GenomeInfoDb’ could not be loaded or installed
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ettore64 • 0
@ettore64-15533
Last seen 5 hours 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?

>library(minfi)
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:
    CRAN: https://cran.rstudio.com/

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 '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:  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
    ‘/private/var/folders/sp/d2rnn1m90dddcc13jjs_1k3m0000gn/T/RtmpcLXAD9/downloaded_packages’
Old packages: 'clue', 'cluster', 'mgcv', 'tibble'
Update all/some/none? [a/s/n]: 
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

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

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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!

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@herve-pages-1542
Last seen 4 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 https://cran.r-project.org/bin/macosx/), 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!

Cheers,

H.

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ettore64 • 0
@ettore64-15533
Last seen 5 hours 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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