[R] [BioC] BioC 2.3 standard installation

[Hervé Pagès]

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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
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