Question

Couldn't load org.Hs.eg.db

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Chen ▴ 30

@3b92b260

Last seen 4.5 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 • 7.4k views

ADD COMMENT • link updated 4.5 years ago by Will • 0 • written 4.5 years ago by Chen ▴ 30

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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...

ADD REPLY • link 4.5 years ago Audrey • 0

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

ADD REPLY • link 4.5 years ago Michelle • 0

score 3 · Accepted Answer · 2021-04-14

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Charlotte Soneson ▴ 170

@csoneson-7887

Last seen 3 months 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.

ADD COMMENT • link 4.5 years ago Charlotte Soneson ▴ 170

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Thanks a lot

ADD REPLY • link 4.5 years ago Chen ▴ 30

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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.

ADD REPLY • link 4.5 years ago Michelle • 0

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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")).

ADD REPLY • link 4.5 years ago Charlotte Soneson ▴ 170

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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

ADD REPLY • link 4.5 years ago Sareh • 0

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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.

ADD REPLY • link 4.5 years ago Charlotte Soneson ▴ 170

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

ADD REPLY • link 4.5 years ago Xulei Huo • 0

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

ADD REPLY • link 4.5 years ago Xulei Huo • 0

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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

ADD REPLY • link 4.5 years ago Sina ▴ 10

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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

ADD REPLY • link 4.5 years ago R • 0

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Any follow-up on this?

ADD REPLY • link 4.5 years ago Alexander • 0

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

ADD REPLY • link 4.5 years ago Xulei Huo • 0

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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

ADD REPLY • link 4.5 years ago Will • 0