[R-SIG-Mac] Can't load Matrix 0.995-1 for lme4

Martin Henry H. Stevens HStevens at MUOhio.edu
Thu Jan 19 18:16:16 CET 2006

Dear Mac useRs,
I can no longer run lme4 because I think I upgraded lme4 without  
being able to upgrade Matrix.

I am using:
Mac OS 10.4.4
C compiler -- gcc 3.3
Fortran compiler -- g77 3.4.2 (with R install)
R v. 2.2.1 (updated from 2.2.0 this morning)
lme4 v. 0.995-1

I tried to use the RGUI  to load the package source of Matrix 0.995-1  
but it fails.

It begins...

trying URL 'http://cran.us.r-project.org/src/contrib/ 
Content type 'application/x-tar' length 2458826 bytes
opened URL
downloaded 2401Kb

* Installing *source* package 'Matrix' ...
** libs
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c Csparse.c -o  
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c HBMM.c -o HBMM.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c Metis_utils.c - 
o Metis_utils.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c R_ldl.c -o  
...and ends...
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include  -I. -fno-common  -g -O2 -c  
kwayvolrefine.c -o kwayvolrefine.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include  -I. -fno-common  -g -O2 -c kwayvolfm.c  
-o kwayvolfm.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include  -I. -fno-common  -g -O2 -c  
subdomains.c -o subdomains.o
ar -rucs ../Metis.a coarsen.o fm.o initpart.o match.o ccgraph.o  
memory.o pmetis.o pqueue.o refine.o util.o timing.o debug.o  
bucketsort.o graph.o stat.o kmetis.o kwayrefine.o kwayfm.o balance.o  
ometis.o srefine.o sfm.o separator.o mincover.o mmd.o mesh.o  
meshpart.o frename.o fortran.o myqsort.o compress.o parmetis.o  
estmem.o mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o  
mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o mrefine2.o  
minitpart2.o mbalance2.o mfm2.o kvmetis.o kwayvolrefine.o kwayvolfm.o  
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c ldl.c -o ldl.o
ar -rucs ../LDL.a ldl.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - 
o Matrix.so Csparse.o HBMM.o Metis_utils.o R_ldl.o Tsparse.o init.o  
lmer.o Mutils.o chm_common.o dense.o dCholCMatrix.o dgCMatrix.o  
dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o  
dsTMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o  
dtrMatrix.o dtpMatrix.o factorizations.o iohb.o ldense.o  
lCholCMatrix.o lgCMatrix.o lgTMatrix.o lsCMatrix.o ltCMatrix.o mmio.o  
triplet_to_col.o   CHOLMOD.a UMFPACK.a COLAMD.a CCOLAMD.a AMD.a  
Metis.a LDL.a  -framework vecLib -lcc_dynamic -F/Library/Frameworks/ 
R.framework/.. -framework R
ld: multiple definitions of symbol _c
Csparse.o definition of _c in section (__DATA,__common)
Tsparse.o definition of _c in section (__DATA,__common)
init.o definition of _c in section (__DATA,__common)
lmer.o definition of _c in section (__DATA,__common)
chm_common.o definition of _c in section (__DATA,__common)
dense.o definition of _c in section (__DATA,__common)
dgCMatrix.o definition of _c in section (__DATA,__common)
dgTMatrix.o definition of _c in section (__DATA,__common)
dsCMatrix.o definition of _c in section (__DATA,__common)
ld: warning multiple definitions of symbol _signgam
definition of _signgam
/usr/lib/libSystem.dylib(gamma9.o) definition of _signgam
** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/ 
** Restoring previous '/Library/Frameworks/R.framework/Versions/2.2/ 
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package 'Matrix'

The downloaded packages are in

I would very grateful for any assistance.


Dr. Martin Henry H. Stevens, Assistant Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
"E Pluribus Unum"

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