[R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

[Hervé Pagès]

FWIW I also get the same thing (i.e. R crashes on loading CRAN binary 
packages) if I configure R 4.0 alpha like here 
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4/conf.high-sierra-x86_64, 
that is, if all the compilers use -mmacosx-version-min=10.13 and I set 
--build=x86_64-apple-darwin17.0

In that case I end up with the following sessionInfo():

   > sessionInfo()
   R version 4.0.0 alpha (2020-04-01 r78132)
   Platform: x86_64-apple-darwin17.0 (64-bit)
   Running under: macOS Mojave 10.14.6

   Matrix products: default
   BLAS:   /Users/biocbuild/bbs-3.11-bioc/R/lib/libRblas.dylib
   LAPACK: /Users/biocbuild/bbs-3.11-bioc/R/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] stats     graphics  grDevices utils     datasets  methods   base

   loaded via a namespace (and not attached):
   [1] compiler_4.0.0

H.


On 4/1/20 23:47, Hervé Pagès wrote:
> Hi Simon,
> 
> After installing R 4.0 alpha from source on a macOS Mojave system, R 
> won't let me use type="both" to install CRAN packages. I get:
> 
>    Error in install.packages("rJava", type = "both", repos = 
> "https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=H0XG-BbaqC0wtDJVNafEVTuhS6RZzzjXrTCwAq3rYGg&s=iXhmlQ7VZsVt9PcHpO66FPP66TY_GHko8gQqVv_CCNw&e= 
> ") :
>      type == "both" can only be used on Windows or a CRAN build for macOS
> 
> OK so this suggests that the CRAN binary packages for R 4.0 are not 
> compatible with my R. Surprisingly though using type="mac.binary" 
> doesn't complain and lets me install these binaries. But then trying to 
> load them causes segfaults. I've tried this with rJava, Rcpp, ggplot2, 
> and doing library() on any of them crashes my session. Note that 
> installing all these packages from source works without any problem.
> 
> So my questions are: is it the case that CRAN binary packages are not 
> meant to be used with an R 4.0 installed from source? If yes then why 
> isn't type="mac.binary" blocking this like type="both" does?
> 
> Thanks,
> H.
> 
>  > sessionInfo()
> R version 4.0.0 alpha (2020-04-01 r78132)
> Platform: x86_64-apple-darwin18.7.0 (64-bit)
> Running under: macOS Mojave 10.14.6
> 
> Matrix products: default
> BLAS:   /Users/biocbuild/bbs-3.11-bioc/R/lib/libRblas.dylib
> LAPACK: /Users/biocbuild/bbs-3.11-bioc/R/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] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0
> 
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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