R SIG Debian - Dec 2008 - Ubuntu 8.10: Package installation fails (lf77blas problem)

I just upgraded to Ubuntu 8.10 (i386) from 8.04. After the upgrade, I ran
update.packages(.libPaths()[1]) in R to get the packages installed from source
up to date too. Unfortunately, two packages could not be updated: mclust and
mboost. In both cases, the error I got mentioned lf77blas. Here's the output
for
mboost:

* Installing *source* package 'mboost' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mboost.c -o mboost.o
gcc -std=gnu99 -shared  -o mboost.so mboost.o -lf77blas -latlas -lgfortran -lm 
-L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lf77blas
collect2: ld returned 1 exit status
make: *** [mboost.so] Error 1
ERROR: compilation failed for package 'mboost'

I guess this has something to do with the removal of the g77 package from Ubuntu
8.10. Is there anything I can do short of compiling g77 and/or R myself?

Hello Ulrich,

maybe the installation of the packages 'r-base-core-ra' and
'r-cran-jit'
(the former package is suggested by the latter) will solve your problem.
I ran into to the same problem, though for different CRAN packages and
IIRC after installation of the two deb-packages all was fine.

Best,
Bernhard
>
>I just upgraded to Ubuntu 8.10 (i386) from 8.04. After the 
>upgrade, I ran
>update.packages(.libPaths()[1]) in R to get the packages 
>installed from source
>up to date too. Unfortunately, two packages could not be 
>updated: mclust and
>mboost. In both cases, the error I got mentioned lf77blas. 
>Here's the output for
>mboost:
>
>* Installing *source* package 'mboost' ...
>** libs
>gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c 
>mboost.c -o mboost.o
>gcc -std=gnu99 -shared  -o mboost.so mboost.o -lf77blas 
>-latlas -lgfortran -lm 
>-L/usr/lib/R/lib -lR
>/usr/bin/ld: cannot find -lf77blas
>collect2: ld returned 1 exit status
>make: *** [mboost.so] Error 1
>ERROR: compilation failed for package 'mboost'
>
>I guess this has something to do with the removal of the g77 
>package from Ubuntu
>8.10. Is there anything I can do short of compiling g77 and/or 
>R myself?
>
>_______________________________________________
>R-SIG-Debian mailing list
>R-SIG-Debian at r-project.org
>https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>
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On 8 December 2008 at 07:25, Ulrich Keller wrote:
| I just upgraded to Ubuntu 8.10 (i386) from 8.04. After the upgrade, I ran
| update.packages(.libPaths()[1]) in R to get the packages installed from source
| up to date too. Unfortunately, two packages could not be updated: mclust and
| mboost. In both cases, the error I got mentioned lf77blas. Here's the
output for
| mboost:
| 
| * Installing *source* package 'mboost' ...
| ** libs
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mboost.c -o
mboost.o
| gcc -std=gnu99 -shared  -o mboost.so mboost.o -lf77blas -latlas -lgfortran -lm
| -L/usr/lib/R/lib -lR
| /usr/bin/ld: cannot find -lf77blas
| collect2: ld returned 1 exit status
| make: *** [mboost.so] Error 1
| ERROR: compilation failed for package 'mboost'
| 
| I guess this has something to do with the removal of the g77 package from
Ubuntu
| 8.10. Is there anything I can do short of compiling g77 and/or R myself?

It is not g77 itself (which was replaced by the improved gfortran), it
appears to be a Fortran-built BLAS library for linear algebra. 

As I have no issue building these package, let's see where this library
comes from:

  edd at joe:~$ locate libf77blas.so
  /usr/lib/libf77blas.so
  /usr/lib/libf77blas.so.3gf
  /usr/lib/libf77blas.so.3gf.0

and hence 
  
  edd at joe:~$ dpkg -S /usr/lib/libf77blas.so
  libatlas-base-dev: /usr/lib/libf77blas.so

So 'sudo apt-get install libatlas-base-dev' should fix it for you.  

This is a tricky area because we try to depend on a virtual BLAS
implementation that can be provided by either the atlas packages, or the
reference blas.  Something may changed there and made the dependency
'concrete' onto just the libatlas package.  We will have a look --
thanks
for the heads-up.

In the meantime, libatlas-base-dev should provide you with libf77blas.so to
build packages containing Fortran code.

Dirk

-- 
Three out of two people have difficulties with fractions.