R SIG Debian - Dec 2008 - update.packages() for R 2.7.1: mgcv fails

Hi
I just upgraded my debian/stable to R 2.7.1 via apt-get install r-base 
r-base-core r-base-dev, and then
began to update.packages()

 > update.packages(lib.loc="/usr/local/lib/R/site-library")
 > update.packages(lib.loc="/usr/lib/R/library")
but I get:
  ....
* Installing *source* package 'mgcv' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c gcv.c -o gcv.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c gdi.c -o gdi.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c magic.c -o 
magic.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mat.c -o mat.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c matrix.c -o 
matrix.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c qp.c -o qp.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c tprs.c -o tprs.o
gcc -std=gnu99 -shared  -o mgcv.so gcv.o gdi.o init.o magic.o mat.o 
matrix.o mgcv.o qp.o tprs.o -llapack -lblas -lgfortran -lm  
-L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package 'mgcv'
** Removing '/usr/lib/R/library/mgcv'
** Restoring previous '/usr/lib/R/library/mgcv'
*

I'm not sure which version of lapack is missing or where to find it.
Also, for r-cran-* packages, whether 
update.packages(lib.loc="/usr/lib/R/library")
is equivalent to apt-get install r-cran-mgcv etc.

thanks,
-Michael


 > sessionInfo()
R version 2.7.1 (2008-06-23)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_CA;LC_NUMERIC=C;LC_TIME=en_CA;LC_COLLATE=en_CA;LC_MONETARY=C;LC_MESSAGES=en_CA;LC_PAPER=en_CA;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.7.1
 >

-- 
Michael Friendly     Email: friendly at yorku.ca 
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

Hi Michael,

On 9 December 2008 at 10:33, Michael Friendly wrote:
| Hi
| I just upgraded my debian/stable to R 2.7.1 via apt-get install r-base 
| r-base-core r-base-dev, and then

Did you get them from Debian, or from CRAN ?  I presume it is CRAN?

| began to update.packages()
| 
|  > update.packages(lib.loc="/usr/local/lib/R/site-library")
|  > update.packages(lib.loc="/usr/lib/R/library")
| but I get:
|   ....
| * Installing *source* package 'mgcv' ...
| ** libs
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c gcv.c -o gcv.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c gdi.c -o gdi.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c init.c -o init.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c magic.c -o 
| magic.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mat.c -o mat.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c matrix.c -o 
| matrix.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mgcv.c -o mgcv.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c qp.c -o qp.o
| gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c tprs.c -o tprs.o
| gcc -std=gnu99 -shared  -o mgcv.so gcv.o gdi.o init.o magic.o mat.o 
| matrix.o mgcv.o qp.o tprs.o -llapack -lblas -lgfortran -lm  
| -L/usr/lib/R/lib -lR
| /usr/bin/ld: cannot find -llapack
| collect2: ld returned 1 exit status
| make: *** [mgcv.so] Error 1
| ERROR: compilation failed for package 'mgcv'
| ** Removing '/usr/lib/R/library/mgcv'
| ** Restoring previous '/usr/lib/R/library/mgcv'
| *
| 
| I'm not sure which version of lapack is missing or where to find it.

You need liblapack-dev with a version of 3.1 or greater.  You may need to point
apt to backports.org -- not sure as I do not run Debian stable (but only
testing).

However the README on CRAN in the bin/linux/debian directory mentions
pre-built packages for r-recommended, so for mgcv you could

	  sudo apt-get install r-cran-mgcv

to get working.  You'd still need liblapack I suppose.

| Also, for r-cran-* packages, whether 
| update.packages(lib.loc="/usr/lib/R/library")
| is equivalent to apt-get install r-cran-mgcv etc.

Versions can be different between the two. It is a tradeoff choice you need
to make.  'apt-cache policy somepackage' will always tell you what
version
you'd get from the different (if any) repos you are lined up to.  Doing R
directly via install.packages() is completely independent to that though but
should stay clear of trouble as non-overlapping directory trees are used.

Hope this helps, Dirk

| 
| thanks,
| -Michael
| 
| 
|  > sessionInfo()
| R version 2.7.1 (2008-06-23)
| i486-pc-linux-gnu
| 
| locale:
|
LC_CTYPE=en_CA;LC_NUMERIC=C;LC_TIME=en_CA;LC_COLLATE=en_CA;LC_MONETARY=C;LC_MESSAGES=en_CA;LC_PAPER=en_CA;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA;LC_IDENTIFICATION=C
| 
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
| 
| loaded via a namespace (and not attached):
| [1] tools_2.7.1
|  >
| 
| -- 
| Michael Friendly     Email: friendly at yorku.ca 
| Professor, Psychology Dept.
| York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
| 4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
| Toronto, ONT  M3J 1P3 CANADA
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

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