R SIG Debian - Jun 2010 - 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
> >>
> >> _______________________________________________
> >> R-SIG-Debian mailing list
> >> R-SIG-Debian at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> >
> > 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
> > 
> > _______________________________________________
> > R-SIG-Debian mailing list
> > R-SIG-Debian at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> 
> 
> 
> ------------------------------
> 
> 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.
> 
> | 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
> | 
> | _______________________________________________
> | R-SIG-Debian mailing list
> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> 
> -- 
>   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 
>