I am not sure if this is an R development problem or not. I am starting
with completely clean OS and and installing the latest version of R
without trying to anything special but I am having trouble with the
LAPACK library linking when I try to build packages that require them.
I thought perhaps my problem may be if interest here.
I just dumped Vista off a laptop formatted the disk 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. The libs seem to be installed
and there are links to them, but perhaps they are the wrong links. 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
---------The
/usr/bin/ld: cannot find -lf77blas
/usr/bin/ld: cannot find -latlas
errors are common to any other packages that use these libraries so it
not an lme4 package problem.
---------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.
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
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