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

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?

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

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Hi, I am also searching for this solution, and came across the following post. Just posting to be helpful for someone else.

https://support.bioconductor.org/p/9139604/#9139615

Copied from this post: " I think the easiest solution would be to update your version of R to the latest (4.1.1) and then reinstall the ggtree package.

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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This post does not fit the theme of this forum. Please ask this on https://support.bioconductor.org/

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3 months ago

The problem is that rvcheck v0.2.0 removed the function get_fun_from_pkg which clusterProfiler depends on. Until the package author removes this dependency you can install rvcheck v0.1.8 to get around the issue.

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This solution worked for me. Just FYI, the vresion is not v1.8.0, but v0.1.8 (rvcheck versions). I didn't check whether downgrading rvcheck breaks something else, though. To downgrade rvcheck:

require(devtools)
install_version("rvcheck", version = "0.1.8", repos = "http://cran.us.r-project.org")

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Thanks, I've corrected my post!