R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
1
Entering edit mode
Dan • 10
@Dan-24445
Last seen 2 days ago

Hallo,

I need to analyze RNA-Seq data, and I have trouble when loading DESeq2, I get the error: package ‘GenomeInfoDb’ could not be loaded. I read some other comments that the library path might be the issue, but I am not sure how to do this on my MacBook Pro, I found only for PC.

Any help is appreciated. Thanks a lot, Dan


> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_2.24.1      S4Vectors_0.28.1    BiocGenerics_0.36.0 limma_3.46.0       

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3         RCurl_1.98-1.2      bitops_1.0-6       
> 


> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("GenomeInfoDb")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'GenomeInfoDb'
also installing the dependency ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/GenomeInfoDb_1.26.2.tgz'
Content type 'application/x-gzip' length 4025755 bytes (3.8 MB)
==================================================
downloaded 3.8 MB


The downloaded binary packages are in
    /var/folders/p9/r4271j_934z40lq4stc9276c0000gn/T//RtmpgM24FP/downloaded_packages
installing the source package ‘GenomeInfoDbData’

trying 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

Warning in file(con, "r") :
  cannot open file '/var/db/timezone/zoneinfo/+VERSION': No such file or directory
dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34:  1461 Done                    echo 'tools:::.install_packages()'
      1462 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
    ‘/private/var/folders/p9/r4271j_934z40lq4stc9276c0000gn/T/RtmpgM24FP/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

> 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


  > .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"''
error mac DESeq2 GenomeInfoDb R • 104 views
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@martin-morgan-1513
Last seen 3 days ago
United States

this sort of looks like a problem with your R installation. How did you install R?

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Hi Martin,

thanks for the reply. I downloaded the latest version from https://cran.r-project.org/bin/macosx/ Any suggestion is welcome, as I am stuck with it.

Many thanks, Dan

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I'm really not sure how to help, but I see that the error message includes Mac OS X 10.13 but from sessionInfo you have Running under: macOS Sierra 10.12.6 -- it seems like there is a version mismatch at the OS level, but i don't know how this would arise or how to solve it. `

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