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

[Martin Maechler]

>>>>> "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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