Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
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@e41f4f96
Last seen 8 weeks 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 • 2.3k views
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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!

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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")

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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.

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5
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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")
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It works! Thank you ~

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Mike Smith ★ 5.2k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg / de.NBI

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.

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Thank you so much!!

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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!

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