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Warning message #4650

ale07alvarez opened this issue Jul 28, 2020 · 2 comments · Fixed by #4662

Warning message #4650

ale07alvarez opened this issue Jul 28, 2020 · 2 comments · Fixed by #4662


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ale07alvarez commented Jul 28, 2020

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
shared object ‘’ not found
Error: loading failed
Execution halted
ERROR: loading failed

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/data.table’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/data.table’

The downloaded source packages are in
R data.table package has been updated to NA (1.12.8)
Warning message:
In utils::install.packages(pkg, repos = repo, type = type, lib = lib, :
installation of package ‘data.table’ had non-zero exit status

# Minimal reproducible example

# Output of sessionInfo()

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ale07alvarez commented Jul 28, 2020

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.3 tools_3.6.3 data.table_1.12.8

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mattdowle commented Jul 28, 2020

Thanks. Seems the same as #4640. If you have time to wade through it all, it would help us anything you can work out. Otherwise, we'll try and get to it.
We don't know the fix yet. Is pkg-config installed and does it return 1 (see that issue for output). Perhaps try upgrading to R 4 for which the macos binary on CRAN appears to be available and passing. Our Travis OSX build here on GitHub is passing fine and I wonder if you can get the binary from that, or see what's different. Mind you, a binary built using R 4 won't work in R 3, so that probably doesn't help you.

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