I have R under Linux Kubuntu Hardy Heron 8.04 LTS.
I am trying to install package 'lme4' and get the following error:
----
* installing *source* package ‘lme4’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"
-fpic -g -O2 -c
init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"
-fpic -g -O2 -c
lmer.c -o lmer.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"
-fpic -g -O2 -c
local_stubs.c -o local_stubs.o
gcc -std=gnu99 -shared -o lme4.so init.o lmer.o
local_stubs.o -L/usr/lib64/R/lib -lRlapack -lblas -lgfortran -lm -lgcc_s
-L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lRlapack
collect2: ld devolvió el estado de salida 1
make: *** [lme4.so] Error 1
ERROR: compilation failed for package ‘lme4’
* removing ‘/usr/local/lib/R/site-library/lme4’
The downloaded packages are in
‘/tmp/Rtmp7uCMsh/downloaded_packages’
Mensajes de aviso perdidos
In install.packages("lme4") :
installation of package 'lme4' had non-zero exit status
-----
Surfing on internet and R hel system it seems the problem is related to
LAPACK, LBAS. ATLAS libraries. R tries to find unsuccessfully " -lRlapack "
I have checked which libraries R is pointing to:
---
bu...@temisto:~$ ldd /usr/lib/R/bin/exec/R
linux-vdso.so.1 => (0x00007fff1e100000)
libR.so => /usr/lib/R/lib/libR.so (0x00007f9157c54000)
libc.so.6 => /lib/libc.so.6 (0x00007f91578f2000)
libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f9156f42000)
libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00007f9156c83000)
libm.so.6 => /lib/libm.so.6 (0x00007f9156a02000)
libreadline.so.5 => /lib/libreadline.so.5 (0x00007f91567c2000)
libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00007f915659c000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007f9156385000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f9156181000)
/lib64/ld-linux-x86-64.so.2 (0x00007f91581c0000)
libncurses.so.5 => /lib/libncurses.so.5 (0x00007f9155f46000)
---
Also if I have the LAPACK and ATLAS libraries installed:
bu...@temisto:~$ dpkg -l | grep lapack
ii lapack3 3.0.20000531a-6.1ubuntu1
ii liblapack-dev 3.1.1-0.3ubuntu2
ii liblapack3gf 3.1.1-0.3ubuntu2
bu...@temisto:~$ dpkg -l | grep atlas
ii atlas3-base 3.6.0-20.6
ii libatlas-base-dev 3.6.0-21.1ubuntu3
ii libatlas-headers 3.6.0-21.1ubuntu3
ii libatlas3gf-base 3.6.0-21.1ubuntu3
---
R CMD config BLAS_LIBS
-lblas
R CMD config LAPACK_LIBS
-L/usr/lib64/R/lib -lRlapack
R seems to be looking for LAPACK in "/usr/lib64/R/lib -lRlapack", probably the
wrong place.
Can somebody point me to a possible solution?
--
Dr Javier Bustamante
Estación Biológica de Doñana, CSIC
Dept. Wetland Ecology
Américo Vespucio s/n
41092 - Sevilla
Spain
voice: +34 954 466700 ext. 1217
fax: +34 954 621125
e-mail: jbustama...@ebd.csic.es
http://www.ebd.csic.es/bustamante/index.html
-----other links-------
http://last-ebd.blogspot.com/
http://euroconbio.blogspot.com/
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