gmane.comp.lang.r.debian

Re: MASS is blocked for R 2.15.0

Michael Rutter — 2012-05-15T17:12:59


On 05/15/2012 10:12 AM, Michael Friendly wrote:

Remove r-cran-vr.  This was a virtual package that made sure class, 
MASS, nnet, and spatial were installed.  It is no longer needed.  So if 
you remove that, you should be good to go.  Or use "apt-get upgrade".

Michael

Re: MASS is blocked for R 2.15.0

Michael Friendly — 2012-05-15T14:12:18

Sorry;  I was using aptitude safe-upgrade.


uclid: ~ # apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages have been kept back:
   r-cran-mass
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.

Searching a bit, I discovered aptitude why-not:

aptitude why-not r-cran-mass
i   r-base        Depends   r-recommended (= 2.15.0-1lucid0)
i A r-recommended Depends   r-cran-mass
p A r-cran-mass   Conflicts r-cran-vr
p A r-cran-mass   Provides  r-cran-vr
euclid: ~ #

But now I'm not sure what to do to fix this.  Any ideas?

-Michael

Re: MASS is blocked for R 2.15.0

Michael Rutter — 2012-05-15T13:08:10


On 05/15/2012 08:50 AM, Michael Friendly wrote:

The issue may be the use of the the "safe-upgrade" option.  The first 
thing is that I don't think apt-get has a "safe-upgrade" option.  Are 
you using aptitude or the "dist-upgrade" option in apt-get?  I think you 
can solve the problem by just using "apt-get upgrade".  I don't know why 
it is blocking MASS, but something in the "safe/dist-upgrade" procedure 
is holding it back.

Hope this helps,
Michael

Re: MASS is blocked for R 2.15.0

Michael Friendly — 2012-05-15T12:50:27

I'm using CRAN.  In /etc/apt/sources.list

deb http://probability.ca/cran/bin/linux/ubuntu lucid/

I guess what I'm asking is, first how can I tell *why* MASS is being 
blocked;  then maybe I can figure out how to fix it.

Re: MASS is blocked for R 2.15.0

Michael Rutter — 2012-05-14T14:11:57


On 05/14/2012 09:16 AM, Michael Friendly wrote:

What repository are you using for R: default Ubunut, CRAN, or the PPA? 
Note, a new version has been released (7.3-18) and I just uploaded it 
(available soon on PPA, next 12-24 hours on CRAN).  That may fix the issue.

Michael

MASS is blocked for R 2.15.0

Michael Friendly — 2012-05-14T13:16:52

I updated R to R 2.15.0 via apt-get and received the message that 
r-cran-mass was blocked.
I recently tried apt-get update/ apt-get safe-upgrade and received the 
same message, for
r-cran-mass-7.3.16-1lucid0

I currently have MASS 7.3-7 installed

How can I figure out what is wrong and correct it?

thx,

Re: GotoBLAS2 breaks lapack

Sergei Petrov — 2012-05-09T17:53:16

2012/5/9 Dirk Eddelbuettel <edd< at >debian.org>:

Removing atlas* completely repaired lapack. Thank you!

Re: GotoBLAS2 breaks lapack

Dirk Eddelbuettel — 2012-05-09T16:35:59

On 9 May 2012 at 19:17, Sergei Petrov wrote:
| 2012/5/9 Dirk Eddelbuettel <edd< at >debian.org>:
| > I recommend using the (already packaged) libopenblas-base / libopenblas-dev
| > package.
| >
| > In casual benchmarking it outperformed the gotoblas2 package it was
| > originally based on.
| >
| 
| apt-get install libopenblas-base libopenblas-dev
| 
| LANG=en update-alternatives --config libblas.so.3gf

I never ever play by hand with update-alternatives to override (and I can
simply install or remove as needed to get my preferred choice working), and
guess what, nothing is borked on my system.  

I recommend you simply purge the related BLAS packages, install again and
enjoy the (very well working) defaults.

Dirk

Re: GotoBLAS2 breaks lapack

Sergei Petrov — 2012-05-09T16:17:42

2012/5/9 Dirk Eddelbuettel <edd< at >debian.org>:

apt-get install libopenblas-base libopenblas-dev

LANG=en update-alternatives --config libblas.so.3gf

There are 3 choices for the alternative libblas.so.3gf (providing
/usr/lib/libblas.so.3gf).

  Selection    Path                                      Priority   Status
------------------------------------------------------------
* 0            /usr/lib/openblas-base/libopenblas.so.0    40        auto mode
  1            /usr/lib/atlas-base/atlas/libblas.so.3gf   35        manual mode
  2            /usr/lib/libblas/libblas.so.3gf            10        manual mode
  3            /usr/lib/openblas-base/libopenblas.so.0    40        manual mode


LANG=en update-alternatives --config liblapack.so.3gf
There are 2 choices for the alternative liblapack.so.3gf (providing
/usr/lib/liblapack.so.3gf).

  Selection    Path                                        Priority   Status
------------------------------------------------------------
* 0            /usr/lib/atlas-base/atlas/liblapack.so.3gf   35        auto mode
  1            /usr/lib/atlas-base/atlas/liblapack.so.3gf   35
manual mode
  2            /usr/lib/lapack/liblapack.so.3gf             10
manual mode


R

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/lib/R/library/stats/libs/stats.so':
  /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv


liblapack.so missed in  libopenblas-base :(

Re: GotoBLAS2 breaks lapack

Dirk Eddelbuettel — 2012-05-09T15:18:03

On 9 May 2012 at 17:41, Sergei Petrov wrote:
| Dirk Eddelbuettel <edd <at> debian.org> writes:
| 
| > One last follow-up.  Debian's Atlas maintainer has started to work in the
| > OpenGoto packaging.  There will be proper Goto packages now that the license
| > is better, but it may take a while. It took years to get Atlas packaged
| > 'right' so don;t expect anything too soon.  The gotoblas2-helper package is
| > still useful for the 'here and now'.
| 
| Unfortunately it is broken :(
| 
| Link not found at ./getGotoBLAS2 line 83

I recommend using the (already packaged) libopenblas-base / libopenblas-dev
package.  

In casual benchmarking it outperformed the gotoblas2 package it was
originally based on.

Dirk

Re: GotoBLAS2 breaks lapack

Sergei Petrov — 2012-05-09T14:41:00


Unfortunately it is broken :(

Link not found at ./getGotoBLAS2 line 83

Re: Installing LaTeX class files not available inDebian packages

Sebastian P. Luque — 2012-05-08T17:40:38

On Tue, 8 May 2012 12:27:13 -0500,
Douglas Bates <bates< at >stat.wisc.edu> wrote:









There's also apt-file, which I'm very fond of:

,-----[ apt-file search tufte-handout.cls ]
| texlive-lang-arabic: /usr/share/texlive/texmf-dist/tex/latex/bidi/biditufte-handout.cls
| texlive-pictures: /usr/share/texlive/texmf-dist/tex/latex/tufte-latex/tufte-handout.cls
| texlive-pictures: /usr/share/texmf-texlive/tex/latex/tufte-latex/tufte-handout.cls
`-----

Cheers,

Re: Installing LaTeX class files not available in Debian packages

Douglas Bates — 2012-05-08T17:27:13

I have some luck with

wajig search <foo>

and also

wajig whichpkg <filename>

(which I neglected to use in this case and would have given me the
answer I needed).

Re: Installing LaTeX class files not available in Debian packages

Dirk Eddelbuettel — 2012-05-08T17:20:40

On 8 May 2012 at 11:48, Douglas Bates wrote:
| Thanks, Dirk.  I should have thought to run locate.

Locate of course only works when you already have the file. What I do when I
don't have the file yet (but suspect it is packaged) is to go here:

   http://packages.ubuntu.com/

   http://packages.debian.org

Dirk

Re: Installing LaTeX class files not available in Debian packages

Douglas Bates — 2012-05-08T16:48:07

Thanks, Dirk.  I should have thought to run locate.

It turns out that I am still having problems processing the knitr
examples that use the tufte-handout class but I'm not entirely sure
why that is.

Re: Installing LaTeX class files not available inDebian packages

Sebastian P. Luque — 2012-05-08T16:30:20

On Tue, 8 May 2012 10:56:10 -0500,
Douglas Bates <bates< at >stat.wisc.edu> wrote:



AFAIK, the standard approach is to duplicate the directory structure of
/usr/share/texmf under /usr/local/share/texmf and then place the
different files of the package (LaTeX) where they belong (Peter Flynn's
book, available online, has a good overview of this) under the latter.
cpio is great to replicate directory structures in one fell swoop.  By
default in Debian, /usr/local/share/texmf is inspected by mktexlsr to
update the LaTeX database, so it's run automatically by Debian packages
that need to do so.  However, you'd need to run it manually after
placing and building the files (if necessary) to make the package
immediately available.

Cheers,

Re: Installing LaTeX class files not available inDebianpackages

Dirk Eddelbuettel — 2012-05-08T16:15:28

Doug,

On 8 May 2012 at 10:56, Douglas Bates wrote:
| I apologize for abusing the list somewhat but there is some connection
| to R.  Several of the example files in the knitr package for R use the
| tufte-handout class, which, AFAICS, is not available in Ubuntu or
| Debian packages (please correct me if I am wrong).

Always glad to be of assistance:

  edd< at >max:~$ locate tufte-handout.cls
  /usr/share/texmf-texlive/tex/latex/tufte-latex/tufte-handout.cls
  edd< at >max:~$ dpkg -S `locate tufte-handout.cls`
  texlive-pictures: /usr/share/texmf-texlive/tex/latex/tufte-latex/tufte-handout.cls
  edd< at >max:~$ 

The package is arguably named a little awkwardly but there you go: "of
course" it is Debian.   I reckon that the aggregate file space of all the
texlive package I have installed is in excess of the disk size of my first
Linux computers...

edd< at >max:~$ dpkg -l|grep texlive|grep ^ii|cut -c-78
ii  texlive-base                                  2009-13
ii  texlive-bibtex-extra                          2009-10ubuntu1
ii  texlive-binaries                              2009-11ubuntu1
ii  texlive-common                                2009-13
ii  texlive-doc-base                              2009-2
ii  texlive-extra-utils                           2009-10ubuntu1
ii  texlive-font-utils                            2009-10ubuntu1
ii  texlive-fonts-extra                           2009-10ubuntu1
ii  texlive-fonts-extra-doc                       2009-10ubuntu1
ii  texlive-fonts-recommended                     2009-13
ii  texlive-fonts-recommended-doc                 2009-13
ii  texlive-generic-recommended                   2009-13
ii  texlive-latex-base                            2009-13
ii  texlive-latex-base-doc                        2009-13
ii  texlive-latex-extra                           2009-10ubuntu1
ii  texlive-latex-extra-doc                       2009-10ubuntu1
ii  texlive-latex-recommended                     2009-13
ii  texlive-latex-recommended-doc                 2009-13
ii  texlive-pictures                              2009-13
ii  texlive-pictures-doc                          2009-13
ii  texlive-pstricks                              2009-10ubuntu1
ii  texlive-pstricks-doc                          2009-10ubuntu1
ii  texlive-science                               2009-10ubuntu1
ii  texlive-science-doc                           2009-10ubuntu1
edd< at >max:~$

Dirk

Installing LaTeX class files not available in Debianpackages

Douglas Bates — 2012-05-08T15:56:10

I apologize for abusing the list somewhat but there is some connection
to R.  Several of the example files in the knitr package for R use the
tufte-handout class, which, AFAICS, is not available in Ubuntu or
Debian packages (please correct me if I am wrong).

The source files are available at tufte-latex.googlecode.com (a.k.a.
code.google.com/p/tufte-latex) and I presume they should end up in a
subdirectory of /usr/local/share/texmf or something like that.  Is
there a standard approach to adding unpackaged class files?

Re: A guide to R packages for Ubuntu

Michael Rutter — 2012-04-30T23:45:17


On 04/30/2012 01:54 AM, Liviu Andronic wrote:

That is a possibility.  Once I get all the bugs worked out, it will be 
something to consider.

Michael

Re: ez package installation fails - ubuntu 12.04

Douglas Bates — 2012-04-30T21:05:07

Go back and reread the description that Dirk mentioned.  He is
suggesting using the CRAN archive, not the Ubuntu archive.  Because of
the release schedules of R and Ubuntu, the Rpackages on the Ubuntu
archive are usually 9-15 months behind the releases on CRAN.

The Brazil mirrors for CRAN are listed at
http://cran.R-project.org/mirrors.html.  If you used the one in Rio
the line to add to sources.list would be

deb http://cran.fiocruz.br/bin/linux/ubuntu precise/

Re: ez package installation fails - ubuntu 12.04

Flavio Bastos — 2012-04-30T20:26:23

Problem solved.
Probably, the mirror I first tried was not updated. I changed the mirror
and the installation ocurred without problems.

Thanks a lot for the help!



On Mon, Apr 30, 2012 at 4:50 PM, Flavio Bastos <bastosfh< at >gmail.com> wrote:


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