Couldn't load org.Hs.eg.db
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Chen ▴ 30
@3b92b260
Last seen 3.6 years ago
Hong Kong

Couldn't load org.Hs.eg.db

library(org.Hs.eg.db) Error: package or namespace load failed for ‘org.Hs.eg.db’: onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: Call: l$contains Error: $ operator is invalid for atomic vectors
org.Hs.eg.db • 6.5k views
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As you can see here (.onLoad failed in loadNamespace() for 'org.Hs.eg.db'), it is a recurrent problem since Monday...

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I'm having the same issue. Pathview, org.Mm.eg.db, and org.Hs.eg.db won't load anymore.

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@csoneson-7887
Last seen 18 hours ago
Switzerland

If this is happening in RStudio, it is likely an issue with the current version of RSQLite. See

for more details. Installing an older version of RSQLite (e.g. v2.2.5) should solve the problem for now.
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Thanks a lot

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None of these solutions worked for me, i.e., options(connectionsObserver = NULL) or remotes::install_version("RSQLite", version = "2.2.5")

I get the same error as before.

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Try restarting your R session, and make sure that you have the intended version of RSQLite installed (e.g. with packageVersion("RSQLite")).

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I'm having the same problem, It won't load. It installs fine but when I do library(org.Hs.eg.db) it won't load

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Did you try the suggested solutions mentioned in the posts above? I.e., restart your R session, then set options(connectionObserver = NULL) or install an old version of RSQLite.

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remotes::install_version("RSQLite", version = "2.2.5")

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This will work for my computor, and i thought it should be restarted after you install this package.

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I get this error when I try to install a previous version with R:

Error in download_version_url(package, version, repos, type) : version '2.2.5' is invalid for package 'RSQLite'

When I try to manually install 2.2.5 via R studio by first downloading the .tar file, it tells me that my R studio is not supporting the older version.

Any idea how I can fix this?

I would like to run ChIPseeker and I need the org.Hs.eg.db library..

EDIT: installing RSQLite version 2.2.4 worked for me and library is running again

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Hi, I've tried all of these things and am still having this problem.

library(org.Hs.eg.db) Error: package or namespace load failed for ‘org.Hs.eg.db’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors

library(pathview) Error: package or namespace load failed for ‘pathview’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors

Any suggestions? I am trying to run a KEGG pathway analysis

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Any follow-up on this?

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Maybe, I thought you should check your data. $ operator is invalid for atomic vectors.

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This worked for me: remotes::install_version("RSQLite", version = "2.2.5") and then just library(org.Hs.eg.db) with R version of 4.0.3

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