Hervé,
what Brian was referring to was
> .Platform$pkgType
[1] "mac.binary"
Cheers,
Simon
> On 2/04/2020, at 10:20 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
>
>
>
> 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
>>>>
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>>>>
>>>
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>>>
>
> --
> 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
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