lme4 0.999375-20 installation error
On previous post I had tried to install with R CMD INSTALL and failed. This morning I installed using install.packages and everything worked fine for some reason. Thanks for your time.
sessionInfo()
R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base
install.packages("lme4_0.999375-20.tar.gz", repos=NULL)
Warning in install.packages("lme4_0.999375-20.tar.gz", repos = NULL) :
argument 'lib' is missing: using '/home/e38302/r_library'
* Installing *source* package 'lme4' ...
** libs
gcc -std=gnu99 -I/apps/R/R270/lib64/R/include -I/usr/local/include
-I"/home/lyman/r_library/Matrix/include" -fpic -g -O2 -c init.c -o
init.o
gcc -std=gnu99 -I/apps/R/R270/lib64/R/include -I/usr/local/include
-I"/home/lyman/r_library/Matrix/include" -fpic -g -O2 -c lmer.c -o
lmer.o
gcc -std=gnu99 -I/apps/R/R270/lib64/R/include -I/usr/local/include
-I"/home/lyman/r_library/Matrix/include" -fpic -g -O2 -c
local_stubs.c -o local_stubs.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o lme4.so init.o lmer.o
local_stubs.o -L/apps/R/R270/lib64/R/lib -lRlapack
-L/apps/R/R270/lib64/R/lib -lRblas -lg2c -lm
Mark Lyman, Statistician
ATK Launch Systems
mark.lyman at atk.com
(435) 863-2863
-----Original Message-----
From: dmbates at gmail.com [mailto:dmbates at gmail.com] On Behalf Of Douglas
Bates
Sent: Wednesday, July 09, 2008 3:55 PM
To: Lyman, Mark
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] lme4 0.999375-20 installation error
I'm not sure exactly what is happening on the Suse system but there
should be an additional -I clause in the call to gcc. When I compile
on a Red Hat system the transcript includes
gcc -I/unsup/R-2.7.0/lib/R/include -I/usr/local/include
-I"/u/b/a/bates/R/i686-pc-linux-gnu-library/2.7/Matrix/include"
-fpic -Wall -pedantic -g -O3 -std=gnu99 -c init.c -o init.o
It is the last -I clause that provides the location to find Matrix.h,
which is what you are missing here.
On Wed, Jul 9, 2008 at 4:24 PM, Mark Lyman <mark.lyman at atk.com> wrote:
I am attempting to install lme4 0.999375-20 on a SUSE 9.1 machine. I
have
already installed Matrix 0.999375-10. However, the lme4 install fails.
Do you
have any suggestions on what might be wrong? My output follows: * Installing *source* package 'lme4' ... ** libs gcc -std=gnu99 -I/apps/R/R270/lib64/R/include -I/usr/local/include
-fpic -
g -O2 -c init.c -o init.o init.c:3:20: Matrix.h: No such file or directory In file included from init.c:4: Syms.h:3: error: parse error before "lme4_ASym" Syms.h:3: warning: type defaults to `int' in declaration of
`lme4_ASym'
Syms.h:4: warning: type defaults to `int' in declaration of
`lme4_CmSym'
Syms.h:5: warning: type defaults to `int' in declaration of
`lme4_CxSym'
Syms.h:6: warning: type defaults to `int' in declaration of
`lme4_DimSym'
Syms.h:7: warning: type defaults to `int' in declaration of
`lme4_GpSym'
Syms.h:8: warning: type defaults to `int' in declaration of
`lme4_LSym'
Syms.h:9: warning: type defaults to `int' in declaration of
`lme4_RXSym'
Syms.h:10: warning: type defaults to `int' in declaration of
`lme4_RZXSym'
Syms.h:11: warning: type defaults to `int' in declaration of
`lme4_STSym'
Syms.h:12: warning: type defaults to `int' in declaration of
`lme4_VSym'
Syms.h:13: warning: type defaults to `int' in declaration of
`lme4_XSym'
Syms.h:14: warning: type defaults to `int' in declaration of
`lme4_ZtSym'
Syms.h:15: warning: type defaults to `int' in declaration of
`lme4_devianceSym'
Syms.h:16: warning: type defaults to `int' in declaration of
`lme4_dimsSym'
Syms.h:17: warning: type defaults to `int' in declaration of
`lme4_envSym'
Syms.h:18: warning: type defaults to `int' in declaration of
`lme4_etaSym'
Syms.h:19: warning: type defaults to `int' in declaration of
`lme4_fixefSym'
Syms.h:20: warning: type defaults to `int' in declaration of
`lme4_flistSym'
Syms.h:21: warning: type defaults to `int' in declaration of
`lme4_gradientSym'
Syms.h:22: warning: type defaults to `int' in declaration of
`lme4_iSym'
Syms.h:23: warning: type defaults to `int' in declaration of
`lme4_muEtaSym'
Syms.h:24: warning: type defaults to `int' in declaration of
`lme4_muSym'
Syms.h:25: warning: type defaults to `int' in declaration of
`lme4_ncSym'
Syms.h:26: warning: type defaults to `int' in declaration of
`lme4_nlmodelSym'
Syms.h:27: warning: type defaults to `int' in declaration of
`lme4_offsetSym'
Syms.h:28: warning: type defaults to `int' in declaration of
`lme4_pSym'
Syms.h:29: warning: type defaults to `int' in declaration of
`lme4_pWtSym'
Syms.h:30: warning: type defaults to `int' in declaration of
`lme4_permSym'
Syms.h:31: warning: type defaults to `int' in declaration of
`lme4_ranefSym'
Syms.h:32: warning: type defaults to `int' in declaration of
`lme4_residSym'
Syms.h:33: warning: type defaults to `int' in declaration of
`lme4_sigmaSym'
Syms.h:34: warning: type defaults to `int' in declaration of
`lme4_sqrtXWtSym'
Syms.h:35: warning: type defaults to `int' in declaration of
`lme4_sqrtrWtSym'
Syms.h:36: warning: type defaults to `int' in declaration of
`lme4_uSym'
Syms.h:37: warning: type defaults to `int' in declaration of
`lme4_varSym'
Syms.h:38: warning: type defaults to `int' in declaration of
`lme4_xSym'
Syms.h:39: warning: type defaults to `int' in declaration of
`lme4_ySym'
Syms.h:39: warning: data definition has no type or storage class init.c:37: error: parse error before "c" init.c:37: warning: type defaults to `int' in declaration of `c' init.c:37: warning: data definition has no type or storage class init.c: In function `R_init_lme4': init.c:54: warning: implicit declaration of function
`M_R_cholmod_start'
init.c:55: error: request for member `final_ll' in something not a
structure or
union init.c:57: warning: assignment makes integer from pointer without a
cast
init.c:58: warning: assignment makes integer from pointer without a
cast
init.c:59: warning: assignment makes integer from pointer without a
cast
init.c:60: warning: assignment makes integer from pointer without a
cast
init.c:61: warning: assignment makes integer from pointer without a
cast
init.c:62: warning: assignment makes integer from pointer without a
cast
init.c:63: warning: assignment makes integer from pointer without a
cast
init.c:64: warning: assignment makes integer from pointer without a
cast
init.c:65: warning: assignment makes integer from pointer without a
cast
init.c:66: warning: assignment makes integer from pointer without a
cast
init.c:67: warning: assignment makes integer from pointer without a
cast
init.c:68: warning: assignment makes integer from pointer without a
cast
init.c:69: warning: assignment makes integer from pointer without a
cast
init.c:70: warning: assignment makes integer from pointer without a
cast
init.c:71: warning: assignment makes integer from pointer without a
cast
init.c:72: warning: assignment makes integer from pointer without a
cast
init.c:73: warning: assignment makes integer from pointer without a
cast
init.c:74: warning: assignment makes integer from pointer without a
cast
init.c:75: warning: assignment makes integer from pointer without a
cast
init.c:76: warning: assignment makes integer from pointer without a
cast
init.c:77: warning: assignment makes integer from pointer without a
cast
init.c:78: warning: assignment makes integer from pointer without a
cast
init.c:79: warning: assignment makes integer from pointer without a
cast
init.c:80: warning: assignment makes integer from pointer without a
cast
init.c:81: warning: assignment makes integer from pointer without a
cast
init.c:82: warning: assignment makes integer from pointer without a
cast
init.c:83: warning: assignment makes integer from pointer without a
cast
init.c:84: warning: assignment makes integer from pointer without a
cast
init.c:85: warning: assignment makes integer from pointer without a
cast
init.c:86: warning: assignment makes integer from pointer without a
cast
init.c:87: warning: assignment makes integer from pointer without a
cast
init.c:88: warning: assignment makes integer from pointer without a
cast
init.c:89: warning: assignment makes integer from pointer without a
cast
init.c:90: warning: assignment makes integer from pointer without a
cast
init.c:91: warning: assignment makes integer from pointer without a
cast
init.c:92: warning: assignment makes integer from pointer without a
cast
init.c:93: warning: assignment makes integer from pointer without a
cast
init.c: In function `R_unload_lme4': init.c:100: warning: implicit declaration of function
`M_cholmod_finish'
make: *** [init.o] Error 1 ERROR: compilation failed for package 'lme4' Mark Lyman, Statistician ATK Launch Systems
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