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
On 14 November 2010 at 10:05, Ron Burns wrote:
| 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.
I think you were pretty close by looking at lapack-dev and blas-dev, but you
missed atlas-dev. Simply do
$ sudo apt-get install r-base-dev
to install the meta-package providing R-build dependencies and you should be
set. Substitute your favourite package management front-end for apt-get here.
A nice trick is to also check build-dependencies of existing packages. As you
struggled with lme4, you could compare against the recorded Build-Depends on
the r-cran-lme4 package I maintain:
Build-Depends: debhelper (>= 7.0.0), cdbs, r-base-dev (>= 2.12.0), \
r-cran-matrix (>= 0.999375-31), r-cran-lattice, r-cran-nlme
That's from the most recent package lme4-0.999375-37 which you may also find
built for Ubuntu thanks to the tireless work of Vincent and Michael who port
my Debian (core) packages for R to the CRAN repositories. See the README at
http://cran.r-project.org/bin/linux/ubuntu/
If you need further assistance, feel free to come to r-sig-debian for Debian
and Ubuntu matters.
Hth, Dirk
|
| Thank you all for your consideration.
| Ron Burns
|
|
|
| --
| R. R. Burns
| Physicist (Retired)
| Oceanside, CA
|
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
On 11/14/2010 12:05 PM, Dirk Eddelbuettel wrote:> > On 14 November 2010 at 10:05, Ron Burns wrote: > | I am not sure if this is an R development problem or not. I am starting> I think you were pretty close by looking at lapack-dev and blas-dev, but you > missed atlas-dev. Simply do > > $ sudo apt-get install r-base-dev >Thank you for your kind and radid reply. I thought I had done that and if in fact I had because when I ran this just now I get a message that "r-base-dev is already the newest version" Regards, Ron -- R. R. Burns Physicist (Retired) Oceanside, CA
On November 14, 2010 10:05:24 am Ron Burns wrote:> [ 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.These are soft links. Could you do an 'ls -l' and see what they are linked to? And if it's another link in /etc/alternatives, could you check its target, too? My guess is that the indirection in /etc/alternatives somehow went awry. Davor