On 4/2/20 02:05, Prof Brian Ripley wrote:
On 02/04/2020 09:34, Simon Urbanek wrote:
Hervé,
"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.
It is simple: type = 'both' has to know what the two types are. Only
the CRAN binaries have the default type set to "mac.binary": building
from the sources gives you a default type of "source". See ?.Platform.
AFAIK the CRAN binary has the default type set to "both".
Anyway knowing the defaults is interesting but only orthogonal to the
discussion.
H.
Cheers,
Simon
On 2/04/2020, at 7:47 PM, Hervé Pagès <hpa...@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=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo&s=dwNIQLeXMIf8EpV1P4Y7_Dy14ehDLhEXXodGF8S4pu8&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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo&s=y45lZ-rli7qQ2JViPRCfXMg9UUKbXNAZ8S5y5Kn3IAU&e=
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo&s=y45lZ-rli7qQ2JViPRCfXMg9UUKbXNAZ8S5y5Kn3IAU&e=
--
Hervé Pagès
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
