date:20230424

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Kenneth Knoblauch

Simon,

Thank you.

Ken

Kenneth Knoblauch
Inserm U1208
Stem-cell and Brain Research Institute
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
https://sbri.fr/public-profile/63/single-member/

On 24 Apr 2023, at 23:27, Simon Urbanek  wrote:

This has been fixed a while time ago so I suspect the culprit are outdated 
mirrors. If in doubt, please use

https://mac.R-project.org/bin/macosx

which is the most up-to-date.

Cheers,
Simon



On Apr 25, 2023, at 12:51 AM, Uwe Ligges  
wrote:



On 24.04.2023 14:41, Kenneth Knoblauch wrote:
Hi,
I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to upgrade 
to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to 
be able to run later versions.  I was looking at the Mac binaries at the R for 
mac OS page and it looks like both links
big-sur-x86_64 and big-sur-arm64 lead to a page with header:
Index of /bin/macosx/big-sur-arm64
Is this just a heading error or is there a misdirect in the link?

Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon 
will fix it soon, too.

Best,
Uwe Ligges

The formalities:
sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5
Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
  LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Paris
tzcode source: internal
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
loaded via a namespace (and not attached):
[1] compiler_4.3.0
capabilities()
  jpeg pngtiff   tcltk X11aqua
http/ftp
  TRUETRUETRUETRUETRUETRUE
TRUE
   sockets  libxmlfifo  cledit   iconv NLS   
Rprof
  TRUE   FALSETRUETRUETRUETRUE
TRUE
   profmem   cairo ICU long.double libcurl
  TRUETRUETRUETRUETRUE
Thank you.
best,
Ken
  ___
 Kenneth Knoblauch
Inserm U1208
Stem-cell and Brain Research Institute
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
https://sbri.fr/public-profile/63/single-member/
   ___
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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Simon Urbanek

Kenneth,

type="mac.binary" is not appropriate as forces is only for old High-Sierra 
binaries which don't exist for R 4.3.0 anymore as that build is no longer 
supported. You should leave type="both" (default, recommended) or type="binary".

Cheers,
Simon



> On Apr 25, 2023, at 1:12 AM, Kenneth Knoblauch  
> wrote:
> 
> Thank you Uwe for the rapid response,
> 
> I tried: 
> 
> install.packages(p42[3], .libPaths()[1], repos = 
> "https://cran.r-project.org/bin/macosx/big-sur-x86_64/;, type = "mac.binary")
> 
> Warning: unable to access index for repository 
> https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3:
>  cannot open URL 
> 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES'
> 
> and
> 
> install.packages(p42[3], .libPaths()[1], repos = 
> "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3;, type = 
> "mac.binary")
> 
> Warning: unable to access index for repository 
> https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3:
>  cannot open URL 
> 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES'
> 
> and 
> 
> install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org;, 
> type = "mac.binary")
> 
> Warning: unable to access index for repository 
> https://cran.r-project.org/bin/macosx/contrib/4.3:
>  cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES'
> 
> where p42 was a character vector of the package names that I had installed 
> under 4.2
> 
> Any guidance would be greatly appreciated.
> 
> Thank you, in advance.
> 
> best,
> 
> Ken
> 
>  ___
>  Kenneth Knoblauch
> Inserm U1208
> Stem-cell and Brain Research Institute
> 18 avenue du Doyen Lépine
> 69500 Bron
> France
> tel: +33 (0)4 72 91 34 77
> fax: +33 (0)4 72 91 34 61
> portable: +33 (0)6 84 10 64 10
> https://sbri.fr/public-profile/63/single-member/
> 
> 
> 
> 
> 
> De : Uwe Ligges 
> Envoyé : lundi 24 avril 2023 14:51
> À : Kenneth Knoblauch; r-sig-mac@r-project.org
> Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64
> 
> 
> 
> On 24.04.2023 14:41, Kenneth Knoblauch wrote:
>> Hi,
>> 
>> I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to 
>> upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air 
>> doesn't seem to be able to run later versions.  I was looking at the Mac 
>> binaries at the R for mac OS page and  it looks like both links
>> 
>> big-sur-x86_64 and big-sur-arm64 lead to a page with header:
>> 
>> Index of /bin/macosx/big-sur-arm64
>> 
>> Is this just a heading error or is there a misdirect in the link?
> 
> Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
> Simon will fix it soon, too.
> 
> Best,
> Uwe Ligges
> 
>> 
>> The formalities:
>> 
>> sessionInfo()
>> R version 4.3.0 (2023-04-21)
>> Platform: x86_64-apple-darwin20 (64-bit)
>> Running under: macOS Monterey 12.6.5
>> 
>> Matrix products: default
>> BLAS:   
>> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
>>   LAPACK version 3.11.0
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> time zone: Europe/Paris
>> tzcode source: internal
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.3.0
>>> capabilities()
>>  jpeg pngtiff   tcltk X11aqua
>> http/ftp
>>  TRUETRUETRUETRUETRUETRUE
>> TRUE
>>   sockets  libxmlfifo  cledit   iconv NLS
>>Rprof
>>  TRUE   FALSETRUETRUETRUETRUE
>> TRUE
>>   profmem   cairo ICU long.double libcurl
>>  TRUETRUETRUETRUETRUE
>> 
>>Thank you.
>> 
>> best,
>> 
>> Ken
>> 
>>
>> ___
>> Kenneth Knoblauch
>>Inserm U1208
>>Stem-cell and Brain Research Institute
>>18 avenue du Doyen Lépine
>>69500 Bron
>>France
>>tel: +33 (0)4 72 91 34 77
>>fax: +33 (0)4 72 91 34 61
>>portable: +33 (0)6 84 10 64 10
>>https://sbri.fr/public-profile/63/single-member/
>>   
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Simon Urbanek

This has been fixed a while time ago so I suspect the culprit are outdated 
mirrors. If in doubt, please use

https://mac.R-project.org/bin/macosx

which is the most up-to-date.

Cheers,
Simon



> On Apr 25, 2023, at 12:51 AM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 24.04.2023 14:41, Kenneth Knoblauch wrote:
>> Hi,
>> I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to 
>> upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air 
>> doesn't seem to be able to run later versions.  I was looking at the Mac 
>> binaries at the R for mac OS page and it looks like both links
>> big-sur-x86_64 and big-sur-arm64 lead to a page with header:
>> Index of /bin/macosx/big-sur-arm64
>> Is this just a heading error or is there a misdirect in the link?
> 
> Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
> Simon will fix it soon, too.
> 
> Best,
> Uwe Ligges
> 
>> The formalities:
>> sessionInfo()
>> R version 4.3.0 (2023-04-21)
>> Platform: x86_64-apple-darwin20 (64-bit)
>> Running under: macOS Monterey 12.6.5
>> Matrix products: default
>> BLAS:   
>> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
>>   LAPACK version 3.11.0
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> time zone: Europe/Paris
>> tzcode source: internal
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> loaded via a namespace (and not attached):
>> [1] compiler_4.3.0
>>> capabilities()
>>jpeg pngtiff   tcltk X11aqua
>> http/ftp
>>TRUETRUETRUETRUETRUETRUE  
>>   TRUE
>> sockets  libxmlfifo  cledit   iconv NLS  
>>  Rprof
>>TRUE   FALSETRUETRUETRUETRUE  
>>   TRUE
>> profmem   cairo ICU long.double libcurl
>>TRUETRUETRUETRUETRUE
>>  Thank you.
>> best,
>> Ken
>>___
>>   Kenneth Knoblauch
>>  Inserm U1208
>>  Stem-cell and Brain Research Institute
>>  18 avenue du Doyen Lépine
>>  69500 Bron
>>  France
>>  tel: +33 (0)4 72 91 34 77
>>  fax: +33 (0)4 72 91 34 61
>>  portable: +33 (0)6 84 10 64 10
>>  https://sbri.fr/public-profile/63/single-member/
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Kenneth Knoblauch

Actually, I was able to update everything from source.  I initially didn't 
think that would work because of the need to update Xcode and gfortran, but it 
all worked and none of that was necessary.  Thanks.


best,

Ken


 
  
 
  ___
  Kenneth Knoblauch
 Inserm U1208
 Stem-cell and Brain Research Institute
 18 avenue du Doyen Lépine
 69500 Bron
 France
 tel: +33 (0)4 72 91 34 77
 fax: +33 (0)4 72 91 34 61
 portable: +33 (0)6 84 10 64 10
 https://sbri.fr/public-profile/63/single-member/





De : Kenneth Knoblauch
Envoyé : lundi 24 avril 2023 15:12
À : Uwe Ligges; r-sig-mac@r-project.org
Objet : RE: [R-SIG-Mac] binaries for R 4.3 x86_64
    
Thank you Uwe for the rapid response,

I tried: 

install.packages(p42[3], .libPaths()[1], repos = 
"https://cran.r-project.org/bin/macosx/big-sur-x86_64/;, type = "mac.binary")

Warning: unable to access index for repository  
https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3:
  cannot open URL 
'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES'

and

install.packages(p42[3], .libPaths()[1], repos = 
"https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3;, type = 
"mac.binary")

Warning: unable to access index for repository  
https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3:
  cannot open URL 
'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES'

and 

install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org;, 
type = "mac.binary")

Warning: unable to access index for repository  
https://cran.r-project.org/bin/macosx/contrib/4.3:
  cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES'

where p42 was a character vector of the package names that I had installed 
under 4.2

Any guidance would be greatly appreciated.

Thank you, in advance.

best,

Ken

  ___
  Kenneth Knoblauch
 Inserm U1208
 Stem-cell and Brain Research Institute
 18 avenue du Doyen Lépine
 69500 Bron
 France
 tel: +33 (0)4 72 91 34 77
 fax: +33 (0)4 72 91 34 61
 portable: +33 (0)6 84 10 64 10
 https://sbri.fr/public-profile/63/single-member/
    




De : Uwe Ligges 
Envoyé : lundi 24 avril 2023 14:51
À : Kenneth Knoblauch; r-sig-mac@r-project.org
Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64
    


On 24.04.2023 14:41, Kenneth Knoblauch wrote:
> Hi,
> 
> I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to 
> upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air 
> doesn't seem to be able to run later versions.  I was looking at the Mac 
> binaries at the R for mac OS page and   it looks like both links
> 
> big-sur-x86_64 and big-sur-arm64 lead to a page with header:
> 
> Index of /bin/macosx/big-sur-arm64
> 
> Is this just a heading error or is there a misdirect in the link?

Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.

Best,
Uwe Ligges

> 
> The formalities:
> 
> sessionInfo()
> R version 4.3.0 (2023-04-21)
> Platform: x86_64-apple-darwin20 (64-bit)
> Running under: macOS Monterey 12.6.5
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
>   LAPACK version 3.11.0
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> time zone: Europe/Paris
> tzcode source: internal
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.3.0
>> capabilities()
> jpeg png    tiff   tcltk X11    aqua    
>http/ftp
> TRUE    TRUE    TRUE    TRUE    TRUE    TRUE  
>  TRUE
>  sockets  libxml    fifo  cledit   iconv NLS  
> Rprof
> TRUE   FALSE    TRUE    TRUE    TRUE    TRUE  
>  TRUE
>  profmem   cairo ICU long.double libcurl
> TRUE    TRUE    TRUE    TRUE    TRUE
> 
>   Thank you.
> 
> best,
> 
> Ken
>    
>   
>    ___
>    Kenneth Knoblauch
>   Inserm U1208
>   Stem-cell and Brain Research Institute
>   18 avenue du Doyen Lépine
>   69500 Bron
>   France
>   tel: +33 (0)4 72 91 34 77
>   fax: +33 (0)4 72 91 34 61
>   portable: +33 (0)6 84 10 64 10
>   https://sbri.fr/public-profile/63/single-member/
>  
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
    
___
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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Kenneth Knoblauch

Thank you Uwe for the rapid response,

I tried: 

install.packages(p42[3], .libPaths()[1], repos = 
"https://cran.r-project.org/bin/macosx/big-sur-x86_64/;, type = "mac.binary")

Warning: unable to access index for repository 
https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3:
  cannot open URL 
'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES'

and

install.packages(p42[3], .libPaths()[1], repos = 
"https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3;, type = 
"mac.binary")

Warning: unable to access index for repository 
https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3:
  cannot open URL 
'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES'

and 

install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org;, 
type = "mac.binary")

Warning: unable to access index for repository 
https://cran.r-project.org/bin/macosx/contrib/4.3:
  cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES'

where p42 was a character vector of the package names that I had installed 
under 4.2

Any guidance would be greatly appreciated.

Thank you, in advance.

best,

Ken

  ___
  Kenneth Knoblauch
 Inserm U1208
 Stem-cell and Brain Research Institute
 18 avenue du Doyen Lépine
 69500 Bron
 France
 tel: +33 (0)4 72 91 34 77
 fax: +33 (0)4 72 91 34 61
 portable: +33 (0)6 84 10 64 10
 https://sbri.fr/public-profile/63/single-member/





De : Uwe Ligges 
Envoyé : lundi 24 avril 2023 14:51
À : Kenneth Knoblauch; r-sig-mac@r-project.org
Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64
    


On 24.04.2023 14:41, Kenneth Knoblauch wrote:
> Hi,
> 
> I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to 
> upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air 
> doesn't seem to be able to run later versions.  I was looking at the Mac 
> binaries at the R for mac OS page and  it looks like both links
> 
> big-sur-x86_64 and big-sur-arm64 lead to a page with header:
> 
> Index of /bin/macosx/big-sur-arm64
> 
> Is this just a heading error or is there a misdirect in the link?

Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.

Best,
Uwe Ligges

> 
> The formalities:
> 
> sessionInfo()
> R version 4.3.0 (2023-04-21)
> Platform: x86_64-apple-darwin20 (64-bit)
> Running under: macOS Monterey 12.6.5
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
>   LAPACK version 3.11.0
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> time zone: Europe/Paris
> tzcode source: internal
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.3.0
>> capabilities()
> jpeg png    tiff   tcltk X11    aqua    
>http/ftp
> TRUE    TRUE    TRUE    TRUE    TRUE    TRUE  
>  TRUE
>  sockets  libxml    fifo  cledit   iconv NLS  
> Rprof
> TRUE   FALSE    TRUE    TRUE    TRUE    TRUE  
>  TRUE
>  profmem   cairo ICU long.double libcurl
> TRUE    TRUE    TRUE    TRUE    TRUE
> 
>   Thank you.
> 
> best,
> 
> Ken
>    
>   
>    ___
>    Kenneth Knoblauch
>   Inserm U1208
>   Stem-cell and Brain Research Institute
>   18 avenue du Doyen Lépine
>   69500 Bron
>   France
>   tel: +33 (0)4 72 91 34 77
>   fax: +33 (0)4 72 91 34 61
>   portable: +33 (0)6 84 10 64 10
>   https://sbri.fr/public-profile/63/single-member/
>  
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

___
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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Uwe Ligges





On 24.04.2023 14:41, Kenneth Knoblauch wrote:

Hi,

I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to upgrade 
to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to 
be able to run later versions.  I was looking at the Mac binaries at the R for 
mac OS page and it looks like both links

big-sur-x86_64 and big-sur-arm64 lead to a page with header:

Index of /bin/macosx/big-sur-arm64

Is this just a heading error or is there a misdirect in the link?


Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.


Best,
Uwe Ligges



The formalities:

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Paris
tzcode source: internal

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.3.0

capabilities()

jpeg pngtiff   tcltk X11aqua
http/ftp
TRUETRUETRUETRUETRUETRUE
TRUE
 sockets  libxmlfifo  cledit   iconv NLS   
Rprof
TRUE   FALSETRUETRUETRUETRUE
TRUE
 profmem   cairo ICU long.double libcurl
TRUETRUETRUETRUETRUE

  Thank you.

best,

Ken
   
  
   ___

   Kenneth Knoblauch
  Inserm U1208
  Stem-cell and Brain Research Institute
  18 avenue du Doyen Lépine
  69500 Bron
  France
  tel: +33 (0)4 72 91 34 77
  fax: +33 (0)4 72 91 34 61
  portable: +33 (0)6 84 10 64 10
  https://sbri.fr/public-profile/63/single-member/
 
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[R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Kenneth Knoblauch

Hi,

I am upgrading to R 4.3.  and trying to upgrade the packages.  I had to upgrade 
to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to 
be able to run later versions.  I was looking at the Mac binaries at the R for 
mac OS page and it looks like both links

big-sur-x86_64 and big-sur-arm64 lead to a page with header:

Index of /bin/macosx/big-sur-arm64

Is this just a heading error or is there a misdirect in the link?

The formalities:

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
 
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Paris
tzcode source: internal

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

loaded via a namespace (and not attached):
[1] compiler_4.3.0
> capabilities()
   jpeg pngtiff   tcltk X11aqua
http/ftp 
   TRUETRUETRUETRUETRUETRUE
TRUE 
sockets  libxmlfifo  cledit   iconv NLS   
Rprof 
   TRUE   FALSETRUETRUETRUETRUE
TRUE 
profmem   cairo ICU long.double libcurl 
   TRUETRUETRUETRUETRUE 

 Thank you.

best,

Ken
  
 
  ___
  Kenneth Knoblauch
 Inserm U1208
 Stem-cell and Brain Research Institute
 18 avenue du Doyen Lépine
 69500 Bron
 France
 tel: +33 (0)4 72 91 34 77
 fax: +33 (0)4 72 91 34 61
 portable: +33 (0)6 84 10 64 10
 https://sbri.fr/public-profile/63/single-member/

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Re: [R-SIG-Mac] Problem installing RUcausal library on MAC

2023-04-24 Thread Prof Brian Ripley


On 24/04/2023 07:17, Simon Urbanek wrote:

Varin,

you're missing the Fortran compiler which the package requires. To make the 
life a bit easier on you, upgrade to R 4.3.0 and then install GNU Fortran from 
https://mac.r-project.org/tools/

If you don't want to upgrade R then you'll need the Fortran from here: 
https://github.com/R-macos/gcc-darwin-arm64/releases/tag/R-4.2.0-release


Or if you do have a gfortran installation which does not match that used 
for a binary installation of R you can use a ~/.R/Makevars file, as in 
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation 
.




Cheers,
Simon




On Apr 24, 2023, at 9:05 AM, varin sacha via R-SIG-Mac 
 wrote:

R-experts,

What is going wrong?

At the end of this page there is the installation command :
https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd

Working with a MAC, I have tried to install the RUcausal library (copy and 
paste the installation command).

It is written that the package has been built on Linux using the GNU Compiler 
Collection. To install the package, open an R instance and run:
install.packages('devtools') # required package
devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal')

I get this error message :

  ERROR: package installation failed
Error: Failed to install 'RUcausal' from Git:
  ! System command 'R' failed
0d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’



install.packages('devtools') # required package
--- Please select a CRAN mirror for use in this session ---
trying URL 
'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz'
Content type 'application/x-gzip' length 421790 bytes (411 KB)
==
downloaded 411 KB


The downloaded binary packages are in

/var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T//Rtmp7SUtUd/downloaded_packages

devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal')

Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal
'/usr/bin/git' clone --depth 1 --no-hardlinks 
https://gitlab.science.ru.nl/gbucur/RUcausal 
/var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T//Rtmp7SUtUd/file61a2a8e336a
── R CMD build 
──
─ installing the package to process help pages
  ---ges
─ installing *source* package ‘RUcausal’ ...
  ** using staged installation
  ** libs
  clang++ -arch arm64 -std=gnu++14 
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c 
RcppExports.cpp -o RcppExports.o
  clang++ -arch arm64 -std=gnu++14 
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c 
compute_DAG_probabilities_BGe_fast.cpp -o compute_DAG_probabilities_BGe_fast.o
  clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names 
-undefined dynamic_lookup -single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o 
RUcausal.so RcppExports.o compute_DAG_probabilities_BGe_fast.o 
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack 
-L/Library/Frameworks/R.framework/Resources/lib -lRblas 
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 
-L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath 
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
-Wl,CoreFoundation
  ld: warning: directory not found for option 
'-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
  ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
  ld: library not found for -lgfortran
  clang: error: linker command failed with exit code 1 (use -v to see 
invocation)
  make: *** [RUcausal.so] Error 1
  ERROR: compilation failed for package ‘RUcausal’
─ removing 
‘/private/var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’
  ---
  ERROR: package installation failed
Error: Failed to install 'RUcausal' from Git:
  ! System command 'R' failed
0d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’


Envoyé de mon iPhone
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Re: [R-SIG-Mac] 'Default' macos (x86) download URL now gone?

2023-04-24 Thread Simon Urbanek

Dirk,

thanks - the problem is that there is not a single installer package (for 
several years now), so that URL is ambiguous. Whether the missing link is a 
good or bad depends on how it is used. I would argue that any link to that URL 
is inherently bad, because there is no way of knowing that the link works for a 
particular system - that's why I have originally removed it with the R 4.3.0 
release. I have restored it now, making it point to the R 4.3.0 arm64 release 
since that is arguably the closest to a single "latest R". R releases have not 
been stored in /bin/macosx since 2015, so anyone using a link there is asking 
for trouble.

For any CI I would strongly recommend using the "last-success" links: 
https://mac.r-project.org/big-sur/last-success/ in particular the .xz versions 
are they are specifically designed to be used by CI (small download, fast and 
localized install).

Cheers,
Simon

> On 24/04/2023, at 3:25 AM, Dirk Eddelbuettel  wrote:
> 
> 
> The URL ${CRAN}/bin/macosx/R-latest.pkg is in fairlt widespread use. A quick
> Google query [1] reveals about 1.1k hits. And it happens to be used too in a
> CI job a colleague noticed failing yesterday.
> 
> The bin/macosx/ page now prominently displays both leading flavours
>  R-4.3.0-arm64.pkg
>  R-4.3.0-x86_64.pkg
> which makes sense give the architecture choices. We can of course update the
> CI script, and likely will.
> 
> But given that this was apparently a somewhat widely-used URL to fetch R on
> macOS, may I suggest that the convenience link be reestablished as a courtesy?
> 
> Best,  Dirk
> 
> https://github.com/search?q=macosx%2FR-latest.pkg=code
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> 

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Re: [R-SIG-Mac] Problem installing RUcausal library on MAC

2023-04-24 Thread Simon Urbanek

Varin,

you're missing the Fortran compiler which the package requires. To make the 
life a bit easier on you, upgrade to R 4.3.0 and then install GNU Fortran from 
https://mac.r-project.org/tools/

If you don't want to upgrade R then you'll need the Fortran from here: 
https://github.com/R-macos/gcc-darwin-arm64/releases/tag/R-4.2.0-release

Cheers,
Simon



> On Apr 24, 2023, at 9:05 AM, varin sacha via R-SIG-Mac 
>  wrote:
> 
> R-experts,
> 
> What is going wrong?
> 
> At the end of this page there is the installation command :
> https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd 
> 
> Working with a MAC, I have tried to install the RUcausal library (copy and 
> paste the installation command).
> 
> It is written that the package has been built on Linux using the GNU Compiler 
> Collection. To install the package, open an R instance and run:
> install.packages('devtools') # required package
> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal')
> 
> I get this error message :
> 
>  ERROR: package installation failed
> Error: Failed to install 'RUcausal' from Git:
>  ! System command 'R' failed
> 0d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’
> 
> 
> 
> install.packages('devtools') # required package
> --- Please select a CRAN mirror for use in this session ---
> trying URL 
> 'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz'
> Content type 'application/x-gzip' length 421790 bytes (411 KB)
> ==
> downloaded 411 KB
> 
> 
> The downloaded binary packages are in
>
> /var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T//Rtmp7SUtUd/downloaded_packages
>> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal')
> Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal
> '/usr/bin/git' clone --depth 1 --no-hardlinks 
> https://gitlab.science.ru.nl/gbucur/RUcausal 
> /var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T//Rtmp7SUtUd/file61a2a8e336a
> ── R CMD build 
> ──
> ─ installing the package to process help pages
>  ---ges
> ─ installing *source* package ‘RUcausal’ ...
>  ** using staged installation
>  ** libs
>  clang++ -arch arm64 -std=gnu++14 
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>  
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>  -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall 
> -pedantic -c RcppExports.cpp -o RcppExports.o
>  clang++ -arch arm64 -std=gnu++14 
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>  
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>  -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall 
> -pedantic -c compute_DAG_probabilities_BGe_fast.cpp -o 
> compute_DAG_probabilities_BGe_fast.o
>  clang++ -arch arm64 -std=gnu++14 -dynamiclib 
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module 
> -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib 
> -L/opt/R/arm64/lib -o RUcausal.so RcppExports.o 
> compute_DAG_probabilities_BGe_fast.o 
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack 
> -L/Library/Frameworks/R.framework/Resources/lib -lRblas 
> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 
> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
>  ld: warning: directory not found for option 
> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>  ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
>  ld: library not found for -lgfortran
>  clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>  make: *** [RUcausal.so] Error 1
>  ERROR: compilation failed for package ‘RUcausal’
> ─ removing 
> ‘/private/var/folders/t_/myv0vvms11g40d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’
>  ---
>  ERROR: package installation failed
> Error: Failed to install 'RUcausal' from Git:
>  ! System command 'R' failed
> 0d0bz2p4xg64gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal’
> 
> 
> Envoyé de mon iPhone
> ___
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Re: [R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

[R-SIG-Mac] binaries for R 4.3 x86_64

Re: [R-SIG-Mac] Problem installing RUcausal library on MAC

Re: [R-SIG-Mac] 'Default' macos (x86) download URL now gone?

Re: [R-SIG-Mac] Problem installing RUcausal library on MAC

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