Unable to run "library(DESeq2)" successfully
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Hui • 0
@Hui-24711
Last seen 3.1 years 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 • 1.5k views
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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
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swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 11 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")
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