38. How to install and/or compile wine on debian testing

UPDATE: See here for Wine 1.5.27 using a chroot
http://verahill.blogspot.com.au/2013/04/376-wine-1527-on-debian-i386-chroot.html


UPDATE: there are plenty of more up-to-date guides on this blog. See e.g. here for how to build v 1.5.6. Obviously, the instructions below are still valid, and will give you a working version of wine.

Original post:
Quite some time ago Wine was removed from Debian Testing/Wheezy. If you already had wine installed, this may not have caused any significant problems, but it did cause inconvenience when setting up a new computer.

There are three fairly easy ways of installing wine in Debian testing.

Update: See here for version 1.4-rc4: http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-compiling-wine.html

1. The simplest approach -- Using the Stable version of wine 
Simply add the stable repo to your /etc/apt/sources. list (add -- don't replace your testing repo)

i.e. if you sources.list looks like this:

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-free


then add a line so that it looks like this:

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-free

deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free

Running

sudo apt-get update

followed by

aptitude search wine

should hopefully show wine, wine-bin etc. The current version in the Debian stable repos is 1.0.1-3.1.

You can now install wine by

sudo apt-get install wine


2. The ever so slightly more complex approach -- installing version 1.3.32-0.1
If you want a newer version -- and I'd say that you would since the debian wine packages are OLD -- you can at the moment pull .deb packages from http://dev.carbon-project.org/debian/wine-unstable/

Don't let the 'unstable' fool you -- these are NOT the packages in the debian SID/unstable repos.

Also, pay heed to the following text on the page above: "The amount of traffic this little sub-page generates is quite respectable. If you think this service helpful and want to help cover some of the attached costs, please donate a few Euros". Whether you donate or not, do not download the same packages over and over again.

Download all the .deb files (in my case for amd64) using the following command:

wget -r -l1 --no-parent -A amd64.deb http://dev.carbon-project.org/debian/wine-unstable/

This is an example of using something akin to wildcards in wget.

cd dev.carbon-project.org/debian/wine-unstable

sudo dpkg -i *.deb

You'll see a number of errors being reported and the packages will be left unconfigured -- this is due to missing dependencies. That's easy to fix though:

sudo apt-get -f install

The missing dependencies will now be pulled in and the installation finalised. It's as easy as that!

3. Building your own -- version 1.3.35
It's not as hard as it may look -- I'm not in the habit of compiling my own packages, and chances are that you aren't either, so I'll show the entire process.

Download the source
wget http://prdownloads.sourceforge.net/wine/wine-1.3.35.tar.bz2

Unpack:
tar -xvf wine-1.3.35.tar.bz2

You may have to
sudo apt-get install bzip2 
before running the tar command above if it complains about missing bzip2 etc.

Change to the directory where the files were unzipped
cd wine-1.3.35

Time to start trying to build -- the errors I get may not be the errors you get. The approach to solving them is the same though.

First we need a whole lot of packages:

sudo apt-get install bison flex gcc libc6-dev libfontconfig-dev libfreetype6-dev libglu-dev libgsm1-dev libice-dev libjpeg-dev libldap-dev libmpg123-dev libncurses5-dev libopenal-dev libpng-dev libsm-dev libssl-dev libusb-dev libx11-dev libxcomposite-dev libxcursor-dev libxext-dev libxi-dev libxinerama-dev libxml2-dev libxrandr-dev libxrender-dev libxslt-dev libxt-dev libxxf86vm-dev make libcapi20-dev liblcms-dev libsane-dev libhal-dev libdbus-1-dev valgrind prelink libcups2-dev

sudo apt-get install lib32v4l-dev lib32ncurses5-dev lib32asound2-dev lib32z-dev ia32-libs-dev

Now start:
./configure

which gives**

configure: OpenCL 32-bit development files not found, OpenCL won't be supported.
configure: gstreamer-0.10 base plugins 32-bit development files not found, gstreamer support disabled
configure: OSS sound system found but too old (OSSv4 needed), OSS won't be supported.
configure: libgsm 32-bit development files not found, gsm 06.10 codec won't be supported.

configure: Finished.  Do 'make' to compile Wine.

---

Good enough for me. 

make

Building will take a good 20-30 minutes.

Finally, 'install' the binaries in their proper locations

sudo make install

The first time you start a program in wine you'll be asked to install the gecko engine, which you can go ahead and do.

** I initially had some problems -- one of them being


checking for X... no
configure: error: X 32-bit development files not found. Wine will be built without X support, which probably isn't what you want. You will need to install 32-bit development packages of Xlib/Xfree86 at the very least. Use the --without-x option if you really want this.

This was solved by installing ia32-libs-dev

---

Links to this post:
http://ramalave.blogspot.com.es/2012/10/instalar-wine-155-de-debian-sid.html

http://3n54y0.blogspot.mx/2012/03/xchange-viewer-usando-wine-en-debian.html

37. Making posters in latex

As a scientist you may have discovered how much less swearing occurs when writing articles in latex rather than MS Word or other What You See Isn't Quite What You Wanted  packages (WYSIQWYW -- I guess this is an acronym that won't be taking off anytime soon). The next step is to move from using powerpoint to make posters and presentations, to using latex.

It's never elegant to post the entire code in blog form, but what to do when you can't upload simple files?

The poster style is based on a theme by Rob J Hyndman and is an adapation of i6dv by David Vilar and edited by me.

Here's beamerthemeMyTheme.sty which you should put in the same folder as your post tex file:


\ProvidesPackage{beamerthemeMyTheme} % this style was created by Rob J Hyndman and is an adapation of i6dv by David Vilar. Edited by Someone Else

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\selectcolormodel{cmyk}
\selectcolormodel{rgb}
\mode<presentation>

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% custom colors
%\definecolor{i6blue}{cmyk}{1,0.305,0,0.06}
\definecolor{i6bluedark}{rgb}{0.0156,0.2578,0.5625} 
\definecolor{i6colorscheme1}{HTML}{333333}  %333333 e.g. for block title
\definecolor{i6colorblockbg}{HTML}{555555}
\definecolor{i6colorblockfg}{HTML}{FFFFFF} %block title white
\definecolor{i6colorscheme2}{HTML}{000000}  % e.g. title in headline
\definecolor{i6colorscheme3}{HTML}{F0F0F0} % e.g. for poster background
\definecolor{i6colorscheme4}{HTML}{000000} 
\definecolor{i6colorschemeHeadline}{HTML}{000000}  % for headline bg
\definecolor{i6colorschemeFootline}{HTML}{101010}  % for headline bg

% headline colors and fonts
\setbeamercolor{headline}{fg=yellow,bg=i6colorschemeHeadline}
\setbeamercolor{title in headline}{fg=yellow}
\setbeamercolor{author in headline}{fg=white}
\setbeamercolor{institute in headline}{fg=lightgray}
\setbeamercolor{separation line}{bg=i6colorscheme1}

% footline colors and fonts
\setbeamercolor{footline}{fg=white,bg=i6colorschemeHeadline}
\setbeamerfont{footline}{fg=white, size=\normalsize}

% body colors and fonts
\setbeamercolor*{normal text}{fg=black,bg=i6colorscheme3}

% block environment
\setbeamercolor*{block body}{bg=white,fg=black}
\setbeamercolor*{block title}{fg=i6colorblockfg,bg=i6colorblockbg}
\setbeamerfont{block title}{size=\large,series=\bf}

% example environment
\setbeamercolor*{example title}{fg=white,bg=i6colorscheme1}
\setbeamerfont{example title}{size=\large,series=\bf,bg=i6colorscheme1,fg=white}

\setbeamercolor{alerted text}{fg=i6colorscheme1}

\setbeamertemplate{itemize items}[triangle]
\setbeamertemplate{navigation symbols}{}  % no navigation on a poster

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamertemplate{block begin}{
  \vskip0.5ex %space between boxes
  \begin{beamercolorbox}[rounded=true,shadow=true,leftskip=1ex,colsep*=0.5ex]{block title}%colsep - height block title, leftskip - title text indent
    \usebeamerfont*{block title}{\Large \insertblocktitle}
  \end{beamercolorbox}%
  {\ifbeamercolorempty[bg]{block body}{}{\nointerlineskip\vskip-0.5pt}}%space between head and block
  \usebeamerfont{block body}%
%  \begin{beamercolorbox}[rounded=true,shadow=true,colsep*=0.5ex,sep=0.5ex,vmode]{block body}%colsep, sep - vert margin top and bottom
  \begin{beamercolorbox}[rounded=true,shadow=true,colsep*=0.5ex,sep=0.5ex,vmode]{block body}%colsep, sep - vert margin top and bottom
   \ifbeamercolorempty[bg]{block body}{\vskip-.25ex}{\vskip-.5ex}\vbox{}%
  }
  \setbeamertemplate{block end}{
  \end{beamercolorbox}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamertemplate{headline}{  
  \leavevmode

  \begin{beamercolorbox}[wd=\paperwidth]{headline}
\centering
        \vskip4ex % height above text
        \usebeamercolor{title in headline}{\color{fg}\textbf{\LARGE{\inserttitle}}\\[1ex]}
        \usebeamercolor{author in headline}{\color{fg}\large{\insertauthor}\\[1ex]}
        \usebeamercolor{institute in headline}{\color{fg}\large{\insertinstitute}\\[1ex]}
  \end{beamercolorbox}

  \begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
    \rule{0pt}{2pt}
  \end{beamercolorbox}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamertemplate{footline}{
  \begin{beamercolorbox}[wd=\paperwidth]{upper separation line foot}
    \rule{0pt}{2pt}
  \end{beamercolorbox}
  
  \begin{beamercolorbox}[ht=5ex,leftskip=1cm,rightskip=1cm]{footline}% ht - thickness
    \hfill \raisebox{0.4cm}{\insertfooter} %raisebox - placement of text
    \vskip1ex
  \end{beamercolorbox}

  \begin{beamercolorbox}[wd=\paperwidth]{lower separation line foot}
    \rule{0pt}{0pt}
  \end{beamercolorbox}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\mode<all>

\def\footer#1{\def\insertfooter{#1}}


and here's the poster.tex file:


\documentclass[final]{beamer}
\usetheme{MyTheme}
\usepackage[orientation=portrait,size=a1,scale=1.14,grid,debug]{beamerposter}
\usepackage[absolute,overlay]{textpos}
\setlength{\TPHorizModule}{1.0cm}
\setlength{\TPVertModule}{1.0cm}
\usepackage{ragged2e}
\usepackage{mhchem}
\usepackage{caption}
\captionsetup{labelformat=empty,labelsep=none}


\title{A hypothetical LaTeX poster}
\author{I Am Me\inst{*} \quad She S Someoneelsei\inst{\dag} \quad A. Third Party\inst{\dag}$^{,}$\inst{\ddag}}
\institute[School of Somethingorother]{
\inst{*}%
School of Somethingorother, My University \quad
\inst{\dag}%
Department of Haxx0r
\inst{\ddag}%
Department of 1337, UC Other
}
\footer{url: http://http://www.blogger.com/ \quad email: me@blogger.com}
\date{}

\begin{document}

\begin{textblock}{6}(0.6,0.6)
\includegraphics[height=4.0cm]{mylogo_light.eps}
\end{textblock}

\begin{textblock}{6}(54.9,0.6)
\includegraphics[height=4.0cm]{ucother_logo.eps}
\end{textblock}

\begin{frame}{} 
\begin{textblock}{28.5}(0.6,6.3)

\begin{block}{Introduction}
\justifying
\begin{center}\begin{minipage}{28cm}
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum gravida nisi eget lectus commodo luctus. Pellentesque vitae velit ligula. Nullam diam enim.[1,2]
\end{minipage}\end{center}
\begin{center}
\begin{figure}
\includegraphics[width=23.9cm]{screenshot.eps}
\caption{A caption for  \ce{[Fe4(H2O)8L9]^{-}}}
\end{figure}
\end{center}
\begin{center}\begin{minipage}{28cm}
Integer nec felis massa, ac tincidunt tellus. Phasellus ornare urna nec erat eleifend eu egestas arcu sodales. Cras interdum, lectus vitae ultricies rutrum, orci sapien bibendum orci, ut facilisis lectus velit at risus. Maecenas ut nisi mi. Praesent in nunc vitae justo ullamcorper placerat nec id lectus.  \ce{[[Fe4(H2O)8L9]^{-}} cluster[3]ante ipsum primis {\sc nmr}.[4]\\
\tiny{
\begin{enumerate}
\item G. Romanum, J. Eunt, G. Ite, F. Sum, \emph{A. Journal. Int. Ed.} \textbf{2011}, \emph{8}, 1943--1946.\\
\item A. Graecum, D. Hispanum, F. Molybdenum, R. Verum, H. Ipsum, P. J. Consectetur, G. Lectus, R. Ligula, M. Diam, \emph{Science} \textbf{2011}, \emph{323}, 13--17.
\item A. Graecum, D. Hispanum, F. Molybdenum, R. Verum, H. Ipsum, P. J. Consectetur, G. Lectus, R. Ligula, M. Diam, \emph{Science} \textbf{2011}, \emph{323}, 13--17.
\item A. Graecum, D. Hispanum, F. Molybdenum, R. Verum, H. Ipsum, P. J. Consectetur, G. Lectus, R. Ligula, M. Diam, \emph{Science} \textbf{2011}, \emph{323}, 13--17.
\end{enumerate} }
\end{minipage}\end{center}

\end{block}

\begin{block}{Experimental} \justifying

\begin{center}
\begin{figure}
\includegraphics[width=23.6cm]{screenshot.eps}
\caption{Another figure caption}
\end{figure}
\end{center}

\begin{center}\begin{minipage}{28cm}
Integer nec felis massa, ac tincidunt tellus. In eget lectus a ante hendrerit gravida ut a massa. Nam euismod nisi vel nulla suscipit fermentum. Quisque vel nulla nibh, at bibendum quam. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Nunc tempor pretium blandit. Nulla vulputate odio quis tortor porttitor rhoncus. Vestibulum euismod purus non dolor pharetra non tempus diam pharetra. Nulla nec mauris vitae risus dapibus eleifend eget et ipsum. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Donec aliquam fringilla nulla, et ornare urna blandit id. In blandit lacinia massa quis tempus. Cras vel feugiat mi. Nullam risus nunc, aliquam non facilisis sit amet, condimentum id felis.  \end{minipage}\end{center}
\end{block}


\begin{block}{Data massage} \justifying
\begin{center}\begin{minipage}{28cm}
In eget lectus a ante hendrerit gravida ut a massa. Nam euismod nisi vel nulla suscipit fermentum. Quisque vel nulla nibh, at bibendum quam. Vestibulum ante ipsum primis in faucibus orci. In eget lectus a ante hendrerit gravida ut a massa. Nam euismod nisi vel nulla suscipit fermentum. Quisque vel nulla nibh, at bibendum quam. 

\end{minipage}\end{center}
\end{block}


\end{textblock}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{textblock}{28.5}(30,6.3)

\begin{block}{Data reduction} \justifying
\begin{center}\begin{minipage}{28cm}
 Donec aliquam fringilla nulla, et ornare urna blandit id. In blandit lacinia massa quis tempus. Cras vel feugiat mi. Nullam risus nunc, aliquam non facilisis sit amet, condimentum id felis.\end{minipage}\end{center}
 
\begin{table}
\begin{tabular}{c c}
\begin{minipage}{14cm} 
\begin{center}
\begin{figure}
\includegraphics[width=10.0cm]{adobe.eps}
\caption{A caption}
\end{figure}
\end{center}
\end{minipage} 
&
\begin{minipage}{14cm}
\begin{figure}
\includegraphics[width=10.0cm]{adobe.eps}
\caption{A caption.}
\end{figure}
\end{minipage}

\end{tabular} \end{table}  
\begin{center}\begin{minipage}{28cm}
Donec aliquam fringilla nulla, et ornare urna blandit id. In blandit lacinia massa quis tempus. Cras vel feugiat mi. Nullam risus nunc, aliquam non facilisis sit amet, condimentum id felis.\end{minipage}\end{center}  
 
\begin{center}
\begin{figure}
\includegraphics[width=12.6cm]{screenshot.eps}
\caption{Map of $\displaystyle \sum_{i}^{}(A(\lambda_{i})_{obs.}-A(\lambda_{i})_{calc.})^{2}$ as a function of pK$_{\textrm{a}}$s}
\end{figure}
\end{center}

\end{block}

\begin{block}{Fringilla nulla}
\justifying
Donec aliquam fringilla nulla, et ornare urna blandit id. In blandit lacinia massa quis tempus. Cras vel feugiat mi. Nullam risus nunc, aliquam non facilisis sit amet, condimentum id felis. $\displaystyle \frac{1}{T_{2r}}\approx\frac{C_{m}}{C_{aq}} \cdot k$:
\begin{eqnarray}
-\Delta H^{\ddag} \frac{1}{T} + \Delta S ^{\ddag}&=& R \cdot ln (\frac{\pi}{p_{m}}\frac{h}{k_{b}}\frac{1}{T}\Delta \nu) \nonumber
\end{eqnarray}

\begin{table}
\begin{tabular}{c c}
\begin{minipage}{14cm}
\begin{center}
\begin{figure}
\includegraphics[width=12.6cm]{screenshot.eps}
\caption{Observed $\Delta$H$^{\ddag}$ as a function of pH.}
\end{figure}
\end{center}
\end{minipage}
&
\begin{minipage}{14cm}
\begin{center}
\begin{figure}
\includegraphics[width=12.6cm]{screenshot.eps}
\caption{Observed $\Delta$S$^{\ddag}$ as a function of pH.}
\end{figure}
\end{center}
\end{minipage}
\end{tabular} \end{table}
\begin{center}\begin{minipage}{28cm}
 Ut ultrices ipsum vitae ipsum sagittis eget egestas dui interdum. 
\end{minipage}\end{center}
\end{block}

\begin{block}{Summary}
\begin{center}\begin{minipage}{28cm}
\begin{itemize}
\item Ut ultrices ipsum vitae ipsum sagittis eget egestas dui interdum. Phasellus nec nisl quam. 
\item Ut ultrices ipsum vitae ipsum sagittis eget egestas dui interdum. Phasellus nec nisl quam. 
\end{itemize}
\end{minipage}\end{center}
\end{block}

\begin{block}{Acknowledgements} \justify
\begin{center}\begin{minipage}{28cm}
Ut ultrices ipsum vitae ipsum sagittis eget egestas dui interdum. \\
Phasellus nec nisl quam. \\
\end{minipage}\end{center}
\end{block}


\end{textblock}
\end{frame}
\end{document}

36. PDF and annotation/editing under linux -- no solutions

Update: There are newer posts here and here.


Galley proofs of scientific articles are typically provided in the form of pdf files with ambiguous passages and editorial suggestions marked. You are then expected to add comments to the pdf indicating whether you agree to changes and/or clarifications. Well, good luck doing that.

It does appear that Acrobat Reader (9.4.x under linux, 10.1.1 under windows) does not support annotation/commenting anymore. See picture for security settings:

I fooled around with pdf2ps + ps2pdf, pdftk allow AllFeatures etc. No luck. Still no annotation in acroread.

PDFedit didn't help much. It looks like an advanced piece of software, but it offers no obvious way of making post-it type comments. The best approximation is adding text to the margins, but it's not what I set out to do.

Sadly, using wine + pdf x-change viewer (http://appdb.winehq.org/objectManager.php?sClass=application&iId=5549) is at the time of writing the best solution. You can download the free version here: http://www.tracker-software.com/product/pdf-xchange-viewer (there's also a 'pro' version)

It really is a straightforward piece of software, and does the trick, so no complaints there. However, it is very unfortunate that such a central piece of functionality is unavailable under linux.

Also, it does seem that acrobat reader is intentionally crippled -- from what I understand there is no obvious reason why commenting isn't allowed (i.e. not the fault of the authors of the pdf) other than because Adobe wants you to shill out money for their 'Pro' version (...interesting how FOSS normally doesn't market itself by adding X or Pro to the name...)