Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
Yeah I **guess** so. Even though a close look at ?.Platform doesn't
particularly help clarify the somewhat fuzzy concept of "default type"
or "preferred setting for options('pkgType')":
pkgType: character string, the preferred setting for
‘options("pkgType")’. Values ‘"source"’,
‘"mac.binary.el-capitan"’ and ‘"win.binary"’ are
currently in use.
> options("pkgType")
$pkgType
[1] "both"
Cheers,
H.
On 4/2/20 13:34, Simon Urbanek wrote:
Hervé,
what Brian was referring to was
.Platform$pkgType
[1] "mac.binary"
Cheers,
Simon
On 2/04/2020, at 10:20 PM, Hervé Pagès 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 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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo=dwNIQLeXMIf8EpV1P4Y7_Dy14ehDLhEXXodGF8S4pu8=
") :
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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--
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
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Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
Hervé,
what Brian was referring to was
> .Platform$pkgType
[1] "mac.binary"
Cheers,
Simon
> On 2/04/2020, at 10:20 PM, Hervé Pagès 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 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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo=dwNIQLeXMIf8EpV1P4Y7_Dy14ehDLhEXXodGF8S4pu8=
") :
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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>>> R-SIG-Mac@r-project.org
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo=y45lZ-rli7qQ2JViPRCfXMg9UUKbXNAZ8S5y5Kn3IAU=
>>>
>
> --
> 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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> R-SIG-Mac@r-project.org
>
Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
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 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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MSzgfKtoxGL_KkQlwrc2_nVNhirnKTu8bSZjbK7pWfo=dwNIQLeXMIf8EpV1P4Y7_Dy14ehDLhEXXodGF8S4pu8=
") :
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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--
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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Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
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.
Cheers,
Simon
On 2/04/2020, at 7:47 PM, 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://cran.r-project.org;) :
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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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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Re: [R-SIG-Mac] 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:
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.
Cheers,
Simon
On 2/04/2020, at 7:47 PM, 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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=1-DiLdDSQroIloL3L_LKjjvH_qEO6FioafafYgQlOec=7DtbiQ_hSodOXZfS86zwIWgG79R3q9TbA6wYXp9_Dps=
") :
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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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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Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=H0XG-BbaqC0wtDJVNafEVTuhS6RZzzjXrTCwAq3rYGg=iXhmlQ7VZsVt9PcHpO66FPP66TY_GHko8gQqVv_CCNw=
") :
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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Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
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.
Cheers,
Simon
> On 2/04/2020, at 7:47 PM, 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://cran.r-project.org;) :
>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://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
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[R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R
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://cran.r-project.org;) :
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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