[BioC] [R] BioC 2.3 standard installation
Hervé Pagès
hpages at fhcrc.org
Tue Dec 2 02:06:10 CET 2008
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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, Hervé Pagès <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.
>
>
--
Hervé Pagès
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
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