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 <aloboa...@gmail.com>
Reply-To: aloboa...@gmail.com
To: Dirk Eddelbuettel <e...@debian.org>
CC: Martin Maechler <maech...@stat.math.ethz.ch>,
r-sig-deb...@stat.math.ethz.ch
References: <18953.17704.527898.355...@lynne.math.ethz.ch>
<18953.23458.954016.424...@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:
e...@ron:~> echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save
R> library(robustbase);cat("Hi\n")
Hi
R>
e...@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 <aloboa...@gmail.com>
| To: "r-h...@r-project.org" <r-h...@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.l...@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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