[R-sig-ME] Problem with library(lme4a)

[Ben Bolker]

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On 11-07-12 10:13 PM, zListserv wrote:
> Getting closer?
> 
> $ ls /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
> $ cd /usr/local/lib
> $ sudo ln -s /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
> Password:
> $ ll libgfortran.2.dylib
> lrwxr-xr-x  1 root  wheel  79 Jul 12 22:03 libgfortran.2.dylib -> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
> 
> BUT, R:
> 
> R> library(lme4a)
> Error in get(hookname, envir = env, inherits = FALSE) : 
>   internal error -3 in R_decompress1
> Error: package/namespace load failed for 'lme4a'
> 

 Urgh.

  I know nothing about this error, all I see is what's listed in
<https://stat.ethz.ch/pipermail/r-help/2008-February/154587.html> (where
it referred to an installation of the rgl package): "The message
indicates a damaged copy of something:  either your decompression code,
or rgl."

  Try downloading again? (Sorry not to be more helpful.)

 (Download the file itself from
<http://lme4.r-forge.r-project.org/repos/bin/macosx/leopard/contrib/2.13/lme4a_0.999375-65.tgz>,
rather than installing directly, so you can check out its characteristics.)

  It should match:

 size: 1614159

md5 hash:

66c5c6f45aa543341164fd7b160303d7  lme4a_0.999375-65.tgz

> 
> On 2011-07-09, at 23:50, Ben Bolker wrote:
> 
> On 11-07-12 09:53 PM, zListserv wrote:
>>>>> Hmmm.
>>>>
>>>> Thanks for your prompt reply.  Please see below
>>>>
>>>>
>>>>>
>>>>>  I believe the key is
>>>>>
>>>>> Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>>>>
>>>>>  I think this is happening because I had Xcode installed on my machine,
>>>>> which includes a copy of libfortran.2.dylib in /usr/local/lib, on it
>>>>> when I built the binary, so that's where R is looking for it.  R
>>>>> installs its own version in
>>>>> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/ , but
>>>>> that's not where it's being told to look.
>>>>>
>>>>>  Possible solutions:
>>>>>
>>>>> * see if the binary version on R-forge happens to be working right now
>>>>> (install.packages(...,repos="http://r-forge.r-project.org"))
>>>>
>>>> Tried it but didn't fix it.
>>>>
>>>>> * wait for me to figure out how to build a version that looks in the
>>>>> right place and put it up on the specialized lme4 repository
>>>>
>>>> I would be most grateful if you could do this
>>>>
>>>>> * install Xcode (at which point you should also be able to build your
>>>>> own version from source ... ?)
>>>>
>>>> I could probably figure this out because I already have xcode installed.
>>>>
>>>>> * open a terminal window and
>>>>>  (1) locate libfortran.2.dylib
> 
>  ** this was a typo, as you found out below -- should be
> libgfortran.2.dylib
> 
>>>>>     [confirm that the library is where I think it is]
>>>>>  (2) cd /usr/local/lib
>>>>>  (3) sudo ln -s
>>>>> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
>>>>>
>>>>
>>>> $ ls /usr/local/lib/libfortran.2.dylib
>>>> ls: /usr/local/lib/libfortran.2.dylib: No such file or directory
>>>>
>>>> $ ls /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libfortran.2.dylib
>>>> ls: /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libfortran.2.dylib: No such file or directory
>>>>
>>>> but
>>>>
>>>> $ ls /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
>>>> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
>>>>
>>>> is libgfortran.2.dylib the correct library to which I should link?
> 
>  Yes.  Try following steps #2 and #3 above and see what happens?
> 
> I'm a little surprised you already have Xcode installed -- it falsifies
> a few of my hunches ...
> 
>>>>
>>>> On 2011-07-12, at 17:37, zListserv at gmail.com wrote:
>>>>
>>>>> I'm trying to use lme4a but the library will not load on my Macintosh.  I'd appreciate any advice about how to make this work.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> <snip>
> 
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