[R-SIG-Mac] [R] lme4 + R 2.11.0 + mac unavailable

Fri Jul 30 04:40:52 CEST 2010

It gives "Darwin" on my machine.

This is an issue (binaries unavailable) of a type that is likely to
recur from time to time, and not just for OSX implementations.  
At the very least, ready access to reasonably complete information 
on the status of packages, both on r-forge and on CRAN and
brought together in one place, is surely desirable for widely
used packages.   The packages check summary will seem a
forbidding place fro relative novices.

Thanks to those who are cogitating about how to handle such
issues, and trying to smooth the way ahead.

There might be a link on the relevant CRAN binaries page:
"The binary for the package that you want is not available.  Click 
here for details of the current status, and for a note on your options
for gaining access to it."

While compiling from source is a suitable recourse for those
who are accustomed to compile packages, encouraging
novice to compile from source seems in general a bad idea.

John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm

On 30/07/2010, at 9:51 AM, Martin Maechler wrote:

>>>>>> "KB" == Ken Beath <ken at kjbeath.com.au>
>>>>>>    on Wed, 28 Jul 2010 01:19:34 -0000 (GMT) writes:
> 
>    KB> On Tue, July 27, 2010 11:07 pm, John Maindonald wrote:
>>> Binaries for lme4 are not for the time being available either on
>>> CRAN or on r-forge?
>>> 
> 
>    KB> There was a discussion about this on R-Sig-ME. It fails one of the checks
>    KB> on the machine used to build the mac packages. It may pass on machines
>    KB> with a later version of MacOS, but there didn't seem to be a consensus of
>    KB> whether failing the checks was a problem.
> 
> The underlyign issue seems to remain unresolved.
> My best guess is still to low-level bugs somewhere in the libraries
> used.
> 
> However, to help users,
> I'm willing to *not* run those tests when *running* on the Mac.
> 
> What does  
>     Sys.info()[["sysname"]]
> 
> return on the Mac, i.e., different versions of R running on the
> Mac?
> From grepping around I'd expect it give  "Darwin"  in all cases.
> Is that true?
> 
> Regards,
> Martin Maechler
> 
> 
> 
>>> John Maindonald             email: john.maindonald at anu.edu.au
>>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>>> Centre for Mathematics & Its Applications, Room 1194,
>>> John Dedman Mathematical Sciences Building (Building 27)
>>> Australian National University, Canberra ACT 0200.
>>> http://www.maths.anu.edu.au/~johnm
>>> 
>>> On 27/07/2010, at 9:57 PM, Martin Maechler wrote:
>>> 
>>>> Dear Peter,
>>>> note that I am CC'ing this reply to the "R - Mac" mailing list, on
>>>> which there are knowledgable people for helping you with some of the
>>>> Mac specific problems
>>>> (more inline below).
>>>> 
>>>> On Sun, Jul 25, 2010 at 20:36, Peter Goff <peter.t.goff at vanderbilt.edu>
>>>> wrote:
>>>>> Martin,
>>>>> 
>>>>> I saw your series of posts on this topic, but sadly I am still unable
>>>>> to
>>>>> install lme4.
>>>>> 
>>>>> I am in the nascent stages of learning R and, at this point, I cannot
>>>>> even
>>>>> load the program "arm" that is key to my program of study (I'm working
>>>>> with
>>>>> Gelman & Hill's Data Analysis using Regression and
>>>>> Multilevel/Hierarchical
>>>>> Models to get acclimated to R).
>>>>> 
>>>>> Here's my quandary thus far:
>>>>> 
>>>>> (1) I download and install R for Macs (version 2.11.1)
>>>>> (2) I try to find lme4 through the "Package Installer" only to find
>>>>> that it
>>>>> does not exist.
>>>>> (3) I find your string of postings on the web and try to install using:
>>>>> install.packages("lme4", type = "source")
>>>>> and I get the following error message:
>>>>> 
>>>>> --- Please select a CRAN mirror for use in this session --- (I chose
>>>>> USA,
>>>>> MI)
>>>> 
>>>> Ok, I assume that's close enough to Vanderbilt ..
>>>> 
>>>>> trying URL 'http://cran.mtu.edu/src/contrib/lme4_0.999375-34.tar.gz'
>>>>> Content type 'application/x-gzip' length 1028012 bytes (1003 Kb)
>>>>> opened URL
>>>>> ==================================================
>>>>> downloaded 1003 Kb
>>>>> 
>>>>> * installing *source* package ‘lme4’ ...
>>>>> ** libs
>>>>> *** arch - i386
>>>>> gcc -arch i386 -std=gnu99
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> -I/Library/Frameworks/R.framework/Resources/include/i386
>>>>> -I/usr/local/include
>>>>> -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Matrix/include"
>>>>> -I"/Library/Frameworks/R.framework/Resources/library/stats/include"
>>>>> -fPIC
>>>>> -g -O2 -c init.c -o init.o
>>>>> /bin/sh: gcc: command not found
>>>> 
>>>> See, that's a clue:  'gcc' is the GNU C compiler and that (and more)
>>>> are absolutely musts for installing many R packages from source.
>>>> 
>>>> The readers of R-SIG-Mac will be able to give more exact details,
>>>> but in order to get a version of gcc (and other tools) working nicely
>>>> with your version of R,
>>>> you'll need to install (parts of) the "Xcode" development tools that
>>>> Apple provides to you (for free, but you need to "get them").
>>>> 
>>>> Best regards,
>>>> Martin
>>>> 
>>>>> make: *** [init.o] Error 127
>>>>> ERROR: compilation failed for package ‘lme4’
>>>>> * removing
>>>>> ‘/Library/Frameworks/R.framework/Versions/2.11/Resources/library/lme4’
>>>>> 
>>>>> The downloaded packages are in
>>>>> 
>>>>> ‘/private/var/folders/ty/tyL1SdtKGlObzhxQbBUTek+++TI/-Tmp-/Rtmpt4fli2/downloaded_packages’
>>>>> Updating HTML index of packages in '.Library'
>>>>> Warning message:
>>>>> In install.packages("lme4", type = "source") :
>>>>> installation of package 'lme4' had non-zero exit status
>>>>> 
>>>>> 
>>>>> 
>>>>> Days and hours later I am at a loss as to how I should proceed. Any
>>>>> advice
>>>>> would be greatly appreciated!
>>>>> 
>>>>> Thanks,
>>>>> ~Peter
>>>>> 
>>>>> Peter Trabert Goff
>>>>> PhD student
>>>>> Department of Leadership, Policy, and Organizations
>>>>> Vanderbilt University
>>>> 
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