[R-sig-ME] FW: Help installing Package lme4

Wed Apr 2 23:32:10 CEST 2008

Please ignore my earlier posting. 

I managed to successfully install the package after specifying the same
-l <target lib dir> for both Matrix & lme4 

Partha 

  _____  

From: Raghavan, Partha (Exchange) 
Sent: Wednesday, April 02, 2008 5:06 PM
To: r-sig-mixed-models at r-project.org
Subject: Help installing Package lme4

I am having trouble installing the lme4 package.

It looks likes the install is having trouble locating a header, Matrix.h

I just installed the Matrix package successfully 

Do I need to set any CPPFLAGS var etc?

This is all on a 64 bit LINUX box

[pbfastprepay1 /a/praghava/out/R/lib/R/library 1128] R CMD INSTALL
lme4_0.99875-9.tar.gz
<

* Installing to library '/a/praghava/out/R/lib/R/library/'

* Installing *source* package 'lme4' ...

** libs

gcc -std=gnu99 -I/usr/local/public/R-2.6.1_LINUX_VS9/lib64/R/include
-I/usr/local/public/R-2.6.1_LINUX_VS9/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c glmer.c -o glmer.o

In file included from lmer.h:4,

                 from glmer.h:4,

                 from glmer.c:1:

lme4_utils.h:12:20: Matrix.h: No such file or directory

In file included from lmer.h:4,

                 from glmer.h:4,

                 from glmer.c:1:

lme4_utils.h:40: error: parse error before "c"

lme4_utils.h:40: warning: type defaults to `int' in declaration of `c'

lme4_utils.h:40: warning: data definition has no type or storage class

lme4_utils.h:192: error: parse error before "cholmod_factor"

lme4_utils.h:217: error: parse error before "cholmod_factor"

glmer.c: In function `b_quadratic':

glmer.c:59: warning: implicit declaration of function `M_dpoMatrix_chol'

glmer.c:59: warning: passing arg 1 of `R_do_slot' makes pointer from
integer without a cast

glmer.c: At top level:

glmer.c:180: error: parse error before "cholmod_factor"

glmer.c: In function `internal_Gaussian_deviance':

glmer.c:185: error: `CHM_SP' undeclared (first use in this function)

glmer.c:185: error: (Each undeclared identifier is reported only once

glmer.c:185: error: for each function it appears in.)

glmer.c:185: error: parse error before "Lm"

glmer.c:186: error: `CHM_FR' undeclared (first use in this function)

glmer.c:188: error: `q' undeclared (first use in this function)

glmer.c:188: error: `p' undeclared (first use in this function)

glmer.c:189: error: `CHM_DN' undeclared (first use in this function)

glmer.c:189: error: parse error before "Ltb"

glmer.c:193: error: subscripted value is neither array nor pointer

glmer.c:193: error: `betahat' undeclared (first use in this function)

glmer.c:194: error: `b' undeclared (first use in this function)

glmer.c:194: error: `bhat' undeclared (first use in this function)

glmer.c:195: error: `Lcp' undeclared (first use in this function)

glmer.c:195: warning: implicit declaration of function
`M_cholmod_copy_factor'

glmer.c:195: error: `L' undeclared (first use in this function)

glmer.c:196: error: `Lm' undeclared (first use in this function)

glmer.c:196: warning: implicit declaration of function
`M_cholmod_factor_to_sparse'

glmer.c:196: warning: implicit declaration of function
`M_cholmod_free_factor'

glmer.c:197: warning: implicit declaration of function
`M_cholmod_sdmult'

glmer.c:197: error: `Ltb' undeclared (first use in this function)

glmer.c:200: warning: implicit declaration of function
`M_cholmod_free_sparse'

glmer.c:200: warning: implicit declaration of function
`M_cholmod_free_dense'

glmer.c:201: error: `RZX' undeclared (first use in this function)

glmer.c:204: error: `RXX' undeclared (first use in this function)

glmer.c: In function `internal_bhat':

glmer.c:396: error: `CHM_FR' undeclared (first use in this function)

glmer.c:396: error: parse error before "L"

glmer.c:403: error: `L' undeclared (first use in this function)

glmer.c: In function `glmer_MCMCsamp':

glmer.c:657: error: `CHM_FR' undeclared (first use in this function)

glmer.c:657: error: parse error before "L"

glmer.c:680: error: `L' undeclared (first use in this function)

make: *** [glmer.o] Error 1

ERROR: compilation failed for package 'lme4'

** Removing '/n/fast-fast/praghava/out/R/lib/R/library/lme4'

/************** GCC VERSION  *****************/

[pbfastprepay1 /a/praghava/out/R/lib/R/library 1129] gcc -v

Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs

Configured with: ../configure --enable-threads=posix --prefix=/usr
--with-local-prefix=/usr/local --infodir=/usr/share/info
--mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
--disable-checking --libdir=/usr/lib64 --enable-libgcj
--with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib64
--with-system-zlib --enable-shared --enable-__cxa_atexit
x86_64-suse-linux

Thread model: posix

gcc version 3.3.3 (SuSE Linux)

/************ LINUX VERSION *****************/

[pbfastprepay1 /a/praghava/out/R/lib/R/library 1130]uname -a 

Linux pbfastprepay1 2.6.5-7.244-smp #1 SMP Mon Dec 12 18:32:25 UTC 2005
x86_64 x86_64 x86_64 GNU/Linux

Partha Raghavan

F.A.S.T.

Bear Stearns & Co. Inc.

383 Madison Avenue 

New York, NY 10179 

Ph. 212 272 3454 

Fax 212 272 7310

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