be present, and then fails when it isn't.

ADD COMMENT • link 3.1 years ago Mike Smith ★ 6.6k

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Thank you so much!!

ADD REPLY • link 3.1 years ago R user Muuchi • 0

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I updated R to versoin 4.2 but still met the same error when library(clusterProfiler). Well R 4.1 worked!

ADD REPLY • link 3.1 years ago mmcui0018 • 0