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

[Ron Burns]

With help from Dirk Eddelbuettel we found that I needed to explicitly 
install libatlas-base-dev.  After doing this everything worked with no 
further fuss.

Best Regards,
     Ron

On 11/13/2010 11:10 AM, Ron Burns wrote:
> 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