[R-sig-Debian] [Fwd: Re: ubuntu problem with 'r-cran-robustbase' [FWD Agustin Lobo]]

[Agustin Lobo]

Subject: Re: [R-sig-Debian] ubuntu problem with 'r-cran-robustbase' [FWD
Agustin Lobo]
Date: Tue, 12 May 2009 13:30:49 +0200
From: Agustin Lobo <aloboaleu at gmail.com>
Reply-To: aloboaleu at gmail.com
To: Dirk Eddelbuettel <edd at debian.org>
CC: Martin Maechler <maechler at stat.math.ethz.ch>,
R-SIG-Debian at stat.math.ethz.ch
References: <18953.17704.527898.355877 at lynne.math.ethz.ch>
<18953.23458.954016.424944 at ron.nulle.part>

Dirk,
> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase 
from CRAN
> sources.  And file a bug report with Ubuntu.

That's the first thing I did: tried to install using
install.packages("robustbase"), which downloads the source and tries to
compile. But the gcc step fails:
gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o
qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib
-lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm
-L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lRlapack
collect2: ld returned 1 exit status

Also, when you say "fill a bug with Ubuntu", is there an r-sig-ubuntu or
the Launchpad for general bug reports in Ubuntu?

Thanks

Agus


Dirk Eddelbuettel escribió:
> On 12 May 2009 at 11:45, Martin Maechler wrote:
> | Agustin, posted on R-help.
> | I think the problem is one of the debian/ubuntu package
> | 'r-cran-robustbase' and its setup or (missing?) dependencies.
> | 
> | I can confirm Agustin's problem, working on Ubuntu 8.04.2
> | (8.04 is a "LTS" = long time support version).
> | 
> |   apt-get install r-cran-robustbase
> | 
> | works fine, but when trying to load the package,
> | there's a DLL - dependency on libRlapack.so 
> | which is not fulfilled (and not fulfillable: There's *no*
> | libRlapack.so).
> | 
> | For me,
> | 
> |   $ /usr/bin/R CMD config LAPACK_LIBS
> |   -llapack
> | 
> | and lapack.so is found inside /usr/lib/R/modules/ 
> | and liblapack.so from the 'lapack3' Debian/Ubuntu package 
> | is simply in /usr/lib/libpack.so  
> | 
> | Could it be that this is caused by an Ubuntu / Debian 
> | mismatch?
> 
> Scratch Debian here. It works there:
> 
> edd at ron:~> echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save
> R> library(robustbase);cat("Hi\n")
> Hi
> R>
> edd at ron:~>
> 
> It looks like Ubuntu failed to rebuild the package. The Rlapack.so vs
> lapack.so is an old one from the Atlas 3.6 / gfortran transition well over a
> year ago and had affected other package.
> 
> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase from CRAN
> sources.  And file a bug report with Ubuntu.
> 
> Dirk
> 
> 
> | Thank you in advance,
> | 
> | Martin Maechler, ETH Zurich
> | 
> | ------- start of forwarded message -------
> | From: Agustin Lobo <aloboaleu at gmail.com>
> | To: "r-help at r-project.org" <r-help at r-project.org>
> | Subject: [R] robustbase: cannot install
> | Date: Mon, 11 May 2009 18:20:14 +0200
> | 
> | This is really odd,
> | I've installed the binary of robustbase through synaptic on an ubuntu 
> | 8.04 machine and get:
> |  > library(robustbase)
> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |    unable to load shared library 
> | '/usr/lib/R/site-library/robustbase/libs/robustbase.so':
> |    libRlapack.so: cannot open shared object file: No such file or directory
> | Error: package/namespace load failed for 'robustbase'
> |  >
> | 
> | The package is where it is suposed to be:
> | /usr/lib/R/site-library/robustbase
> | 
> | is this not a problem at compiling?
> | 
> | The problem is that if I try to install the source with 
> | install.packages("robustbase"), I get:
> | gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o 
> | qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib 
> | -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm 
> | -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR
> | /usr/bin/ld: cannot find -lRlapack
> | collect2: ld returned 1 exit status
> | 
> | Despite the fact that I do have Rlapack:
> | ~$ R CMD config LAPACK_LIBS
> | -L/usr/lib/R/lib -lRlapack
> | 
> | Am I doing something wrong?
> | 
> | Thanks
> | 
> | Agus
> | -- 
> | Dr. Agustin Lobo
> | Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> | LLuis Sole Sabaris s/n
> | 08028 Barcelona
> | Spain
> | Tel. 34 934095410
> | Fax. 34 934110012
> | email: Agustin.Lobo at ija.csic.es
> | http://www.ija.csic.es/gt/obster
> | 
> | ______________________________________________
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> | https://stat.ethz.ch/mailman/listinfo/r-help
> | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> | and provide commented, minimal, self-contained, reproducible code.
> | ------- end of forwarded message -------
> | 
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