R-SIG-Debian Digest, Vol 58, Issue 3

food now? or after work in the library?

On Wed, 2010-06-02 at 12:00 +0200, r-sig-debian-request at r-project.org
wrote:
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Today's Topics:

   1. Re: R 2.11.0 for Ubuntu 10.04 Lucid Lynx on CRAN
      (Mauricio Zambrano)
   2. Re: building rpy against lenny-cran (Johannes Ranke)
   3. Re: TSA package dependencies (Scott Brogan)
   4. Re: Compiling R-2.11.0 with ATLAS-tuned BLAS and	LAPACK
      (Paul Johnson)
   5. Re: Compiling R-2.11.0 with ATLAS-tuned BLAS	and	LAPACK
      (Dirk Eddelbuettel)
   6. Re: Compiling R-2.11.0 with ATLAS-tuned BLAS and	LAPACK
      (Andrew Piskorski)

----------------------------------------------------------------------

Message: 1
Date: Tue, 1 Jun 2010 15:13:24 +0200
From: Mauricio Zambrano <hzambran.newsgroups at gmail.com>
To: mar36 at psu.edu
Cc: r-sig-debian <r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] R 2.11.0 for Ubuntu 10.04 Lucid Lynx on
	CRAN
Message-ID:
	<AANLkTil89IpynWfXUIz5iw_uiTKz7b2iATtJCV-SjM6- at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Carlos and Michael,

2010/6/1 Michael Rutter <mar36 at psu.edu>:

On 06/01/2010 07:05 AM, Carlos J. Gil Bellosta wrote:

Hello,

What runs underneath is the download.file() function.

Can you download a file with it? For instance, I can do

download.file( "http://www.google.com/index.html", "index.html" )

Can you?

Best regards,

Carlos J. Gil Bellosta
http://www.datanalytics.com

2010/6/1 Mauricio Zambrano<hzambran.newsgroups at gmail.com>:

2010/6/1 Carlos J. Gil Bellosta<cgb at datanalytics.com>:

Hello,

Did you try an alternative CRAN mirror?

Yes, I have tried some of Spain, UK and Italy, but I still get the
same error message....

Kinds

Mauricio

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Mauricio,

I was successfully able to use 'update.packages' using mirrors in both Spain
and the UK, so I can't replicate the problem right now. ?I do recall having
a similar issue a couple of weeks ago, but the problem fixed itself within a
couple of hours. ?I just assumed that the mirror I was using was having some
downtime.

I was also assuming some problems with the mirror, but this should not
be correct if you could update your packages with mirrors in Spain and
UK (Bristol).

Are you updating packages under your username or sudo? ?I think Carlos is on
the correct track in that the account or session you are using doesn't have
access to the internet for some reason. ?Have you rebooted your machine
lately? ?That may fix a problem another update created.

I'm running R with sudo, and I've rebooted my Pc several times today,
but still nothing....

I would like to know if there are other user experiencing the same
problem, to find out if the problem is on my machine or on the mirror.

Hope this helps,
Michael

Thanks for your help.

Kinds,

Mauricio

-- 
?==========================
Dept. of Civil and Env. Engineering
University of Trento, Italy

--
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

------------------------------

Message: 2
Date: Tue, 1 Jun 2010 21:07:33 +0200
From: Johannes Ranke <jranke at uni-bremen.de>
To: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] building rpy against lenny-cran
Message-ID: <201006012107.34234.jranke at uni-bremen.de>
Content-Type: Text/Plain;  charset="iso-8859-1"

Hi Kouros,

mhm, did we go to Cedar Cliff together? Did we go to model UN together? In this 
case I remember you as both intelligent and ambitious :)

I am doing fine, working in an commercial environment since almost two years, 
but trying to keep up good science as well as possible.

What have you been up to?

Im am sure you know Ken Gehosky who was my best friend at Cedar Cliff is now 
teaching there - I thought this was kind of funny...

Sincerely,

Johannes

Am Dienstag, 1. Juni 2010, um 14:50:14 schrieb owzar001:
----------------------------------------------------------------------

Message: 1
Date: Tue, 1 Jun 2010 00:58:30 +0200
From: Johannes Ranke <jranke at uni-bremen.de>
To: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] building rpy against lenny-cran
Message-ID: <201006010058.31443.jranke at uni-bremen.de>
Content-Type: Text/Plain;  charset="iso-8859-1"

Hi Kouros,

I can not tell you why building rpy on amd64 did not work in your case.
Anyway, I have reincluded rpy into the list of supported packages for
the factory fresh backport of R 2.11.1 to lenny. The packages should
arrive at CRAN tomorrow.

Hi Johannes.

I hope that you are well (I thought about you two weeks ago as I was
driving  past Cedar Cliff enroute to my parents).

I was able to build the rpy package against lenny-cran thanks to two
suggestions by Dirk (documented in my reply to Dirk).

Thanks for contributing rpy deb packages to CRAN. These will be very
helpful.

Take care, Kouros

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------------------------------

Message: 3
Date: Tue, 1 Jun 2010 22:23:30 +0100
From: Scott Brogan <s.d.brogan at gmail.com>
To: mar36 at psu.edu, R-SIG-Debian at r-project.org
Subject: Re: [R-sig-Debian] TSA package dependencies
Message-ID:
	<AANLkTikoVXpE-n8ErCcWYLm2eAqTP1s2UV7ux9hdICPo at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Thanks; I should've read the manual.

------------------------------

Message: 4
Date: Tue, 1 Jun 2010 22:27:12 -0500
From: Paul Johnson <pauljohn32 at gmail.com>
To: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Compiling R-2.11.0 with ATLAS-tuned BLAS
	and	LAPACK
Message-ID:
	<AANLkTiktiSdb7oE1lvB_6FhxyfUdiWxg9CSLwN8esgsP at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Fri, May 28, 2010 at 1:35 PM, Avraham Adler <avraham.adler at gmail.com> wrote:
Thank you both very much for the advice. It is obviously significantly
more complicated than I first thought (although I /did/ manage to
compile both ATLAS and R under windows following the instructions, go
figure :). ) so I'll stop trying to bite off more than I can chew.

Thank you again,

--Avraham

This question reminded me I never understood BLAS linkage with R when
I asked about it 2 months ago and I forgot to follow up.  I am looking
at

http://127.0.0.1:11224/doc/manual/R-admin.html#Shared-BLAS

It seems (to my untrained eye) to say that default R is  built with a
shared library based on a nonoptimized version of BLAS that is
distributed with R itself.  It says the recommended R

If one has a different BLAS shared library on my system, one does not
recompile. Rather move R's libRblas.so and then make a symlink from
the new shared BLAS to where the old one was.

The doc has this example:

ln -s /opt/acml4.4.0/gfortran64_mp/lib/libacml_mp.so R_HOME/lib/libRblas.so

So I'd just have to figure out which shared library is the right one
and put it where libRblas used to be.

Here's what I don't understand about the current R packaging.

In the deb packages,  I download from CRAN, there is no file
libRblas.so, so I don't see how to make that new link to test  a
different BLAS.

Oh, and while I'm asking, in the source for the R package, I find a
comment from Doug Bates (README.Debian) about stripping the R binary
and possible adverse effect on --debugger. That comment is pretty old,
perhaps it is before the day when there used to be a separate package
of debugging symbols?

pj

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

------------------------------

Message: 5
Date: Tue, 1 Jun 2010 22:56:47 -0500
From: Dirk Eddelbuettel <edd at debian.org>
To: Paul Johnson <pauljohn32 at gmail.com>
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Compiling R-2.11.0 with ATLAS-tuned BLAS
	and	LAPACK
Message-ID: <19461.54911.791091.788248 at ron.nulle.part>
Content-Type: text/plain; charset=us-ascii

On 1 June 2010 at 22:27, Paul Johnson wrote:
| On Fri, May 28, 2010 at 1:35 PM, Avraham Adler <avraham.adler at gmail.com> wrote:
| > Thank you both very much for the advice. It is obviously significantly
| > more complicated than I first thought (although I /did/ manage to
| > compile both ATLAS and R under windows following the instructions, go
| > figure :). ) so I'll stop trying to bite off more than I can chew.
| >
| > Thank you again,
| >
| > --Avraham
| 
| This question reminded me I never understood BLAS linkage with R when
| I asked about it 2 months ago and I forgot to follow up.  I am looking
| at
| 
| http://127.0.0.1:11224/doc/manual/R-admin.html#Shared-BLAS
| 
| It seems (to my untrained eye) to say that default R is  built with a
| shared library based on a nonoptimized version of BLAS that is
| distributed with R itself.  It says the recommended R
| 
| If one has a different BLAS shared library on my system, one does not
| recompile. Rather move R's libRblas.so and then make a symlink from
| the new shared BLAS to where the old one was.

Ignore the 'move' part -- the manual is written for a generic Unix system
without apt-get et al.

Do the following, as per the old /usr/share/doc/r-base-core/README.Atlas.gz:

    > mm <- matrix(rnorm(10^6), ncol = 10^3)
    > system.time(crossprod(mm))
    [1] 2.38 0.04 2.84 0.00 0.00

(but these days use a bigger size than 10^6 and 10^3)

Then uninstall all your libatlas packages and make do with refblas3 and
liblapack3gf.  Rerun the matrix multiplation. Note the time.

Now install a libatlas* for you architecture, or just libatlas3gf-base and
re-run the same matrix multiplication. You will see a speed up.

And you didn't have to recompile R.  

All this brought to you by the wizardry of the former (Camm) and current
(Sylvestre) Atlas maintainers in Debian.  We owe them a drink. Or two.

| The doc has this example:
| 
| ln -s /opt/acml4.4.0/gfortran64_mp/lib/libacml_mp.so R_HOME/lib/libRblas.so
| 
| So I'd just have to figure out which shared library is the right one
| and put it where libRblas used to be.
| 
| Here's what I don't understand about the current R packaging.
| 
| In the deb packages,  I download from CRAN, there is no file
| libRblas.so, so I don't see how to make that new link to test  a

Who says you need libRblas.so?  We no longer do.

-- 
  Regards, Dirk

------------------------------

Message: 6
Date: Wed, 2 Jun 2010 02:08:48 -0400
From: Andrew Piskorski <atp at piskorski.com>
To: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Compiling R-2.11.0 with ATLAS-tuned BLAS
	and	LAPACK
Message-ID: <20100602060848.GA97381 at piskorski.com>
Content-Type: text/plain; charset=us-ascii

Dirk, that reminds me.  I DO build R myself from scratch, but it often
ends up not using Atlas even though I told it "--with-blas".

In particular, I just built R 2.11.1 on an x86-64 server running
Ubuntu 8.04.4 LTS (Hardy), and it doesn't want to use Atlas.  This
machine has both these Atlas packages installed, although I'm not sure
what the 3gf stuff is:

  ii  atlas3-base       3.6.0-20.6         Automatically Tuned Linear Algebra Software, 
  ii  libatlas3gf-base  3.6.0-21.1ubuntu3  Automatically Tuned Linear Algebra Software, 

Below is my configure command and some of the relevant output.  Am I
doing anything obviously wrong?  Or could this be some sort of
limitation of the older Atlas packages on this machine?  Is R deciding
not to use Atlas because of the "checking whether double complex BLAS
can be used... no"?

------------------------------------------------------------

LIBnn=lib r_arch=x86_64 LIBS=-lpthread ../configure  -with-x=yes --enable-R-shlib --enable-R-profiling --with-tcltk=/usr/lib/tcl8.4 --with-tcl-config=/usr/lib/tcl8.4/tclConfig.sh --enable-threads=posix --with-blas 

checking build system type... x86_64-unknown-linux-gnu 
checking host system type... x86_64-unknown-linux-gnu 

checking whether C99 double complex is compatible with Rcomplex... yes 
yes 
checking for cblas_cdotu_sub in vecLib framework... no 
checking for dgemm_... no 
checking for ATL_xerbla in -latlas... no 
checking for dgemm_ in -lblas... yes 
checking for dgemm_ in -ldgemm... no 
checking for dgemm_ in -lblas... (cached) yes 
checking for dgemm_ in -lessl... no 
checking for dgemm_ in -lblas... (cached) yes 
checking whether double complex BLAS can be used... no 

  C compiler:                gcc -std=gnu99  -g -O2 
  Fortran 77 compiler:       gfortran  -g -O 
  C++ compiler:              g++  -g -O2 
  Fortran 90/95 compiler:    gfortran -g -O 
  Obj-C compiler:              
  Interfaces supported:      X11, tcltk 
  External libraries:        readline 
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo 
  Options enabled:           shared R library, shared BLAS, R profiling, Java 
  Recommended packages:      yes 