[R-sig-Debian] ubuntu problem with 'r-cran-robustbase' [FWD Agustin Lobo]
Agustin Lobo
alobolistas at gmail.com
Tue May 12 16:18:51 CEST 2009
Dirk Eddelbuettel wrote:
> 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?
Synaptic
repository http://cran.r-project.org/bin/linux/ubuntu hardy
> Which Ubuntu release?
Ubuntu 8.04
> Which R release?
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu
>
> 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:~$
>
And I have:
alobo at alobo-laptop:~$ ldd /usr/lib/R/bin/exec/R
linux-gate.so.1 => (0xb7f44000)
libR.so => /usr/lib/R/lib/libR.so (0xb7c21000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7ad2000)
libblas.so.3gf => /usr/lib/libblas.so.3gf (0xb7a53000)
libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0xb79bc000)
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7997000)
libreadline.so.5 => /lib/libreadline.so.5 (0xb7966000)
libpcre.so.3 => /usr/lib/libpcre.so.3 (0xb793f000)
libz.so.1 => /usr/lib/libz.so.1 (0xb792a000)
libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb7926000)
/lib/ld-linux.so.2 (0xb7f45000)
libncurses.so.5 => /lib/libncurses.so.5 (0xb78f5000)
> 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) ...
If I do the same, I just get:
$ sudo wajig install r-cran-robustbase
[sudo] password for alobo:
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-cran-robustbase is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> edd at joe:~$ echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save
>> library(robustbase);cat("Hi\n")
> Hi
> edd at joe:~$
>
In my case:
$ echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save
> library(robustbase);cat("Hi\n")
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'
Execution halted
> So scratch Ubuntu too. The error is local to Augustin's system, and as per
> Martin, possibly other older Ubuntu sytems. Just upgrade.
Ubuntu 8.04 is an LTS
> | 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.
I did not break anything. I made the link because a (bad) advice here:
https://stat.ethz.ch/pipermail/r-sig-debian/2009-March/000650.html
and then just removed it because I was told this was not a good idea.
Can you upgrade to 9.04 ?
I could, but rather put my time on other things, this is why I stick to
LTS distributions. So if there is no alternative, I'll have to do it.
> So to sum up: No bug on current Debian testing or Ubuntu jaunty.
No. The complete summary must include: + bug on Ubuntu 8.04
Thanks
Agus
> 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 -------
> | > |
> | > | _______________________________________________
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> | > | R-SIG-Debian at r-project.org
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> | >
>
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