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

[Loren Engrav]

Cool, let us hope this 123 lasts for a time, I must store it

I sudo tar'd it and the warnings went away

Will go on with 5455s as the 5426s fail on this Snow Leopard

Thank you

-- 
Loren Engrav, MD
Professor and Chief, Plastic Surgery, 1977-2001
Associate Director, Burn Center, 1977-2001
Univ Washington
Seattle



> From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
> Date: Mon, 14 Sep 2009 18:54:05 -0400
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "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
> 
> 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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> _______________________________________________
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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
>