Problem while uploading DESeq2 library
0
0
Entering edit mode
5 weeks ago
Amr ▴ 20

Problem while uploading DESeq2 library:

library(DESeq2) Loading required package: GenomicRanges Loading required package: GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’ Error: package ‘GenomeInfoDb’ could not be loaded

Please help Thanks in advance

DESeq2 R • 252 views
ADD COMMENT
0
Entering edit mode
 there is no package called ‘GenomeInfoDbData’

try installing that package. Then try loading package ‘GenomeInfoDb’

ADD REPLY
0
Entering edit mode

I tried to install GenomeInfoDbData by this below command:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GenomeInfoDbData")

I got that message although I cant find that directory C:\Users\Amr\AppData\Local\Temp\RtmpWiEsQe\downloaded_packages:

Error in setwd(exdir) : cannot change working directory Warning in install.packages(...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status

The downloaded source packages are in ‘C:\Users\Amr\AppData\Local\Temp\RtmpWiEsQe\downloaded_packages’ Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.1/library packages: nlme Old packages: 'IRanges', 'S4Vectors' Update all/some/none? [a/s/n]:

ADD REPLY
0
Entering edit mode

Have your tried to close and reload your R session ? After you can try to reinstall

ADD REPLY
0
Entering edit mode

Solved !! by run Rstudio as adminstrator and the packages are installed smoothly.

ADD REPLY
0
Entering edit mode

That is a problem. Every time you install a package, you will have to run Rstudio as admin. Try configuring user directory for library installation.

ADD REPLY

Login before adding your answer.

Traffic: 1811 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6