Unable to run "library(DESeq2)" successfully
1
0
Entering edit mode
Hui • 0
@Hui-24711
Last seen 5 months ago

Hi guys, I am new to R and DESeq2. When I am trying to install DESeq2 in R4.0.3, I encountered below problem. When I run "library(DESeq2)", it says can not load the package of "GenomeInfoDbData", then I download the package of GenomeInfoDbData to my local disk, and choose to install from disk and install GenomeInfoDbData successfully , it still tell me can not load that package. Sorry I don't know how to change the language setting back to English. Any advices? Thank you!

Code should be placed in three backticks as shown below


> library("DESeq2")
载入需要的程辑包:GenomicRanges
载入需要的程辑包:GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 不存在叫‘GenomeInfoDbData’这个名字的程辑包
错误: 无法载入程辑包‘GenomeInfoDb’
> utils:::menuInstallLocal()
程序包‘GenomeInfoDb’打开成功,MD5和检查也通过
> library(DESeq2)
载入需要的程辑包:GenomicRanges
载入需要的程辑包:GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 不存在叫‘GenomeInfoDbData’这个名字的程辑包
错误: 无法载入程辑包‘GenomeInfoDb’

sessionInfo( )
DESeq2 • 224 views
ADD COMMENT
0
Entering edit mode

I have tried ,same failure

> BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

试开URL’https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GenomeInfoDbData_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10673545 bytes (10.2 MB)
downloaded 10.2 MB


The downloaded source packages are in
        ‘E:\360MoveData\Users\luohu\Documents\RtmpUlInNN\downloaded_packages’
Old packages: 'Matrix'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is
  later:
       binary source needs_compilation
Matrix 1.2-18  1.3-2              TRUE

  Binaries will be installed
试开URL’https://mirrors.nics.utk.edu/cran/bin/windows/contrib/4.0/Matrix_1.2-18.zip'
Content type 'application/zip' length 4506373 bytes (4.3 MB)
downloaded 4.3 MB

package ‘Matrix’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        E:\360MoveData\Users\luohu\Documents\RtmpUlInNN\downloaded_packages
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
ADD REPLY
0
Entering edit mode
swbarnes2 ▴ 800
@swbarnes2-14086
Last seen 6 hours ago
San Diego

library() does not install packages. It just loads them after they are already installed.

You want

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

BiocManager::install("DESeq2")
ADD COMMENT
0
Entering edit mode

very useful information. Thank you for sharing! friday night funkin

ADD REPLY

Login before adding your answer.

Traffic: 621 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