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

Thu Apr 3 00:02:00 CEST 2008

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:
> 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
>
>
>
>
>
>
>  ***********************************************************************
>  Bear Stearns is not responsible for any recommendation, ...{{dropped:8}}
>
>
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