gmane.comp.lang.r.debian

Re: How to set symbolic link correctly so that LaTeX finds Sweave?

Marius Hofert — 2012-05-25T17:28:00

yes, okay.


yes, I just can't remember what it was again.
okay, good to know.
ahh, that's what the PPA stands for. Makes sense, typically one sees 
real-person's names thereafter.

Something which bothered me (completely off-topic now): Ubuntu Software 
Center removed (!) Emacs 24 (and said that it is not well-maintained in 
comparison to Emacs 23...). I couldn't run Gnus anymore... so I 
reinstalled emacs snapshot and from now on I do all updates in the 
terminal (sudo apt-get update... that does not seem to remove emacs 
snapshot :-) )

this is what I used:

sudo add-apt-repository ppa:cassou/emacs
sudo apt-get update
sudo apt-get install emacs-snapshot


yes, that's what someone told me, too: stick to the package manager as 
often as you can, it saves you trouble on updates etc.
complicated Koma-Script-biblatex stuf...
okay, good, thanks for helping, Dirk.

Cheers,

Marius

Re: How to set symbolic link correctly so that LaTeX finds Sweave?

Dirk Eddelbuettel — 2012-05-25T17:19:57

Marius,

I don't mean to brush you off here but this thread no longer has anything to
do with 'R on Debian'.  I can recommend the http://askubuntu.com site for
generic Ubuntu questions, and there is also http://tex.stackexchange.com for
latex questions.

Now: 

On 25 May 2012 at 18:57, Marius Hofert wrote:
| >  'r-base-dev' should give you everything you need to use CRAN; the build-dep
| >  are only needed if you build R from source, which you should not have to.
| 
| Martin Maechler suggested it at some point (we develop "copula") -- not
| sure anymore why.

I recall talking about related issues with him years ago. There may have been
a depends missing in r-base-dev.  In any event, the build-deps don't hurt :)

| In principle, I agree. However, there are certain things that are simply
| not possible with older versions of software packages (due to
| org-contacts for example, I need emacs-snapshot).

I also used emacs-snapshot (pre emacs-23 I think) and you will be pleased to
learn more about so-called PPA

Re: How to set symbolic link correctly so that LaTeX finds Sweave?

Marius Hofert — 2012-05-25T16:57:35

On 05/25/2012 05:35 PM, Dirk Eddelbuettel wrote:

okay, good (I wasn't sure if it's the "correct" approach, that's why I
mentioned it here).


Martin Maechler suggested it at some point (we develop "copula") -- not
sure anymore why.


:-)

In principle, I agree. However, there are certain things that are simply
not possible with older versions of software packages (due to
org-contacts for example, I need emacs-snapshot).


Something I don't understand: I specified Sweave.sty (via the link) from
the 2009 basic TeXLive installation and it still did not work... (that's
why I wasn't sure I installed R/TeX correctly and that's why I gave the
information above).

(I didn't know this command, thanks).

I have the same output.


Again, same output.


Okay, so I try to achieve something similar by hand:

cd /usr/share/texmf/tex/latex
sudo ln -s /usr/share/R/share/texmf Sweave

Hmmm... still Sweave.sty not found (after texhash&  reboot) -- although
that's the tex tree of the 2009 TeXLive version.

For the 2011 TeXLiv

Re: How to set symbolic link correctly so thatLaTeXfinds Sweave?

Dirk Eddelbuettel — 2012-05-25T15:35:24

On 25 May 2012 at 17:20, Marius Hofert wrote:
| I recently switched from Mac OS X (after 7 years) to Xubuntu 12.04 and I am
| quite happy with it so far. I first installed R from source but I was somehow
| missing certain things and I thus decided (after a new Xubuntu installation
| which I had to make due to other reasons) to install R the "Ubuntu way":

Right.
 
| ,----[ R installation: ]
| | 1) sudo emacs /etc/apt/sources.list
| | 2) add:
| |    deb http://stat.ethz.ch/CRAN/bin/linux/ubuntu precise/
| | 3) in a terminal:
| |    gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
| |    gpg -a --export E084DAB9 | sudo apt-key add -
| | 4) the "standard way":
| |    sudo apt-get update
| |    sudo apt-get install r-base
| |    sudo apt-get install r-base-dev
| |    sudo apt-get build-dep r-base-dev
| `----

'r-base-dev' should give you everything you need to use CRAN; the build-dep
are only needed if you build R from source, which you should not have to.

| I realized that the TeXLive Version which ca

How to set symbolic link correctly so that LaTeXfinds Sweave?

Marius Hofert — 2012-05-25T15:20:11

Hi,

I recently switched from Mac OS X (after 7 years) to Xubuntu 12.04 and I am
quite happy with it so far. I first installed R from source but I was somehow
missing certain things and I thus decided (after a new Xubuntu installation
which I had to make due to other reasons) to install R the "Ubuntu way":

,----[ R installation: ]
| 1) sudo emacs /etc/apt/sources.list
| 2) add:
|    deb http://stat.ethz.ch/CRAN/bin/linux/ubuntu precise/
| 3) in a terminal:
|    gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
|    gpg -a --export E084DAB9 | sudo apt-key add -
| 4) the "standard way":
|    sudo apt-get update
|    sudo apt-get install r-base
|    sudo apt-get install r-base-dev
|    sudo apt-get build-dep r-base-dev
`----

,----[ .libPaths() shows: ]
| "/usr/local/lib/R/site-library"
| "/usr/lib/R/site-library"
| "/usr/lib/R/library"
`----

I realized that the TeXLive Version which can be installed via the Ubuntu Software
Center is quite outdated (2009) for my needs. I therefore installed TeXLive 201

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/a

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,