[R] LAPACK lib problem, lme4, lastest R, Linux

[Ron Burns]

I just dumped Vista off a laptop and installed Ubuntu 10.10 (latest 
release) as the single operating system. I did all of the updates and 
then installed emacs and ess. Next I installed R by following the the 
usual instructions on the CRAN site. At this point all is working I am 
now in the process of installing the packages that I normally have 
installed. I am having a problem with the LAPACK libraries when 
installing lme4, but the problem is not unique to lme4. It is either a 
link to or missing LAPACK libs. I am at a loss as what I am doing wrong 
since I have started with a completely clean machine and am not trying 
to anything special.

-------HERE is the R startup:
  <wow> (ron) R

R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

-------HERE is the final output from trying to install lme4:
* installing *source* package lme4 ...
** libs
gcc -I/usr/share/R/include   -I"/usr/lib/R/library/Matrix/include" 
-I"/usr/lib/R/library/stats/include"   -fpic  -std=gnu99 -O3 -pipe  -g 
-c init.c -o init.o
gcc -I/usr/share/R/include   -I"/usr/lib/R/library/Matrix/include" 
-I"/usr/lib/R/library/stats/include"   -fpic  -std=gnu99 -O3 -pipe  -g 
-c lmer.c -o lmer.o
gcc -I/usr/share/R/include   -I"/usr/lib/R/library/Matrix/include" 
-I"/usr/lib/R/library/stats/include"   -fpic  -std=gnu99 -O3 -pipe  -g 
-c local_stubs.c -o local_stubs.o
gcc -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lf77blas 
-latlas -lgfortran -lm -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lf77blas
/usr/bin/ld: cannot find -latlas
collect2: ld returned 1 exit status
make: *** [lme4.so] Error 1
ERROR: compilation failed for package lme4
* removing /usr/local/lib/R/site-library/lme4

---------BUT
[ 48 ] <wow> (ron) /usr/bin/R CMD config LAPACK_LIBS
-llapack

---------AND
<wow> (ron) dpkg -l | grep lapack
ii  liblapack-dev                        3.2.1-8 
                    library of linear algebra routines 3 - static version
ii  liblapack3gf                         3.2.1-8 
                    library of linear algebra routines 3 - shared version
[ 44 ] <wow> (ron)

--------I did see a message indicating "Also do 'ldd 
/usr/lib/R/bin/exec/R' and make sure you do _not_ have a depends on 
Rlapack.so.  ....":

[ 47 ] <wow> (ron) ldd /usr/lib/R/bin/exec/R
	linux-gate.so.1 =>  (0x00533000)
	libR.so => /usr/lib/libR.so (0x0073e000)
	libc.so.6 => /lib/libc.so.6 (0x00110000)
	libf77blas.so.3gf => /usr/lib/libf77blas.so.3gf (0x00ed4000)
	libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x0026e000)
	libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00cca000)
	libm.so.6 => /lib/libm.so.6 (0x0065f000)
	libreadline.so.6 => /lib/libreadline.so.6 (0x00534000)
	libpcre.so.3 => /lib/libpcre.so.3 (0x00f5b000)
	liblzma.so.2 => /usr/lib/liblzma.so.2 (0x00568000)
	libz.so.1 => /lib/libz.so.1 (0x0058b000)
	libdl.so.2 => /lib/libdl.so.2 (0x005a0000)
	/lib/ld-linux.so.2 (0x00e67000)
	libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x005a4000)
	libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x005c4000)
	libpthread.so.0 => /lib/libpthread.so.0 (0x005e0000)
	libncurses.so.5 => /lib/libncurses.so.5 (0x005fa000)

[ 41 ] <wow> (ron) ls /usr/lib/libatlas*
/usr/lib/libatlas.so.3gf@
[ 42 ] <wow> (ron) ls /usr/lib/libf77blas*
/usr/lib/libf77blas.so.3gf@

-------- so these are there and linked OK and there is no Rlapack.so The 
links look OK.

Should I be linking to static libs and if so they do not seem to on my 
machine anywhere. ( a "find . -name "*f77blas*" (or on atlas) turned up 
so's only)

I am at a loss as to where to go from here.

Thank you all for your consideration.
	Ron Burns

-- 
R. R. Burns
Physicist (Retired)
Oceanside, CA