Monthly Archives: April 2013

Undefined references – LaTeX Warning

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Sometimes LaTeX tells you this:

LaTeX Warning: There were undefined references.

If you get this warning, you will notice some ?? in your document at places where references should be. For references to sections, tables of figures, just run pdflatex again (and check for typos). For bibliography references you need to run bibtex.

Let’s assume you are writing a LaTeX file with the name ‘report.tex’. Do the following:

> pdflatex report.tex
[...]
LaTeX Warning: Citation `Liu2010' on page 1 undefined on input line 39.
[...]
LaTeX Warning: Reference `fig:results' on page 1 undefined on input line 65.
[...]
LaTeX Warning: There were undefined references.
[...]
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
[...]
> bibtex report
[...]
> pdflatex report.tex
[...]
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
[...]
> pdflatex report.tex
[...]

You need to run pdflatex again twice after calling bibtex. Twice, because layout may change and things end up somewhere else after you inserted the references.

Replace newlines with sed

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Sed is a commandline linux tool to replace text in a file or input stream. Typically sed works line-oriented, i.e., a line is read, the expression applied, then the next line is read. Say we have a file where one line is one word. We want to reconstruct the sentence. How to replace all linebreaks in the file with a space? Simple:

sed "{:q;N;s/\n/ /g;t q}"

The regular expression ‘s/\n/ /’ says substitute linebreaks (\n) by a space. ‘g’ says apply this globally. ‘N’ says append the next line to what is processed. Using only ‘N’ would replace linebreaks in every second line. The rest of the thing is a trick to join all lines together. We define the label q (‘:q;’), then we say that in case that there was a sucessfull substitution, go to label q (‘t q’).

Now we have all words in one line. Across sentences! Sentences are separed by an empty line. So easy – replace linebreaks by spaces, replace two adjacent spaces by a linebreak. Gives you one sentence per line, words separated by spaces. Voila:

cat  | sed "{:q;N;s/\n/ /g;t q}" | sed "{s/  /\n/g}"

The most important commands for SVN

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Here are the most important commands for using SVN in the command line on Linux. You have to be inside your local folder where you put the svn else it won’t work (most common source for error “Skipping .'” or “. is not a working copy”).

update

To update your local working copy to the newest version that exists on the server (ALWAYS do this before you start to change things or your teammates will kill you!!):

svn update

add

Files you move into the local working copy folder are not added automatically. If you want the file to be part of the SVN, you have to add it. It works for multiple files or folders, too.

svn add

delete

To delete files from the repository, first mark them for deletion:

svn rm

On the next commit, the file will be deleted from the repository and from your local copy! If you want to keep the local copy, do

svn rm --keep-local

revert

With revert, you can undo pending changes in your working copy (e.g. add, delete) before the next commit.

svn revert

Also handy in case you forgot what local changes you made and you want to return to the latest “safe” version from the repository.
Note that this does NOT enable you to go back to a previous already-commited version. To do that, you can checkout the specific version of your repository at some other place (with the option -r) and manually get what you need or follow the procedure outlined here.

commit (changes to the repository)

If you have changed a file, added or deleted something and want to put the changes into the SVN you have to commit it, without that the changes are only in your working copy and not on the server!

svn ci -m ""

log

It is good practice to write log messages with commits. You can review these log messages with

svn log

You should do an update of your working copy before this command, otherwise you will not get all messages. In case this is a lot of messages, you can add a limit, e.g., display only the latest 5 log entries:

svn log -l 5

status

To see which files of your working copy haven’t been committed yet:

svn status

Common SVN status codes:

diff

To see what has changed in a file from the last version to the current version:

svn diff

More resources: You can always use “svn help” to see what else is there or take a look at the excellent book.

A typical SVN session

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We assume you have created a working copy and there is already some content in your SVN that you share with others. All of this assumes that you are using some linux shell and are in the folder of your working copy. If you are in the wrong folder else it won’t work (most common source for error “Skipping .'” or “. is not a working copy”).

First thing you do is update (i.e. get the latest changes from the server), in case your teammates changed something. You don’t want to work on an old version!

svn update

Then you open some files, change some things (in "main.adb"), add a new file ("list.adb") and delete a different file ("array.adb"). After two hours work you need a coffee and it’s always a good idea to commit (i.e. send your changes to the server) before taking a longer break. Before you commit, you want to know what changed:

svn status

The message you get will look more or less like this:

M    main.adb
?    list.adb
!    array.adb

This means, you have modified "main.adb", there is a file "list.adb" that SVN doesn’t really know about and "array.adb" should be there, but SVN cannot find it.

If you just commit, only "main.adb" will get changed and on the next update "array.adb" will be restored in your working copy. Why? Because you need to tell SVN explicitly that you want a file to be added or deleted. So let’s do that.

svn add list.adb
svn del array.adb

Now let’s check the status again, the result will be:

M    main.adb
A    list.adb
D    array.adb

We are satisfied and commit the whole thing:

svn ci -m "Replaced array with list, added list.adb, deleted array.adb"

It is always a very good idea to write a meaningful commit message (the parameter -m), so that your teammates know what has been changed. It also makes it easier to go back to a specific version, e.g. the version just before you removed the array.

Creating a SVN working copy (checkout)

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You will need to do this once to get the first working copy from the server to your computer.

svn co server_url folder_where_you_want_to_have_your_working_copy

The "server url" isn’t actually a URL like in the internet most of the time. It can be a path to a file (this would work if e.g. if you are inside the IMS and want to access a SVN that is located in a folder that you have mounted) or something with svn+ssh or the like. The one who created the SVN for you should tell you the server URL.

What is SVN?

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To say it in very simple terms, SVN allows you to store your files on a server with a change history and have a "working copy" on any computer you like. You only work in your working copy and at some intervals tell SVN to copy the changes you make to the server. SVN will then overwrite the files on the server, but at the same time keep a record of what has changed. This means, that you can always go back to some earlier version – no more need for manual backup!

Also, SVN is great for working in groups. Because the files are on the server and everybody can have his own working copy on his own computer, you need not send around files with the changes you make. Every group member just makes her changes whenever she is ready to get the changes to the group, she just tells SVN to copy them to the server. The other group members only have to update their working copy with the newest version on the server and all have the same version of the code.

That’s actually about it, if you only want to use the basic functionalities. Just some terminology: Creating a working copy is called "checkout", copying code from the server to your working copy is called "update" and copying your changes from your working copy to the server is called "commit".

Installing a LaTeX package

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Let’s say you want to create a A0 poster with LaTeX. You find an example on the internet that starts like this: 

\documentclass[final]{beamer}
\usepackage[orientation=landscape,size=a0,scale=1]{beamerposter}
\usepackage{lipsum} % lorem ipsum

You download the example ‘example.tex’, run pdflatex on it and it fails like this:

me@mycomputer: pdflatex example.tex
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 restricted \write18 enabled.
entering extended mode
(./example.tex
LaTeX2e <2011/06/27>
Babel  and hyphenation patterns for english, dumylang, nohyphenation, lo
aded.
(/usr/share/texlive/texmf-dist/tex/latex/beamer/beamer.cls

[...]

! LaTeX Error: File `beamerposter.sty' not found.

Type X to quit or  to proceed,
or enter new name. (Default extension: sty)

Enter file name:

This means, that this particular LaTeX package ‘beamerposter’ is not installed on your machine. Bad luck.

What to do if you have admin permissions

On linux, open your favourite package manager (e.g., Synaptic), type the name of the LaTeX package (in this case ‘beamerposter’). If the result shows a linux package like ‘texlive-latex-extra’ install it and be happy.

What to do if you do not have admin permissions

1. Download the package

Go to CTAN. Search for the missing package name and click on the best result. In the beamerposter case, you will end up here. To get to a page where you can actually download the package, you need to follow the link listed under CTAN path in the box at the bottom of the page. Click on ‘Download’ and save the ‘beamerposter.zip’ somewhere on your computer.

We will also assume that the second package, ‘lipsum’, is also missing, you would find it on CTAN here.

2. Extract the package to the correct location

The READMEs of LaTeX package usually contain "Put it in your tex folder" or "Put it somewhere where LaTeX can find it" (if they contain anything on installation at all). What this actually means is, that there are several possibilities. LaTeX searches for sources in a few directories, depending on your system and LaTeX distribution. Some examples for linux and texlive are:

/usr/share/texmf/
/usr/share/texlive/texmf/
/usr/local/share/texmf/tex/latex/
~/texmf/

If you don’t have admin permissions, the easiest is to create a folder ‘texmf’ in your home directory (~). You will need in this folder a subfolder ‘tex’, and then ‘latex’. So in total you should have:

~
   |- texmf/
      |- tex
         |- latex

In this folder, i.e., ~/texmf/tex/latex/, you can put any style files and latex will find them. It is advisable to create separate folders for separate packages, so we will extract the ‘beamerposter.zip’ that we downloaded into the folder ~/texmf/tex/latex/beamerposter/ and ‘lipsum.zip’ into the folder ~/texmf/tex/latex/lipsum/. This is what the folder looks like now:

~
   |- texmf/
      |- tex
         |- latex
            |- beamerposter
               |- beamerposter.pdf
               |- beamerposter.sty
               |- beamerposter.tex
               |- example.tex
               |- README
            |- lipsum
               |- lipsum.dtx
               |- lipsum.ins
               |- lipsum.pdf
               |- README

As you can see, we now have a ‘beamerposter.sty’. So if this were the only package we needed, we could skip step 3. Unfortunately we are still missing ‘lipsum.sty’, so this is what step 3 is about.

3. Create a style file

As we see, there is no style file ‘lipsum.sty’. There is only a ‘lipsum.ins’ and a ‘lipsum.dtx’ file. The .dtx file is only to create the documentation and we can ignore it here. To create the style file, run latex (latex, not pdflatex!) on ‘lipsum.ins’:

me@mycomputer: latex lipsum.ins

The result should look like this:

~
   |- texmf/
      |- tex
         |- latex
            |- beamerposter
               |- ...
            |- lipsum
               |- lipsum.dtx
               |- lipsum.ins
               |- lipsum.log
               |- lipsum.pdf
               |- lipsum.sty
               |- README

4. Try pdflatex again

And it should work (unless of course a different package is missing…).

Updating the Database

If you install fonts and in some other cases you need to update the LaTeX package database. On linux/texlive this is done with ‘texhash’: 

me@mycomputer: texhash

More

This works for regular LaTeX packages. Bibtex packages go to texmf/bibtex. If there are fonts involved, you will need to put them in texmf/fonts and it might get tricky.

LaTeX at Wikibooks