This looks very much like a permissions problem. I've encountered this when I've done an installation using tlmgr, though I'm surprised at its rearing its ugly head when installation is done using apt-get.
The Likely Problem
At some point in the installation, files were installed that were only usable by the root account. That is, ordinary users do not have permission to read the necessary files for latex to work.
In brief, every file and directory on a UNIX system has three sets of three permissions (sort of). The three sets are: owner, group, world and the three permissions are read, write, execute. In order to use a file or directory you have to have sufficient permissions to carry out the activity. Which permissions apply depend on your relationship to the file (or directory) in question. For the files installed in a TeXLive installation, the most likely situation is that you do not own the files (root does) nor are you in the same group as the files (probably something like admin) so the world permissions apply to you. When you do ls -l <file name> then the first block looks something like -rw-r--r--. It is the last three that therefore concern you. What you need is to have r-- for ordinary files and r-x for directories and executable files.
Diagnosing the Problem
To check this hypothesis, you need to find the permissions of (some of) the files. From the comments, the first thing to try is:
ls -l /usr/share/texmf-texlive/tex/latex/base/article.cls
With a bit of luck, this will complain:
cannot access /usr/share/texmf-texlive/tex/latex/base/article.cls: Permission denied
If so, it's a permissions problem. (It might be that the message is cannot open directory and that the path is only a part of the path given.)
Making sure it doesn't happen again
When software is installed, it tries to install it as permissively as possible so that any user can use it. However, when you create a file in your own directory you don't want this behaviour: you want it so that you can use it, but no other user can do so. Unfortunately, the system can't tell the difference between these two cases and just sees the instruction "Create a file/directory". Now you can say "Create a file/directory with these permissions" but then that's hard for a user to override if they want to do a local installation. So what happens is the request is "Create a file/directory and suggest these permissions". The "suggestion" is then matched against something called the umask to get the real permissions. You can think of the umask as a polariser: it only allows certain permissions to get through.
Permissions are stored as octal numbers, with 4 = read, 2 = write, 1 = executable. An installer might say "This is an executable file, I suggest permissions 755" meaning everyone can read and execute it, and the owner can write to it. This is then checked against the umask to see which of these permissions can be set. A common user umask is 077. This allows through all user permissions but none of the others so the resulting file permissions are 700. On the other hand, the standard umask for a system installation is 022. This guards against files being writeable by non-owners but otherwise lets everything else through. Then the 755 would work.
What is likely to have happened here is that the umask in effect was 077 instead of 022. This can sometimes happen when using sudo since then the umask is not changed from its user setting. To avoid this happening again, the command umask 022 changes the umask to 022 (umask by itself displays the current setting) so this can be done before the installation, and then reset afterwards.
(However, as I said, I'm a little surprised at this happening with apt-get since I would expect that to be umask-savvy and sort itself out. tlmgr does not, though.)
Fixing Things Afterwards
Deleting and reinstalling is one option, but given the size of TeXLive it's a bit of a sledgehammer. A little more refined is fixing the permissions.
The first thing to do is work out where the problem starts. To do that, start with the article.cls path that you have and find out where you first lose permission:
ls -l /usr/share/texmf-texlive/tex/latex/base/article.cls
ls -ld /usr/share/texmf-texlive/tex/latex/base
ls -ld /usr/share/texmf-texlive/tex/latex
ls -ld /usr/share/texmf-texlive/tex
ls -ld /usr/share/texmf-texlive
ls -ld /usr/share
(If you get to the bottom one and still have problems, then you have big problems.)
Most likely, it is /usr/share/texmf-texlive. Next is to get a sense of the scale of the problem:
sudo find /usr/share/texmf-texlive -not -perm -004
This gives you a list of all the files and folders below texmf-texlive which are not world-readable. It might just be that it is only the top directory that has the wrong permissions, if so then do the following:
- Give a small "whoop" of joy
sudo chmod 755 /usr/share/texmf-texlive
If the list is very short, you can do something similar to the above on each of the files/directories. The rules are that the permission to give is whatever the owner has without the writeable one. chmod can take "symbolic" permissions so you don't have to remember the octal notation (symbolic is actually better here as the syntax for adding permissions is simple). In short:
- Do
sudo ls -l <filename>
- Examine the first bit, it will start with one of
drwx, -rwx, or -rw-
- If one of the first two, do
sudo chmod go+rx <filename>
- If the last one, do
sudo chmod go+r <filename>
If the list is quite long, going through each one is a pain. Fortunately, find can iterate through the list of files and execute a command on each one. We have to do it twice to fix the two situations.
First, we go through and add the read bit to all files and folders.
sudo find /usr/share/texmf-texlive -not -perm -004 -exec chmod go+r {} ';'
Then, we go through and add the execute bit to all executable files and all folders.
sudo find /usr/share/texmf-texlive -perm +100 -not -perm -001 -exec chmod go+x {} ';'
At this point, everything should have the right permissions.
Caveat
There is a faint chance that there are some files which aren't meant to be world readable in the TeXLive tree, or executable files which aren't meant to be executable by anyone but root. However, I doubt that.
(Unfortunately, as I can't guarantee that my last TL installation didn't need this permission fix, I can't trust that the permissions in my installation are all as they were intended so I can't test this myself.)
Best Answer
@jon, thanks for the tips (and everybody else). I was able to piece it all together with all your guy's help. For anybody else reading this this is what you need to do to get the latest version of LaTeX working w/ biblatex (something you need if you're wanting to use references)
Steps to take to install LaTeX and Biblatex so that you can use references in your documents. (this is using Ubuntu, Linux)
wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gztar -zxvf install-tl-unx.tar.gzsudo ./install-tlexport PATH=/usr/local/texlive/2012/bin/x86_64-linux:$PATHNOTE: your last directory might be different. Mine was "x86_64-linux" but you should first check to see if that exists. (Also don't forget to close your shell and reopen it so that the changes to the PATH settings are added)You are now completed with the set up process. Time to actually write out a damn Tex document now.
Please download this fully working example file http://pastebin.com/download.php?i=fLWQ93Ly. Save that file to your local disk as the following filename "test1.tex" and run the following in your shell:
pdflatex test1.tex(This will generate a few warnings, but you can ignore them)biber test1pdflatex test1.tex(This will then generate a PDF file for you which should look like this:Please let me know if anybody has any troubles with this.