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Help installing Package lme4

2 messages · Raghavan, Partha (Exchange), Douglas Bates

Original
Raghavan, Partha (Exchange)
# 
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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***********************************************************************
Bear Stearns is not responsible for any recommendation, ...{{dropped:8}}
Douglas Bates
# 
You need to have the Matrix package installed before you can install
the lme4 package.  The missing header files are found in the installed
Matrix package.

If you have the Matrix package installed then the R CMD INSTALL script
should find the directory with those headers and put it on the include
path for the compilations.

On Wed, Apr 2, 2008 at 4:32 PM, Raghavan, Partha (Exchange)
<Praghavan at bear.com> wrote: