Question: failing to install the package org.Hs.eg.db in R (version 3.5.2 )
1
gravatar for biojun
9 months ago by
biojun0
biojun0 wrote:

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
annotationdbi org.hs.eg.db • 278 views
ADD COMMENTlink modified 9 months ago by Martin Morgan ♦♦ 24k • written 9 months ago by biojun0
Answer: failing to install the package org.Hs.eg.db in R (version 3.5.2 )
1
gravatar for Martin Morgan
9 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

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")
ADD COMMENTlink written 9 months ago by Martin Morgan ♦♦ 24k

It works. Thank you.

ADD REPLYlink written 9 months ago by biojun0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 200 users visited in the last hour