[move to r-devel, put maintainer in loop] Patrick Connolly <[EMAIL PROTECTED]> writes:
> On Mon, 30-Oct-2006 at 04:44PM -0500, Duncan Murdoch wrote: > > > |> Try "R CMD printenv R_HOME" and you'll find which R home directory it is > |> using. You can see a lot more with "R CMD printenv" or various options > |> to "R CMD config". > > Thanks for that information. It knocks my theory on the head. Pity > that, because I might have been able to do something about it if that > was the problem. Now I'm at a loss to work out why lme4 installation > cannot find Matrix, and more strangely, why nothing else gave a > similar problem. I think I've tried every version of lme4 and Matrix > that has emerged since R-2.4.0 has been released. > > The fact that no other Red hat user has a problem indicates the > problem is this end; but I'm short of ideas about where to look. > Looks like it's back to versions 6 months old -- like proprietary > software users have to put up with. :-( Hmmm, I can provoke this on SUSE too (I was going to ask you to try this!): mkdir foo MY_R=~/misc/r-release-branch/BUILD/bin/R R_LIBS=foo $MY_R --vanilla << EOF options(repos=c(CRAN="http://cran.dk.r-project.org";)) install.packages("lme4", depend=TRUE) EOF This installs Matrix alright, then dies with Warning in install.packages("lme4", depend = TRUE) : argument 'lib' is missing: using foo trying URL 'http://cran.dk.r-project.org/src/contrib/lme4_0.9975-8.tar.gz' Content type 'application/x-tar' length 235617 bytes opened URL ================================================== downloaded 230Kb * Installing *source* package 'lme4' ... ** libs gcc -I/usr/local/src/pd/r-release-branch/BUILD/include -I/usr/local/src/pd/r-release-branch/BUILD/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -c Wishart.c -o Wishart.o In file included from Wishart.h:4, from Wishart.c:1: lme4_utils.h:9:20: Matrix.h: No such file or directory In file included from Wishart.h:4, from Wishart.c:1: lme4_utils.h:25: error: syntax error before "c" lme4_utils.h:25: warning: type defaults to `int' in declaration of `c' lme4_utils.h:25: warning: data definition has no type or storage class lme4_utils.h:163: error: syntax error before "cholmod_factor" lme4_utils.h:177: error: syntax error before "cholmod_factor" make: *** [Wishart.o] Error 1 ERROR: compilation failed for package 'lme4' And Matrix.h is sitting happily in foo/Matrix/include/ but obviously not getting included. Should there have been a copy inside lme4? What is not obvious to me is how this can work anywhere... I also tried unpacking the lme4 directory from its tarball, dropping all files from the Matrix installed include dir into lme4/src and then $MY_R CMD INSTALL -l foo lme4 but no go gcc -shared -L/usr/local/lib64 -o lme4.so Matrix_stubs.o Wishart.o glmer.o init.o lme4_utils.o lmer.o local_stubs.o pedigree.o -L/usr/local/src/pd/r-release-branch/BUILD/lib -lRlapack -L/usr/local/src/pd/r-release-branch/BUILD/lib -lRblas -lg2c -lm -lgcc_s local_stubs.o(.text+0x0): In function `M_numeric_as_chm_dense': /home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: multiple definition of `M_numeric_as_chm_dense' Matrix_stubs.o(.text+0x0):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: first defined here local_stubs.o(.text+0x70): In function `M_dpoMatrix_chol': /home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: multiple definition of `M_dpoMatrix_chol' Matrix_stubs.o(.text+0x70):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: first defined here ..etc.. -- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
