R SIG Debian - May 2013 - clean wheezy, R intrigue, squeeze-cran3 requires liblzma2?

Hi.

On the release version of Debian Wheezy, I am missing symbols for left and
right brackets in plotmath. Anybody see similar trouble while reviewing
demo(plotmath)?

This is a completely clean, fresh install.  I've not installed any peculiar
libraries or packages, except R, the installation of which still puzzles
me.

I configured a CRAN mirror for packages using squeeze-cran3 folder, and
that's where the first funny thing happened.  I noticed same when R-2.15.3
came out, but I thought I had this trouble because my system was all junked
up with unusual libraries.  But now, on a clean system, I get this error,
which indicates I need a package liblzma2, which does not exist in Debian:


pauljohn@pjlap-d7:amd64$ sudo apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or ||been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base-core : Depends: liblzma2 (>= 4.999.9beta+20091116) but it is not
installable
               Recommends: r-recommended but it is not going to be installed
               Recommends: r-base-dev but it is not going to be installed
               Recommends: r-doc-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

This appears to be a packaging error, but I don't understand why all of the
Debian users on earth don't see it too.

See what I mean?:

pauljohn@pjlap-d7:bin$ dpkg -l | grep lzma
ii  liblzma-dev:amd64
5.1.1alpha+20120614-2              amd64        XZ-format compression
library - development files
ii  liblzma5:amd64
5.1.1alpha+20120614-2              amd64        XZ-format compression
library


My work around for that is to get the R source packaging from the CRAN and
build my own R packages. They install fine, run fine, except for that
plotmath display hassle that prompts me to write today.

When I run demo(plotmath), most of the output is fine, but the left and
right brackets in the output are displayed in little "domino" shaped
boxes,
like

_____
|  F8  |
|  EE  |
_____

This only happens, so far as I can tell, in plotmath code creating
multi-line brackets or parens. If you have seen that one, I would be glad
to know if there is a fix.

pj

ps. I installed this new Debian release because I was more-and-more having
the trouble that Evince did not display plotmath symbols correctly. I was
getting infinity where mu should be, for example.  Adobe acroread could
display the same PDF more-or-less correctly.  I found many forum posts with
help, and even did some prospecting for bugs in the poppler development
group. The fontconfig tip in ?pdf didn't make a difference. However, I did
find that embedding the fonts into the pdf files that R creates does give
Evince enough information to show the results. I had trouble understanding
the options required for R's embedFonts(), so I took a simpler approach of
using ghostscript directly.

* This is inconvenient, it must be run to embed fonts before pdflatex is
run.  So far as I can tell, it is same/similar to what R's embedFonts does,
except that it works in the shell, rather than inside R.

#!/bin/bash

## Paul Johnson
## 2013-05-11
##
## R creates pdf files that do not have fonts embedded. This
## uses ghostscript to fix that. It takes all pdf in a directory
## and embeds fonts.
##
## Todo: Make command line argument smarter, so that if user
## gives whatever.pdf, it will handle that, or
## if user gives a directory name, it will go in there and do it.


for i in *.pdf; do
base=`basename $i .pdf`;
basenew="${base}newtemp.pdf"

  /usr/bin/gs -o $basenew -dNOPAUSE -dPDFSETTINGS=/prepress
-sDEVICE=pdfwrite $i

mv -f $basenew $i
done;


-- 
Paul E. Johnson
Professor, Political Science      Assoc. Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas
http://pj.freefaculty.org               http://quant.ku.edu

	[[alternative HTML version deleted]]

Le Sat, May 11, 2013 at 04:25:14PM -0500, Paul Johnson a ?crit
:
> 
> This is a completely clean, fresh install.  I've not installed any
peculiar
> libraries or packages, except R, the installation of which still puzzles
> me.
> 
> I configured a CRAN mirror for packages using squeeze-cran3 folder, and
> that's where the first funny thing happened.  I noticed same when
R-2.15.3
> came out, but I thought I had this trouble because my system was all junked
> up with unusual libraries.  But now, on a clean system, I get this error,
> which indicates I need a package liblzma2, which does not exist in Debian:
 
> The following packages have unmet dependencies:
>  r-base-core : Depends: liblzma2 (>= 4.999.9beta+20091116) but it is not
> installable
>                Recommends: r-recommended but it is not going to be
installed
>                Recommends: r-base-dev but it is not going to be installed
>                Recommends: r-doc-html but it is not going to be installed
Dear Paul,

the packages in the squeeze-cran3 folder are built for the Debian
"Squeeze"
(6.0) distribution.  The liblzma2 package exists in Squeeze, but not in Wheezy
(Debian 7.0, the distribution you used for your fresh install).  Downgrades
are not supported, as exemplified by your problem.

Debian Wheezy was released just one week ago, so I guess it is only a matter of
time before a "wheezy-cran" folder will be provided.

Best regards,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan