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

[Simon Urbanek]

On Jul 29, 2010, at 7:51 PM, 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?
> 

... why don't you just compare the values with tolerance? That seems to make more sense that to disable the test altogether ...

Cheers,
Simon


> 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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