[R-sig-Debian] R-SIG-Debian Digest, Vol 58, Issue 3
Christoph Ungemach
c.ungemach at warwick.ac.uk
Wed Jun 2 14:32:10 CEST 2010
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
>
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