GenomeInfoDb’ could not be loaded or installed
Entering edit mode
ettore64 • 0
Last seen 1 day ago
Istituto Superiore di Sanità /Rome

Hi all, I get a weird error. After R (4.0.5) and Rstudio fresh install on macos Sierra I reinstalled Bioconductor and then minfi and ChAMP packages for DNA methylation analysis. Note, I already had the packages working on the same mac with previous R versions, this was just meant to be an update, and currently have them working on my pc under R 4.0.4. Now when I load minfi or ChAMP I get an error message concerning GenomeInfoDb and GenomeInfoDbData. So I tried to install GenomeInfoDbData separately but the installation had a non-zero exit status. Any idea?

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

> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:

Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL ''
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:  1854 Done                    echo 'tools:::.install_packages()'
      1855 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
Old packages: 'clue', 'cluster', 'mgcv', 'tibble'
Update all/some/none? [a/s/n]: 
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

sessionInfo( )
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_2.24.1      S4Vectors_0.28.1    BiocGenerics_0.36.1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_4.0.5      tools_4.0.5         RCurl_1.98-1.3     
[5] bitops_1.0-6
GenomeInfoDbData • 164 views
Entering edit mode

This seems like it could be a system configuration issue. Would something like this thread help for installing the needed system dependency:

Entering edit mode

The thread you suggested helped me consider it could be a macos system issue, so I tried upgrading my system and solved my problem. Thanks!

Entering edit mode
Last seen 15 hours ago
Seattle, WA, United States

Looks like some Xcode related issue or something like that. But why would you install packages from source on a Mac? I don't know how you installed R but if you did this _the proper way_ (i.e. by using the official distribution from, install.packages() and BiocManager::install() should install Mac binaries by default. Doing so tends to spare people a lot of headache. It's also _much_ faster!



Entering edit mode
ettore64 • 0
Last seen 1 day ago
Istituto Superiore di Sanità /Rome

Well, it looks like it was a macos system issue. I upgraded macos Sierra to High Sierra and could install the minfi packages (including GenomeInfoDb and GenomeInfoDbData w/o problems. Thanks anyway for your suggestions!


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