R SIG Debian - May 2009 - ubuntu problem with 'r-cran-robustbase' [FWD Agustin Lobo]

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?

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 -------

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

-- 
Three out of two people have difficulties with fractions.

On 12 May 2009 at 13:30, Agustin Lobo wrote:
| 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

Where is your R from?  Which Ubuntu release?  Which R release?

On a just-upgraded Ubuntu 9.04 which CRAN-port-for-Ubuntu packages thanks to
Vincent and Michael, I have

edd at joe:~$ ldd /usr/lib/R/bin/exec/R
        linux-gate.so.1 =>  (0xb7f07000)
        libR.so => /usr/lib/R/lib/libR.so (0xb7bd9000)
        libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7a76000)
        libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0xb76f9000)
        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb7645000)
        libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb761f000)
        libreadline.so.5 => /lib/libreadline.so.5 (0xb75ed000)
        libpcre.so.3 => /lib/libpcre.so.3 (0xb75bb000)
        libbz2.so.1.0 => /lib/libbz2.so.1.0 (0xb75aa000)
        libz.so.1 => /lib/libz.so.1 (0xb7593000)
        libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb758f000)
        /lib/ld-linux.so.2 (0xb7f08000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7580000)
        libncurses.so.5 => /lib/libncurses.so.5 (0xb754e000)
edd at joe:~$

As I recall, Rlapack.so disappeared from my system a long time ago.  You may
need to sort some things out on your system.

And with that, here is the test I should have done earlier but didn't for
lack of time:

edd at joe:~$ wajig install r-cran-robustbase
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  [...]
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
  r-cran-robustbase
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 639kB of archives.
After this operation, 2187kB of additional disk space will be used.
Get:1 http://ron jaunty/universe r-cran-robustbase 0.4-3-1 [639kB]
Fetched 639kB in 6s (94.9kB/s)
Selecting previously deselected package r-cran-robustbase.
(Reading database ... 345584 files and directories currently installed.)
Unpacking r-cran-robustbase (from .../r-cran-robustbase_0.4-3-1_i386.deb) ...
Setting up r-cran-robustbase (0.4-3-1) ...
edd at joe:~$  echo 'library(robustbase);cat("Hi\n")' | R
--silent --no-save
> library(robustbase);cat("Hi\n")
Hi
>
edd at joe:~$

So scratch Ubuntu too.  The error is local to Augustin's system, and as per
Martin, possibly other older Ubuntu sytems.  Just upgrade.
 
| Also, when you say "fill a bug with Ubuntu", is there an
r-sig-ubuntu or
| the Launchpad for general bug reports in Ubuntu?

Launchpad.  But first get your ducks in a row. You may just have done
something to your system. Frankly, mails like your earlier 

	  Although
	  I did remove the ln
	  libRlapack.so -> ./lapack.so

don't install a lot of confidence in me that your system is still standard
enough for us to diagnose in a meaningful way. If you break it, you get to
keep the pieces.  Can you upgrade to 9.04 ?

So to sum up:  No bug on current Debian testing or Ubuntu jaunty.

Dirk

| 
| Thanks
| 
| Agus
| 
| 
| Dirk Eddelbuettel escribi :
| > 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
| > 

-- 
Three out of two people have difficulties with fractions.