[back to the lists] So it seems that r-base-dev forgets to depend on libatlas-base-dev You can fix this by installing libatlas-base-dev manually: apt-get install libatlas-base-dev This should solve the compilation/linking problem with KernSmooth, preprocessCore and any other package that needs to be linked against the BLAS/ATLAS/LAPACK libraries on Ubuntu 8.10 (Intrepid Ibex). Note that this problem only affects people that get their R-2.8 from r-base + r-base-dev Cheers, H.
Tiandao Li wrote:
This is my installation:
> install.packages("KernSmooth")
Warning in install.packages("KernSmooth") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://cran.fhcrc.org/src/contrib/KernSmooth_2.22-22.tar.gz'
Content type 'application/x-gzip' length 28422 bytes (27 Kb)
opened URL
==================================================
downloaded 27 Kb
* Installing *source* package 'KernSmooth' ...
** libs
gfortran -fpic -g -O2 -c blkest.f -o blkest.o
gfortran -fpic -g -O2 -c cp.f -o cp.o
gfortran -fpic -g -O2 -c dgedi.f -o dgedi.o
gfortran -fpic -g -O2 -c dgefa.f -o dgefa.o
gfortran -fpic -g -O2 -c dgesl.f -o dgesl.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o
gfortran -fpic -g -O2 -c linbin2D.f -o linbin2D.o
gfortran -fpic -g -O2 -c linbin.f -o linbin.o
gfortran -fpic -g -O2 -c locpoly.f -o locpoly.o
gfortran -fpic -g -O2 -c rlbin.f -o rlbin.o
gfortran -fpic -g -O2 -c sdiag.f -o sdiag.o
gfortran -fpic -g -O2 -c sstdiag.f -o sstdiag.o
gcc -std=gnu99 -shared -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o
dgesl.o init.o linbin2D.o linbin.o locpoly.o rlbin.o sdiag.o sstdiag.o
-lf77blas -latlas -lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lf77blas
collect2: ld returned 1 exit status
make: *** [KernSmooth.so] Error 1
ERROR: compilation failed for package 'KernSmooth'
** Removing '/usr/local/lib/R/site-library/KernSmooth'
The downloaded packages are in
/tmp/RtmpqCLrkQ/downloaded_packages
Warning message:
In install.packages("KernSmooth") :
installation of package 'KernSmooth' had non-zero exit status
On Mon, Dec 1, 2008 at 4:05 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:
I'm taking this off-list for now.
Tiandao Li wrote:
[...]
library()
[...]
KernSmooth Functions for kernel smoothing for Wand & Jones
(1995)
yes this shows that you have KernSmooth but my suggestion was that you
try to install it *from source*. I don't know how you got this
KernSmooth, maybe you installed the Ubuntu pkg r-cran-kernsmooth,
which is a binary package (precompiled), so the fact that you were
able to install it doesn't tell me anything useful...
Thanks!
H.
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319