Hank,
you're right. Strangely enough, exactly this bug was fixed in one of
the previous releases of Matrix, but apparently crept back in (hence
the CC to the maintainers - it is in 0.995-2, too). The patch is
really simple (attached). For now I have fixed it manually and re-ran
the build, so the fixed OS X binary should by available on CRAN by
tomorrow.
Cheers,
Simon
diff -ur Matrix/src/chm_common.c Matrix.fixed/src/chm_common.c
--- Matrix/src/chm_common.c 2006-01-16 15:03:48.000000000 -0500
+++ Matrix.fixed/src/chm_common.c 2006-01-19 15:51:16.000000000
-0500
@@ -1,6 +1,8 @@
#include "chm_common.h"
#include "Mutils.h"
+cholmod_common c;
+
static R_INLINE int
check_class(char *class, char **valid)
{
diff -ur Matrix/src/chm_common.h Matrix.fixed/src/chm_common.h
--- Matrix/src/chm_common.h 2006-01-13 18:47:38.000000000 -0500
+++ Matrix.fixed/src/chm_common.h 2006-01-19 15:16:12.000000000
-0500
@@ -4,7 +4,7 @@
#include "CHOLMOD/Include/cholmod.h"
#include "Mutils.h"
-cholmod_common c;
+extern cholmod_common c;
cholmod_sparse *as_cholmod_sparse(SEXP x);
cholmod_triplet *as_cholmod_triplet(SEXP x);
Begin forwarded message:
> From: "Martin Henry H. Stevens" <[EMAIL PROTECTED]>
> Date: January 19, 2006 12:16:16 PM EST
> To: [email protected]
> Subject: [R-SIG-Mac] Can't load Matrix 0.995-1 for lme4
>
> 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/
> Matrix_0.995-1.tar.gz'
> 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
> Csparse.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
> R_ldl.o
> ....more...
> ...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
> subdomains.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
> /Library/Frameworks/R.framework/../R.framework/R(lgamma.lo)
> definition of _signgam
> /usr/lib/libSystem.dylib(gamma9.o) definition of _signgam
> ** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/
> library/Matrix'
> ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.2/
> Resources/library/Matrix'
> make: *** [Matrix.so] Error 1
> ERROR: compilation failed for package 'Matrix'
>
> The downloaded packages are in
> /private/tmp/RtmpyMhutL/downloaded_packages
>>
>
>
> I would very grateful for any assistance.
>
> Cheers,
> Hank
>
>
> 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
> http://www.cas.muohio.edu/~stevenmh/
> http://www.muohio.edu/ecology/
> http://www.muohio.edu/botany/
> "E Pluribus Unum"
>
> _______________________________________________
> R-SIG-Mac mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
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