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R 3.4.3 binaries

15 messages · Luis Puerto, Uwe Ligges, Federico Calboli +6 more

Original
Federico Calboli
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Hi All,

I know that I can get the latest and greatest binaries from http://r.research.att.com/ but I am puzzled why there are still no OSX R 3.4.3 binaries on CRAN.  The Windows installer has been up a few days already.  Is there anything I am missing concerning this delay?  

Cheers

F
Peter Dalgaard
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I would guess that either Uwe/CRAN is swamped or Simon is traveling to NZ, or both... 

-pd

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Luis Puerto
    

    

      
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Hi Federico, 

I know that it isn?t recommended by R Core Group, but you can always instal it from source using Homebrew. I?ve believe that there is even a bottle already and you don?t need to compile. I?m not sure. 

I?ve using a pure Homebrew install in my Mac and runs faster then the CRAN one, with openBlas and OpenMP.

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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On 06.12.2017 11:22, peter dalgaard wrote:

            

      
      
      
    

        
Yes, both, but not related to this issue. ;-)

            

      
      
      
    

        
You have to ask Simon, CRAN simply mirrors from his site.

Best,
Uwe

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Federico Calboli
    

    

      
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Well, fist off thanks to Uwe and Simon for their work ? my question was motivated by concern of a last minute issue caused by High Sierra, which I am finding riddled with bugs.

Cheers

F

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
--
Federico Calboli
Ecological Genetics Research Unit
Department of Biosciences
PO Box 65 (Biocenter 3, Viikinkaari 1)
FIN-00014 University of Helsinki
Finland

federico.calboli at helsinki.fi

  
  


  


      

    

    

      
      

        


  

        

      Luis Puerto
    

    

      
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I?ve under High Sierra and I?ve noticed zero issues on my install. I want to stress that I?ve in particularly noticed zero issues. Perhaps we use different R packages and use it in different way. :)

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
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Homebrew is not particularly unrecommended either, but you could get in trouble with compatibility vs. CRAN package binaries. "Unsupported" is more precise: None of us are trying these builds so if they break, you could be on your own. (From the Open Source perspective, the more people who know how to deal with R at source code level, the better; and homebrew does appear to have a substantially better reputation than the older MacPorts system did.)

  
  


  


      

    

    

      
      

        


  

        

      Luis Puerto
    

    

      
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You?re right Peter. At least from my perception, I?m quite novice, Homebrew is quite good covered and supported. Besides, right now R is part of Homebrew core, so there is a good amount of people taking care of the installation scripts. I?ve had myself some problems in the past, and rJava and Java, like any other installation, give you problems from time to time. But usually are they are fixed in a couple of days. 

It?s very true that if you use the Homebrew to install R, you aren?t free of problems down that road, and you need to know more or less what are you doing. When you compile R you need to compile most of the packages you download and sometimes there is problems from time to time. 

Anyhow, I agree, that the more people knowing R at lower level the better. 

There are several tutorials out there about how to install R with Homebrew and get you what some people call a ?100% Homebrew R Edition?. I want to write my own soon since there is none there for High Sierra. 

If people is interested I can share here too. 

Finally, have a good Finnish Independence and Spanish Constitution day to you all. 

Best Regards
Luis Puerto
http://luisspuerto.net

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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Hi,

FWIW, the key R related issue with High Sierra, fixed in 3.4.3, relates to the setting of the time zone in R.

An easy work around was posted some time ago, which is to put:

  Sys.setenv(TZ = "YourTime/Zone")

in your ~/.Rprofile, so that the TZ is set with a new R session.

A list of TZ's is available here:

  https://en.wikipedia.org/wiki/List_of_tz_database_time_zones <https://en.wikipedia.org/wiki/List_of_tz_database_time_zones>

Regards,

Marc Schwartz

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Balamuta, James Joseph
    

    

      
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Greetings and Salutations All,

First off, I want to say I really appreciate all the work that goes into making R available on macOS. I realize that this is a time intensive process. However, this is now the second consecutive time the macOS binary release has lagged behind other platforms. As a result, would it be possible to add another maintainer? Even more so, could we please update the macOS section of CRAN to reflect the present status of the build? Some information is severely outdated. In particular, on the tools page, there still is a link to gfortran-4.2.3 ? which hasn?t been used since R 3.0.0 (?) --  and an installer for the custom compiler clang4 toolchain has yet to appear. If there is a public repository or a means to submit a patch to address these issues I would be more than happy to help since the current setup greatly impacts being able to introduce students to HPC and interfacing with external libraries. 

Sincerely,

JJB

        
On 12/6/17, 4:22 AM, "R-SIG-Mac on behalf of peter dalgaard" <r-sig-mac-bounces at r-project.org on behalf of pdalgd at gmail.com> wrote:

        
I would guess that either Uwe/CRAN is swamped or Simon is traveling to NZ, or both... 
    
    -pd

        
> On 6 Dec 2017, at 10:26 , Federico Calboli <federico.calboli at helsinki.fi> wrote:

        
> 
    > Hi All,
    > 
    > I know that I can get the latest and greatest binaries from http://r.research.att.com/ but I am puzzled why there are still no OSX R 3.4.3 binaries on CRAN.  The Windows installer has been up a few days already.  Is there anything I am missing concerning this delay?  
    > 
    > Cheers
    > 
    > F
    > 
    > _______________________________________________
    > R-SIG-Mac mailing list
    > R-SIG-Mac at r-project.org
    > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
    
    -- 
    Peter Dalgaard, Professor,
    Center for Statistics, Copenhagen Business School
    Solbjerg Plads 3, 2000 Frederiksberg, Denmark
    Phone: (+45)38153501
    Office: A 4.23
    Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
    
    _______________________________________________
    R-SIG-Mac mailing list
    R-SIG-Mac at r-project.org
    https://stat.ethz.ch/mailman/listinfo/r-sig-mac

  
  


  


      

    

    

      
      

        


  

        

      Marc Girondot
    

    

      
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Hi all,
Joseph... you seem to have all the expertize to be the new maintener ;)
Marc

Le 06/12/2017 ? 18:21, Balamuta, James Joseph a ?crit?:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Yes, that is true indeed, I am remote and I had connectivity issues to the build server. Please accept my apologies, I hope to have it sorted out soon.

Thanks,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Mario
    

    

      
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Hi all.

Here a Mac user tester if you need.

Saludos.

Mario

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
10 days later

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Of course everything is a public repository (all of R and CRAN is) and you can always submit a patch - but very few people do. We can only address issues that are known. The toolchain is well documented as well both on the CRAN page as well as in the manuals. If you don't bother to read either, there is very little we can do about it. The Fortran compiler you refer to is still provided for the Mavericks builds which are only few months old. If anyone has suggestions for improvements, we're more than happy to accomodate them, but unfortunately no one has been willing to put the effort into it - idle complaints are of no help at all. If you want to help, a good start would be to start contributing constructively.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Balamuta, James Joseph
    

    

      
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Greetings and Salutations Simon,

Thanks for the response.

            

      
      
      
    

        
I have no issue with spending time to fix different issues. I?ve written at length about solutions to issues that have arisen in relation to compiled code with macOS and actively work to support community packages.

However, I?m not sure how R/CRAN processes patches, bug tickets, or general help.

c.f. macOS toolchain documentation bug

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17331

If you could answer a few quick questions for me, I?ll try to start making improvements:

1. Is there a contributing document that describes the procedure regarding patch submission? 
a. I assume this would govern: https://svn.r-project.org/R/ 
2. If I wanted to update the macOS CRAN page, where is that repository? 
3. To coordinate or propose changes before implementing them, is there a good place to post?


Sincerely,

JJB

        
On 12/17/17, 11:40 PM, "Simon Urbanek" <r at dune.urbanek.info> wrote:

        
Of course everything is a public repository (all of R and CRAN is) and you can always submit a patch - but very few people do. We can only address issues that are known. The toolchain is well documented as well both on the CRAN page as well as in the manuals. If you don't bother to read either, there is very little we can do about it. The Fortran compiler you refer to is still provided for the Mavericks builds which are only few months old. If anyone has suggestions for improvements, we're more than happy to accomodate them, but unfortunately no one has been willing to put the effort into it - idle complaints are of no help at all. If you want to help, a good start would be to start contributing constructively.
    
    Cheers,
    Simon

        
> On 7/12/2017, at 6:21 AM, Balamuta, James Joseph <balamut2 at illinois.edu> wrote:

        
> 
    > Greetings and Salutations All,
    > 
    > First off, I want to say I really appreciate all the work that goes into making R available on macOS. I realize that this is a time intensive process. However, this is now the second consecutive time the macOS binary release has lagged behind other platforms. As a result, would it be possible to add another maintainer? Even more so, could we please update the macOS section of CRAN to reflect the present status of the build? Some information is severely outdated. In particular, on the tools page, there still is a link to gfortran-4.2.3 ? which hasn?t been used since R 3.0.0 (?) --  and an installer for the custom compiler clang4 toolchain has yet to appear. If there is a public repository or a means to submit a patch to address these issues I would be more than happy to help since the current setup greatly impacts being able to introduce students to HPC and interfacing with external libraries. 
    > 
    > Sincerely,
    > 
    > JJB
    > 
    > On 12/6/17, 4:22 AM, "R-SIG-Mac on behalf of peter dalgaard" <r-sig-mac-bounces at r-project.org on behalf of pdalgd at gmail.com> wrote:
    > 
    >    I would guess that either Uwe/CRAN is swamped or Simon is traveling to NZ, or both... 
    > 
    >    -pd
    >

        
>> On 6 Dec 2017, at 10:26 , Federico Calboli <federico.calboli at helsinki.fi> wrote:

        
>> 
    >> Hi All,
    >> 
    >> I know that I can get the latest and greatest binaries from http://r.research.att.com/ but I am puzzled why there are still no OSX R 3.4.3 binaries on CRAN.  The Windows installer has been up a few days already.  Is there anything I am missing concerning this delay?  
    >> 
    >> Cheers
    >> 
    >> F
    >> 
    >> _______________________________________________
    >> R-SIG-Mac mailing list
    >> R-SIG-Mac at r-project.org
    >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
    > 
    >    -- 
    >    Peter Dalgaard, Professor,
    >    Center for Statistics, Copenhagen Business School
    >    Solbjerg Plads 3, 2000 Frederiksberg, Denmark
    >    Phone: (+45)38153501
    >    Office: A 4.23
    >    Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
    > 
    >    _______________________________________________
    >    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