[R-sig-Debian] update.packages() for R 2.7.1: mgcv fails
Dirk Eddelbuettel
edd at debian.org
Tue Dec 9 17:26:51 CET 2008
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
|
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