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Macports installation problem

13 messages · Rainer M Krug, David Winsemius, John +4 more

Original
John
# 
Hi,

   I tried to install Cairo graphics

https://www.cairographics.org/download/

   and I need to install Macports.

   I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
port install cairo", but it did not respond. I haven't seen any file name
or app called Macports, but one file called "port" which is located at

loca/bin/port"

   How should I do it?

   Thanks,

John
*******

Last login: Sun Oct 15 02:52:49 on console
Johns-MacBook-Pro:~ john$ /opt/local/bin/port ; exit;
MacPorts 2.4.2
Entering shell mode... ("help" for help, "quit" to quit)
[Users/john] > sudo port install cairo
Error: Unrecognized action "port sudo"
Rainer M Krug
# 
This is related to Macports and not to R - please post your question on their mailing list. If it would be about errors installing R, that would be different.

Cheers,

Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Z?rich

Cell:       +41 (0)78 630 66 57
email:      Rainer at krugs.de
Skype:      RMkrug

PGP: 0x0F52F982
David Winsemius
# 
I think using MacPorts might actually be the "error" that needs correction. I would suggest an alternate strategy. Go to http://r.research.att.com/libs/ and get the appropriate version of cairo, probably the most recent one. 

http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz

Scroll down to the bottom of that page and an appropriate modification of the two lines for unpacking to the root. 

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /


The Mac version of R does not do well with either MacPorts or homebrew installation of required system packages because those package managers put them in loaction that are not recognized by the static build that is the default.
Rainer M Krug
# 
Using homebrew (and as far as I know Macports as well) works without major problems. The problem start when you mix standard installations / homebrew / Macports. This results in problems. 

So: each of the approaches has it?s own pros and cons - it is only that homebrew and Macports are not officially supported by the R team.

Cheers,

Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Z?rich

Cell:       +41 (0)78 630 66 57
email:      Rainer at krugs.de
Skype:      RMkrug

PGP: 0x0F52F982
David Winsemius
# 
The fact that the original poster had obviously not used MacPorts (and perhaps did not even know what it was) suggests that the appropriate reply should be to discourage him from using it and offer a strategy with greater likelihood of success in combination with the more typical installation method for the Mac R fork.
One of the cons is that both homebrew and MacPorts requires a greater knowledge of the Unix under-pinnings of MacOS. If a poster is asking how to install MacPorts, it suggests that he don't already have such skills and perhaps doesn't even have the motivation to acquire them. (Your earlier response suggested that posting in R-SIG-Mac was the wrong way to do acquire such skills and I agree. Appears the poster has not yet developed the habit of reading supporting online documentation. He certainly did not do so regarding R-SIG-Mac. My opinion: A person who chooses not to read or heed online documentation should be actively discouraged from using either MacPorts of homebrew.) 

Best;
David.
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law
John
# 
Thanks, David and Rainer.

Where should I type them? On RStudio command line?

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /


I got this after typing in RStudio command line
http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
Error: unexpected symbol in "curl -O http"


J

2017-10-18 9:54 GMT-07:00 David Winsemius <dwinsemius at comcast.net>:

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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Those are Unix system functions, not R or RStudio functions. Do some reading regarding Unix bash and the MacOS Terminal.app

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dan Kelley
    

    

      
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John,

You could spin your wheels for a long time on this, because it seems that you lack some basic information, not related to R.  You best plan might be to drop consideration of R for a few weeks, to brush up on the basics. But, if just need to get R working for some particular one-off task, your should consider finding someone local you can help you in-person, in exchange for a coffee / beer / lunch.

Dan Kelley

        
On Oct 18, 2017, at 11:39 PM, David Winsemius <dwinsemius at comcast.net<mailto:dwinsemius at comcast.net>> wrote:

        

        
On Oct 18, 2017, at 6:09 PM, John <miaojpm at gmail.com<mailto:miaojpm at gmail.com>> wrote:

        
Thanks, David and Rainer.

Where should I type them? On RStudio command line?

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

Those are Unix system functions, not R or RStudio functions. Do some reading regarding Unix bash and the MacOS Terminal.app

--
David.


I got this after typing in RStudio command line
curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
Error: unexpected symbol in "curl -O http"


J

2017-10-18 9:54 GMT-07:00 David Winsemius <dwinsemius at comcast.net<mailto:dwinsemius at comcast.net>>:

        
On Oct 18, 2017, at 8:40 AM, Rainer Krug <rainer_krug at icloud.com<mailto:rainer_krug at icloud.com>> wrote:

        

        
On 18 Oct 2017, at 17:17, David Winsemius <dwinsemius at comcast.net<mailto:dwinsemius at comcast.net>> wrote:

        

        
On Oct 17, 2017, at 11:58 PM, Rainer Krug <rainer_krug at icloud.com<mailto:rainer_krug at icloud.com>> wrote:

        
This is related to Macports and not to R - please post your question on their mailing list. If it would be about errors installing R, that would be different.


I think using MacPorts might actually be the "error" that needs correction. I would suggest an alternate strategy. Go to http://r.research.att.com/libs/ and get the appropriate version of cairo, probably the most recent one.

http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz

Scroll down to the bottom of that page and an appropriate modification of the two lines for unpacking to the root.

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /


The Mac version of R does not do well with either MacPorts or homebrew installation of required system packages because those package managers put them in loaction that are not recognized by the static build that is the default.

Using homebrew (and as far as I know Macports as well) works without major problems. The problem start when you mix standard installations / homebrew / Macports. This results in problems.

The fact that the original poster had obviously not used MacPorts (and perhaps did not even know what it was) suggests that the appropriate reply should be to discourage him from using it and offer a strategy with greater likelihood of success in combination with the more typical installation method for the Mac R fork.


So: each of the approaches has it?s own pros and cons - it is only that homebrew and Macports are not officially supported by the R team.

One of the cons is that both homebrew and MacPorts requires a greater knowledge of the Unix under-pinnings of MacOS. If a poster is asking how to install MacPorts, it suggests that he don't already have such skills and perhaps doesn't even have the motivation to acquire them. (Your earlier response suggested that posting in R-SIG-Mac was the wrong way to do acquire such skills and I agree. Appears the poster has not yet developed the habit of reading supporting online documentation. He certainly did not do so regarding R-SIG-Mac. My opinion: A person who chooses not to read or heed online documentation should be actively discouraged from using either MacPorts of homebrew.)

Best;
David.



Cheers,

Rainer



--
David.

Cheers,

Rainer

        
On 18 Oct 2017, at 02:36, John <miaojpm at gmail.com<mailto:miaojpm at gmail.com>> wrote:

        
Hi,

I tried to install Cairo graphics

https://www.cairographics.org/download/

and I need to install Macports.

I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
port install cairo", but it did not respond. I haven't seen any file name
or app called Macports, but one file called "port" which is located at

loca/bin/port"

How should I do it?

Thanks,

John
*******

Last login: Sun Oct 15 02:52:49 on console
Johns-MacBook-Pro:~ john$ /opt/local/bin/port ; exit;
MacPorts 2.4.2
Entering shell mode... ("help" for help, "quit" to quit)
[Users/john] > sudo port install cairo
Error: Unrecognized action "port sudo"


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

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Z?rich

Cell:       +41 (0)78 630 66 57
email:      Rainer at krugs.de<mailto:Rainer at krugs.de>
Skype:      RMkrug

PGP: 0x0F52F982





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

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Z?rich

Cell:       +41 (0)78 630 66 57
email:      Rainer at krugs.de<mailto:Rainer at krugs.de>
Skype:      RMkrug

PGP: 0x0F52F982




David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law







David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

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

  
  


  


      

    

    

      
      

        


  

        

      Robert Baer
    

    

      
      #
    

  


  

      
-- snip --

            

      
      
      
    

        
Even though its not my question, I appreciate the specific 
recommendations on best practices for move ahead.

            

      
      
      
    

        
I? am brand new to this list, but have been using R since about 2000.? 
The reason I'm here is to translate Mac-speak like "homebrew" and 
"MacPorts" into grounded advice that lets me use R as effectively on my 
new Mac as my Windows and Linux machines.? I appreciate John's 
predicament and this approach to answering his question is highly 
informative to me as I lurk and learn.?? Thanks from this newbie Mac user.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rainer M Krug
    

    

      
      #
    

  


  

          

      
      
      
    

        
If you know your way around in Linux, I would suggest looking into homebrew - it essentially brings the approach of apt (in the case of debian) to a Mac. If not, you might be better off with the official R installers. But all work equally after installed.


Cheers,

Rainer

            

      
      
      
    

        
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Z?rich

Cell:       +41 (0)78 630 66 57
email:      Rainer at krugs.de
Skype:      RMkrug

PGP: 0x0F52F982

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
      #
    

  


  

          

      
      
      
    

        
Dear Rainer;

I think it might be a bit more complicated than "just use the same installer all the time", but am not a user of either homebrew or MacPorts so am speaking only from reports I have read in this mailing list and SO. Bob Rudis whom I also respect in such matters has several times made the same suggestion. I think there may need to be supplemental instructions on setting system environment variables and also possibly further changes to Makevars files in some packages being obtained from CRAN or BioC. I have been encouraged by others to switch to homebrew, but have never found a sufficiently complete tutorial that appeared to cover these other issues. If you know of one, Rainer, I think you should share it.

Best;
David.

            

      
      
      
    

        
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

  
  


  


      

    

    

      
      

        


  

        

      MacQueen, Don
    

    

      
      #
    

  


  

      
The OP's question has inspired an interestingly large number of responses.

One thing I'm curious about, and I don't think I've seen in the discussion, is why the OP needed to install Cairo graphics with respect to R (otherwise the question was indeed off-topic for R-sig-Mac).

In summary (and I think this is reasonably consistent with other responses; discussion to support my summary follows):

1)  Use CRAN R, install dependencies needed for extended R capability on the OS as needed, from whatever source you prefer, or whichever is easiest for R to use
2)  If one chooses to install R using MacPorts or homebrew, be prepared to exercise a greater depth of computer science smarts
3)  Feel free to install other useful stuff using MacPorts or homebrew, whichever one prefers; there is unlikely to be any conflict with R


In close to 20 years of using R on Mac, I have always been able to use whatever capabilities R offers that I wanted to use, using the R provided on CRAN. Nothing has ever motivated me to install R using MacPorts or homebrew in order to obtain some capability that I couldn't have using CRAN's binary download for Mac. This includes things like access to remote Oracle databases, using various spatial packages built around sp and rgdal, reading and writing MS Office files (both Word and Excel), building simple tcl/tk interfaces, writing my own packages that link to Fortran, and probably more that I don't remember. I see no necessity to install R from MacPorts or homebrew. Of course, if one wishes to for whatever reason, great! And I'm glad that people have wanted to make R available from those package managers.

I do use MacPorts, however, to get useful software such as an X Windows aware version of emacs, ghostscript, and ImageMagick. Indeed, I even have cairo installed using MacPorts, albeit on a 10.11.6 system, not a 10.12.x system like the OP. (It's probably there as a dependency for some other MacPorts package.) From that point of view, the OP's command to install it using MacPorts was correct. I'd need more information to make a guess at why it didn't succeed.

Some R packages do, of course, depend on external libraries not provided with R. One has to install these from somewhere.  For example, the spatial packages need GDAL. In this case, I use the KyngChaos frameworks, but I'm aware that they're also available from MacPorts (and probably homebrew as well). Could I use them instead? Probably; R is pretty good about letting the user specify where dependencies are found.

I do not know what R extended capability depends on installing Cairo graphics on the OS. The X11() graphics device, as provided (I believe), has a version that uses cairo. There is the Cairo R package, but it has a binary version, at least for R on 10.11.x, so there's no need to install Cairo graphics to install the Cairo package.

-Don

--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509

        
On 10/20/17, 8:34 AM, "R-SIG-Mac on behalf of David Winsemius" <r-sig-mac-bounces at r-project.org on behalf of dwinsemius at comcast.net> wrote:

        

        
> On Oct 19, 2017, at 11:33 PM, Rainer Krug <rainer_krug at icloud.com> wrote:

        
> 
    > 
    >

        
>> On 19 Oct 2017, at 20:25, Robert Baer <rbaer at atsu.edu> wrote:

        
>> 
    >> 
    >> -- snip --
    >> 
    >>>>> I think using MacPorts might actually be the "error" that needs correction. I would suggest an alternate strategy. Go to http://r.research.att.com/libs/ and get the appropriate version of cairo, probably the most recent one.
    >>>>> 
    >>>>> http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
    >>>>> 
    >>>>> Scroll down to the bottom of that page and an appropriate modification of the two lines for unpacking to the root.
    >>>>> 
    >>>>> curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
    >>>>> sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /
    >> Even though its not my question, I appreciate the specific recommendations on best practices for move ahead.
    >> 
    >>>>> 
    >>>>> The Mac version of R does not do well with either MacPorts or homebrew installation of required system packages because those package managers put them in loaction that are not recognized by the static build that is the default.
    >>>> Using homebrew (and as far as I know Macports as well) works without major problems. The problem start when you mix standard installations / homebrew / Macports. This results in problems.
    >>> The fact that the original poster had obviously not used MacPorts (and perhaps did not even know what it was) suggests that the appropriate reply should be to discourage him from using it and offer a strategy with greater likelihood of success in combination with the more typical installation method for the Mac R fork.
    >> I  am brand new to this list, but have been using R since about 2000.  The reason I'm here is to translate Mac-speak like "homebrew" and "MacPorts" into grounded advice that lets me use R as effectively on my new Mac as my Windows and Linux machines. 
    > 
    > If you know your way around in Linux, I would suggest looking into homebrew - it essentially brings the approach of apt (in the case of debian) to a Mac. If not, you might be better off with the official R installers. But all work equally after installed.
    
    Dear Rainer;
    
    I think it might be a bit more complicated than "just use the same installer all the time", but am not a user of either homebrew or MacPorts so am speaking only from reports I have read in this mailing list and SO. Bob Rudis whom I also respect in such matters has several times made the same suggestion. I think there may need to be supplemental instructions on setting system environment variables and also possibly further changes to Makevars files in some packages being obtained from CRAN or BioC. I have been encouraged by others to switch to homebrew, but have never found a sufficiently complete tutorial that appeared to cover these other issues. If you know of one, Rainer, I think you should share it.
    
    Best;
    David.
    > 
    > 
    > Cheers,
    > 
    > Rainer
    > 
    > 
    >> I appreciate John's predicament and this approach to answering his question is highly informative to me as I lurk and learn.   Thanks from this newbie Mac user.
    >> 
    >> -- 
    >> 
    >> 
    >> --
    >> Robert W. Baer, Ph.D.
    >> Professor of Physiology
    >> Kirksville College of Osteopathic Medicine
    >> A T Still University of Health Sciences
    >> 800 W. Jefferson St
    >> Kirksville, MO 63501
    >> 660-626-2321 Department
    >> 660-626-2965 FAX
    >> 
    > 
    > --
    > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
    > 
    > University of Z?rich
    > 
    > Cell:       +41 (0)78 630 66 57
    > email:      Rainer at krugs.de
    > Skype:      RMkrug
    > 
    > PGP: 0x0F52F982
    > 
    > 
    > 
    
    David Winsemius
    Alameda, CA, USA
    
    'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law
    
    _______________________________________________
    R-SIG-Mac mailing list
    R-SIG-Mac at r-project.org
    https://stat.ethz.ch/mailman/listinfo/r-sig-mac

  
  


  


      

    

    

      
      

        


  

        

      美彦 馬場
    

    

      
      #
    

  


  

      
I do not want to mess this ML with yet another option, but Fink, another package manager for macOS, is also an option.  The main reasons I use Fink is to make sure GIS related CRAN packages (e.g. regal) are linked to Fink installed GIS packages (e.g. gdal).

Fink:
1. allows you to have multiple versions of R (e.g. 3.4, 3.3 and 3.2);
2.?has a number of CRAN/BioC packages to be stored in /sw/lib/R/3.4/site-library, /sw/lib/R/3.3/site-library and /sw/lib/R/3.2/site-library respectively
(CRAN/BioC libraries are linked to Fink packages);
3. allows users to use CRAN (saved in user directory) and Fink installed package; and
4. does not depend on non-System/Fink installed shared libraries  (so that regal will not be wrongly linked to user-installed gdal)

$ otool -L /sw/lib/R/3.3/site-library/rgdal/libs/rgdal.dylib 
/sw/lib/R/3.3/site-library/rgdal/libs/rgdal.dylib:
	/sw/lib/R/3.3/site-library/rgdal/libs/rgdal.dylib (compatibility version 0.0.0, current version 0.0.0)
	/sw/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libR.dylib (compatibility version 3.3.0, current version 3.3.1)
	/sw/lib/libgdal.20.dylib (compatibility version 22.0.0, current version 22.1.0)
	/sw/lib/libproj.9.dylib (compatibility version 11.0.0, current version 11.0.0)
	/sw/lib/libintl.8.dylib (compatibility version 10.0.0, current version 10.5.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1348.1.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)