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binaries for R 4.3 x86_64

9 messages · Uwe Ligges, Simon Urbanek, Ken Knoblauch

Original
Ken 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
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 L?pine
 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/
Uwe Ligges
#
On 24.04.2023 14:41, Kenneth Knoblauch wrote:
Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.

Best,
Uwe Ligges
Ken 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 L?pine
 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 <ligges at statistik.tu-dortmund.de>
Envoy? : lundi 24 avril 2023 14:51
? : Kenneth Knoblauch; r-sig-mac at r-project.org
Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64
?
On 24.04.2023 14:41, Kenneth Knoblauch wrote:
Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.

Best,
Uwe Ligges
Ken 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 L?pine
 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
Envoy? : lundi 24 avril 2023 15:12
? : Uwe Ligges; r-sig-mac at 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 L?pine
?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 <ligges at statistik.tu-dortmund.de>
Envoy? : lundi 24 avril 2023 14:51
? : Kenneth Knoblauch; r-sig-mac at r-project.org
Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64
???
On 24.04.2023 14:41, Kenneth Knoblauch wrote:
Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure 
Simon will fix it soon, too.

Best,
Uwe Ligges
???
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
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
Ken Knoblauch
# 
Simon,

Thank you.

Ken

Kenneth Knoblauch
Inserm U1208
Stem-cell and Brain Research Institute
18 avenue du Doyen L?pine
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
http<http://www.sbri.fr/user/1453>s://sbri.fr/public-profile/63/single-member/
On 24 Apr 2023, at 23:27, Simon Urbanek <simon.urbanek at r-project.org> 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 <ligges at statistik.tu-dortmund.de> 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         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 L?pine
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 at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
      #
    

  


  

      
No, you have fixed the direct link to the binary, but further down the 
page there is a link "big-sur-x86_64" that actally point to thw wrong 
directory.
That is not yet fixed on the master.

Best,
Uwe

        
On 24.04.2023 23:19, Simon Urbanek wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
Ah, ok, thanks, It wasn't clear to me from the description, now also fixed.

Cheers,
Simon