[R] lme4 install error

Douglas Bates
2006-11-06T14:07:19Z

On 11/5/06, Shravan Vasishth <shravan.vasishth at gmail.com> wrote:

> I'm trying to install lme4 (after having installed R 2.4.0 from source,
and
> having installed the latest Matrix package). lme4 fails with the following
> message:
>
> pedigree.o definition of _lme4_xSym in section (__DATA,__common)
> pedigree.o definition of _lme4_ySym in section (__DATA,__common)
> make: *** [lme4.so] Error 1
> ERROR: compilation failed for package 'lme4'
> ** Removing
>
'/Library/Frameworks/R.framework/Versions/2.4/Resources/library/lme4'
>
> Others have apparently also had this problem, but their error message
> appeared to signal a missing or unfindable Matrix header file. This does
not
> seem to be the case here. What is likely to be the problem? This install is
> on a Mac OS 10.3.9. I've done R upgrades many times before; this is the
> first time I''ve had a problem.
>
> The full error message for lme4 can be seen at:
>
> http://www.ling.uni-potsdam.de/~vasishth/screen.txt

Thank you for the report and for making the full transcript available.
 It appears that I have neglected an "extern" when moving some code
from the Matrix package to lme4.  The compilers used for Mac OS X
10.4.x don't object to the multiple defintiions as long as they are
consistent but compilers for older versions of Mac OS X do.

I'll upload a fixed version of lme4 later today.

> One other unusual thing was that there were many warning messages during
the
> Matrix install.
>
> ...
> Warning in matchSignature(signature, fdef, where) :
>
>          in the method signature for function "coerce" no
definition for
> class: "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>          in the method signature for function "coerce" no
definition for
> class: "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>          in the method signature for function "coerce" no
definition for
> class: "matrix.csc"
> ...

Those warnings are to be expected.  In the Matrix package we have
utility functions to convert sparse Matrix objects from the SparseM
package to sparse matrix objects for the Matrix package.  We do not
have the Matrix package depend on the SparseM package as it would be,
for the most part, redundant.  The warnings simply indicate that
classes from the SparseM package are used in the signatures of methods
but are not visible at the time that the Matrix package is compiled.

to be loaded when the
> I have put the entire history of that install here:
> http://www.ling.uni-potsdam.de/~vasishth/screen2.txt
>
>
> Thanks,
>
> --
> Shravan Vasishth,    Empirical Methods in Syntax
> Juniorprofessor, Institute for Linguistics, Potsdam
> Tel: +49-(0)331-977-2016, -2457  Fax: -2087
> http://www.ling.uni-potsdam.de/~vasishth
>
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>
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