[R-sig-ME] Failure to load lme4 on Mac

Douglas Bates bates at stat.wisc.edu
Fri Jul 16 00:13:45 CEST 2010 

On Thu, Jul 15, 2010 at 4:53 PM, John Maindonald
<john.maindonald at anu.edu.au> wrote:
> This is odd. Around June 27, I installed version lme4_0.999375-34
> from R-forge, using:
>
> install.packages("lme4", repos="http://R-Forge.R-project.org")

I believe it was the absence of an Mac OS X binary package on CRAN,
not on R-forge, that others were commenting on.  If you check on the
main CRAN site

http://cran.r-project.org/web/packages/lme4/

(or on the equivalent page from your local mirror) you will see that
the source and Windows packages are available but not the Mac OS X
package as it reports errors in one of the package tests.

The place where the error is reported is curious because two models
are being compared and they differ only in whether the implicit
intercept or an explicit intercept is used in the formula.  So once
the model matrices and internal representations have been established,
the models should be identical yet somehow they are producing
discernibly different answers.  It is always possible that there is
something happening much earlier in the tests that corrupted memory
but without access to a system displaying the error I am a bit of a
loss as to how we can proceed.

Perhaps Martin or I can sit down with someone who has a Mac laptop
with the necessary build tools at useR!2010 next week and see if we
can find out what is going on.

The report of the test failure is at
http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/lme4-00check.html

Interestingly Marc Otto was able to build and test the experimental
version, lme4a, on Mac OS X today and it has the same test but did not
trip up on it.

> I checked a moment ago, and this still works:
>
>> install.packages("lme4", repos="http://R-Forge.R-project.org")
> trying URL 'http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.11/lme4_0.999375-34.tgz'
> Content type 'application/x-gzip' length 1281413 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
> I have been happily using it.
>
> I do however have another Mac that I am keeping for my sister,
> and on which I have installed R-2.11.1.  When I try the same command
> there, I get:
>
> "
> Warning: unable to access index for repository index http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.11
> Warning message:
> In getDependencies(pkgs, available, lib) :
>  package 'lme4' is not available.
> "
>
> This other R installation is not as fully configured as my main R machine.
>
> For what it is worth (nothing that I can see), here are the two sessionInfo's
>
> Main Machine:
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> loaded via a namespace (and not attached):
> [1] Matrix_0.999375-41 grid_2.11.1        lattice_0.18-8     lme4_0.999375-34
> [5] nlme_3.1-96        stats4_2.11.1
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>
> Other machine:
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
>
>
> 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 16/07/2010, at 6:54 AM, Douglas Bates wrote:
>
>> On Thu, Jul 15, 2010 at 12:31 PM, Daniel Ezra Johnson
>> <danielezrajohnson at gmail.com> wrote:
>>> I would appreciate it if the lme4 developers could state whether they
>>> plan to ensure that a Mac binary be available at any point in the
>>> future (as it does not seem like the problem is going to fix itself).
>>> As we see, it is not trivial to compile the package from source on the
>>> Mac OS.
>>
>> Neither Martin nor I use Mac OS and we can't reproduce the problem on
>> other operating systems so we are kind of stuck.
>>
>> Apparently it is a matter of one of the tests failing but without
>> access to a system that exhibits the failure I wouldn't know where to
>> start debugging.  Is some kind person using Mac OS were to download
>> and test the package and provide some details about the nature of the
>> failure we might be able to get started.
>>
>>>
>>> Thanks,
>>> Dan
>>>
>>> On Thu, Jul 15, 2010 at 12:58 PM, Christopher Desjardins
>>> <desja004 at umn.edu> wrote:
>>>> Did you see this from Daniel Myall ...
>>>>
>>>> .................
>>>> Hi Sean,
>>>>
>>>> On your Macbook do you have xcode installed? The error "sh: make: command
>>>> not found" indicates that this is not the case.
>>>>
>>>> The best place to get the latest xcode is http://connect.apple.com/ (The
>>>> main Apple site sends you back and forward between two pages for the xcode
>>>> download).
>>>> ................
>>>>
>>>> You need to install Xcode as you don't have the 'make' command.
>>>> http://developer.apple.com/technologies/tools/xcode.html. Unfortunately
>>>> Xcode is about 1 GB in size.
>>>>
>>>> Or you could wait for a binary build of lme4 for Mac.
>>>> Chris
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jul 15, 2010 at 11:01 AM, Sladjana <s-lukic at northwestern.edu> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am having the same problem with loading lme4 on Mac.
>>>>> Can someone guid me through this, I would really appreciate?
>>>>> This is the error message I have been getting:
>>>>> * installing *source* package ‘lme4’ ...
>>>>> ** libs
>>>>> *** arch - i386
>>>>> sh: make: command not found
>>>>> 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/5i/5ineVodYG08abdx7gchSaE+++TI/-Tmp-
>>>>> /Rtmp4Czfel/downloaded_packages’
>>>>>
>>>>> Thank you
>>>>> Sladjana
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-mixed-models at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>>>
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