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

[Michael Rutter]

Agus,

robustbase just installed fine on my stock 8.04 system.  Please make 
sure that you have added all the repositories and packages suggested on 
this page:

http://cran.r-project.org/bin/linux/ubuntu/

Backports are important, and make sure you have r-base-dev
installed.  You may also need to be root (via sudo) to install, although 
there are instructions for local installation.  You can run the 
following commands to see what R related packages you have installed.

dpkg --get-selections | grep r-base
dpkg --get-selections | grep r-cran

Michael

Agustin Lobo wrote:
> 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
>> | | ______________________________________________
>> | R-help at r-project.org mailing list
>> | 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 -------
>> | | _______________________________________________
>> | R-SIG-Debian mailing list
>> | R-SIG-Debian at r-project.org
>> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>
> 
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-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter