Installing CRAN binary packages with R 4.0 installed from source crashes R
Thanks. Only seeing this after I sent my other email about also getting crashes when I use your conf.high-sierra-x86_64 settings. But of course I'm not on Catalina so my setting is not exactly the same as yours. Therefore I should conclude that the CRAN binaries are not meant for me. H.
On 4/2/20 01:34, Simon Urbanek wrote:
Herv?, "both" is a fairly recent addition and my guess would be that it has been guarded specifically since it is the default and installing binaries only works for the CRAN version. I didn't look at the new "both" code to see how it knows that it's the CRAN version - there is really no special "CRAN" flag. At some point we were guarding binary installs in general by checking the OS and R, but it was fragile - you could be building using the same system as we do and yet use a different compiler, so I think it's in general impossible unless we introduce some extra identification of the binaries. So, yes, if you compile R from sources yourself it is not guaranteed to be compatible with CRAN package binaries. Those are only built and tested with the CRAN R binary. Cheers, Simon
On 2/04/2020, at 7:47 PM, Herv? Pag?s <hpages at fredhutch.org> 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=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=1-DiLdDSQroIloL3L_LKjjvH_qEO6FioafafYgQlOec&s=7DtbiQ_hSodOXZfS86zwIWgG79R3q9TbA6wYXp9_Dps&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 -- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319