[R-SIG-Mac] [R] 64-bit OSX binary for 2.9.2

Tue Sep 15 00:54:05 CEST 2009

Hi,

On Sep 14, 2009, at 6:34 PM, Loren Engrav wrote:

> I too would vote for a 1 2 3 set of install instructions

David's post should have all-but-nailed it ... some comments in line:

> , maybe for 32bit and 64bit if they differ

They don't. The R that you install following the instructions below is  
a universal build, so 32bit and 64 bit (ppc + intel) are all installed.

R is then launched in 32 bit or 64 bit mode by the command line args  
sent to it on launch. The various GUI's (if you go that route) take  
care of this for you. The 64 bit gui are the ones w/ 64 at the end of  
their download link, eg:

* http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard.dmg (32  
bit); vs
* http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard64.dmg (64  
bit)

If you launch R from the terminal, it defaults to 32bit.

If you want to launch R form the terminal in 64bit, you would do:

For intel:
$ R --arch x86_64

For ppc:
$ R --arch ppc64

> I did the 123 below and
>
> 1-the were many messages during install like " x
> Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf/:  
> Can't
> update time for
> Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf:  
> Operation
> not permitted, but
>
> 2-2.9.2 seems to function OK after simple testing; is that warning
> insignificant

Long version:

This is because you need to run the "tar" command as a user who has  
privileges to write to the directory that the files are being  
uncompressed to.

Short version:

2c of David's commands should be:

2. c) click on the Terminal window and
   (i) Type (without quotes): "sudo "
   (ii) Paste in the tar command: cmd-V to paste-in that command.

So, the command to execute at 2c in your terminal is:

$ sudo tar fvxz R*.tar.gz -C /

I would do this again to ensure you have all of the 2.9.2 "parts" in  
there (ie, don't assume that everything was OK when you did it and got  
all those "permission denied" warnings/errors).

> 3-R.app available at http://r.research.att.com/ is 5426 but 5455 32  
> and 64
> bit available at
> http://r.research.att.com/R-GUI-5455-2.9-leopard-Leopard.dmg as per  
> 8/6/09
> r-sig-mac discussion so I put in 5455; but why 5426 here and 5455  
> there?

I don't have an answer for that, 5455 is a later build of the .app, so  
if it's working for you, I guess just go ahead and keep using that  
one. Otherwise, fall back to the one on the site.

Hope that helps some,

-steve

>
> Thank you
>
> Loren Engrav, MD
> U Washington
>
>
>> From: David Winsemius <dwinsemius at comcast.net>
>> Date: Mon, 14 Sep 2009 13:00:52 -0400
>> To: Steve Lianoglou <mailinglist.honeypot at gmail.com>
>> Cc: r-help <r-help at stat.math.ethz.ch>, ivo welch  
>> <ivo_welch at brown.edu>,
>> "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
>> Subject: Re: [R-SIG-Mac] [R] 64-bit OSX binary for 2.9.2
>>
>>
>> On Sep 14, 2009, at 11:59 AM, Steve Lianoglou wrote:
>>
>>> Hi,
>>>
>>> On Sep 14, 2009, at 11:44 AM, ivo welch wrote:
>>>
>>>> dear R wizards:  I am looking for a binary package distribution of
>>>> R 2.9.2
>>>> for OSX .  Looking at http://r.research.att.com/ , there seems to
>>>> be only a
>>>> binary for 2.9.0 .  is the 2.9.2 version binary package available
>>>> somewhere?   (at this point, would it make sense to elevate the 64-
>>>> bit
>>>> version to a "standard recommended" rather than just a "boutique"
>>>> version?)
>>>
>>> There isn't a *.pkg / *.dmg install for it, but it's there. In this
>>> section:
>>>
>>> Universal nightly builds for Mac OS X (10.4 Tiger and 10.5 Leopard)
>>>
>>> Third row in the table:
>>>
>>> http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz
>>>
>>> You have to inflate it at the root of your HD. The text right below
>>> the d/l table tells you how to do that:
>>>
>>> """Alternatively you can use the tar-ball (*.tar.gz) which must be
>>> unpacked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't
>>> contain the GUI (see below for a separate download)."""
>>
>> The problem may arise for  *NIX-newbies ( a group in which I still
>> claim membership)  that they are unable to operationalize that
>> message. For one thing they may not even know how to open a Terminal
>> window. For another they may not know that the "/" at the end of that
>> command will take care of "unpacking at the root", so they will not
>> need to navigate away from the place that they find themselves when
>> Terminal opens up a bash session.  The steps broken down would be
>> something along these lines:
>>
>> First : Download the nightly build, and select "Save to file" rather
>> than opening with Stuffit, and then it by default should end up in  
>> the
>> <user>/Downloads/ folder.
>>
>> 1. a-c) Go to the Utilities folder of the Applications folder and
>> double-click on Terminal.app
>> 2. a) Go back to the browser and select the string:  tar fvxz
>> R*.tar.gz -C /
>>
>> (I would solicit some input here from more competent UNIXers  
>> regarding
>> whether one would ever need to prefix this command with sudo.)
>>
>> 2. b) cmd-C to put it in the clipboard
>> 2. c) click on the Terminal window and cmd-V to paste-in that  
>> command.
>> 2 d) use the arrow and backspace keys (since mouse-clicking does not
>> change the cursor position in Terminal sessions) to delete the
>> "R*.tar.gz" on the command line.
>>
>> 3 a) Navigate with the Finder to the Downloads/ folder and locate the
>> R<build>. Click-drag that file to the Terminal window and
>> "unclick" (or is it lift-click) when the pointer is at the place on
>> the command line where the "R*.tar.gz" used to be. A full path  
>> version
>> of the file name will get inserted (an no quotes are needed, unlike
>> what one might expect after working in R regularly.)
>>
>> On my machine, one now sees this on the command line:
>> tar fvxz /Users/davidwinsemius/Downloads/R-2.9-branch-leopard-
>> universal.tar.gz  -C /
>>
>> 4) Hit <return>
>>
>> Sit back and watch the show.
>>
>> You can the separately download the appropriate R-GUI and put in in
>> the /Applications/ folder.
>>
>>>
>>> You'll have to install the R.app GUI separately if you want to use
>>> the 2.9.2 install, otherwise I think the 2.9.0 *.pkg installer
>>> includes it, though I'm not sure.
>>
>> It does, In fact, it has both the 32 bit GUI and the 64 bit GUI. What
>> I did was install that package _first_ which gave me 2.9.0 and then
>> performed the steps above. You really would not want to do it in a
>> reversed order, since you would be replacing R 2.9.2 with R 2.9.0.
>>
>> And of course this message _should_ have gone to r-sig-mac at stat.math.ethz.ch
>>  and any follow up should trim the r-help address.
>>
>> -- 
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>>
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>
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--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact