failing to install the package org.Hs.eg.db in R (version 3.5.2 )
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1
Entering edit mode
biojun • 0
@biojun-20020
Last seen 2.6 years ago

When I tried to install the package org.Hs.eg.db in R (version 3.5.2), I met some problems which are listed as follows.

Do you have any suggestions?

Thank you.

> BiocManager::install('org.Hs.eg.db')
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’

trying URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz'
Content type 'application/gzip' length 77962833 bytes (74.4 MB)
downloaded 74.4 MB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'DBI'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'C:/Users/lijian/Documents/R/win-library/3.5/org.Hs.eg.db'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\lijian\AppData\Local\Temp\RtmpyW47IQ\downloaded_packages’
installation path not writeable, unable to update packages: class, codetools, mgcv
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
org.Hs.eg.db AnnotationDbi • 1.9k views
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1
Entering edit mode
@martin-morgan-1513
Last seen 11 weeks ago
United States

Try to correct the first problem reported, missing 'DBI', with

BiocManager::install("DBI")

Then if successful

BiocManager::install("AnnotationDbi")

and finally

BiocManager::install("org.Hs.eg.db")
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0
Entering edit mode

It works. Thank you.

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