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

[Hervé Pagès]

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 <hpages using 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: hpages using 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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319