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Update: Aug 04, 2013

  • With the current version of TeXLive 2013, the second MWE below still exhibits the same behavior if the \todo[inline] is commented out after the first run.
  • Furthermore, the problem now also does show up if the standalone class is used. Although my update from 2012 indicates the problem did not show up with the standalone class, I can now reproduce it with TeXLive 2012 as well. So, either I did not test carefully enough earlier to notice the problem, or some other package changes occurred after Oct 11, 2012 to cause the problem to come back with the standalone pacakge.

  • As this problem does resolve itself after subsequent runs, perhaps this question should be closed. However, it is not at all obvious what happened when this occurs in a real document. I suspect that a tweak to the todonotes package would be required to correct this.


Update: Oct 11, 2012

  • With the current version of TeXLive 2012, this problem no longer occurs with the standalone class. However using the article class, this problem still reproducible. The MWEs below have been updated.
  • As Joseph Wright pointed out in the comments, this problems does resolve itself upon the 3rd run -- only the output of the 2nd run exhibits the problem.

In a previous question about scaling pgfplots graph, I mentioned that an attempt to scale the graph resulted in the axis labels begin detached from the axis. I haven't gotten an answer that uses released code to that question, but I am seeing similar behavior now even without any scale option applied.

Unfortunately, I am not yet able to reproduce a MWE. This problem only happens sometimes in my larger document, and making changes to unrelated portions of my document either causes or fixes issues where the axis labels are detached from the axis. This time, the problem showed up on a graph which was a place holder and the source code for that is below. This graph below itself works just fine, and most of time works fine when it is included in another file, but does not always work. The outer box is from the geometry package.

When I include this in a test case things work fine. I will continue to hunt for a proper MWE as I fully understand the difficulties in debugging a problem without being able to reproduce it, but was hoping that someone else has seem similar issues and knows that they are related to so I know where to look for the problem.

% This works just fine, but sometimes has problems when included in another file
\documentclass{article}
\usepackage{standalone}
\usepackage{pgfplots}
%
\begin{document}
%
\pgfkeys{/pgfplots/axis labels at tip/.style={
        xlabel style={
            at={(current axis.right of origin)}, 
            xshift=1.5ex, anchor=center
        },
        ylabel style={
            at={(current axis.above origin)}, 
            yshift=1.5ex, anchor=center
        }
    }
}
%
\begin{tikzpicture}
\begin{axis}[
        clip=false,
        minor tick num=0, %
        axis y line=center,
        axis x line=middle, 
        axis on top=true,
        axis labels at tip,
        unbounded coords=jump, %
        tick label style={font=\small}, %
        legend style={font=\footnotesize},
        xmin=-5,
        xmax=5, 
        ymin=-1.0,
        ymax=5.0, 
        xlabel=$x$,
        ylabel=$y$,
    ] 
\end{axis} 
\end{tikzpicture}
\end{document}

The axis labels at tip is from this previous question about scaling. I don't think that is related to the problem here, but I included that as that is how I had this graph set up.


UPDATE: June 20, 2011

I was only seeing this problem when generating a large number of pages, so was difficult to figure out what was causing this. But, have now managed to track this down further and come up with the following MWE.

Run the following using pdflatex, then comment out the \todo line, and re-run. Upon subsequent run, I get a two page document, with the text "Basic axis:" on first page, and the y-axis label at the top of the 2nd page, a small amount of the tip of the y-axis is visible near the bottom of the page. Here is the output of the first run:

enter image description here

and here is the output of the 2nd run:

enter image description here

Note how the top portion of the axis is at the bottom of Page 2, and the y label is near the top right.

To make these images usable I tweaked the MWE below with:

  1. \usepackage[paperheight=10.0cm, paperwidth=12.5cm]{geometry}, and

  2. xlabel=$\textcolor{red}{x}$, ylabel=$\textcolor{red}{y}$.

Code:

\documentclass{article}
\usepackage{pgfplots}
\usepackage{todonotes}
%
\begin{document}
%
\todo[inline]{Something to do}% Comment this line after 1st run
%
Basic axis:

\begin{minipage}{0.55\linewidth}
\begin{tikzpicture}
\begin{axis}[
        axis y line=center, axis x line=middle, 
        xmin=-2.5, xmax=2.5, ymin=-2.5, ymax=2.5, 
        axis on top=true,
        xlabel=$x$, ylabel=$y$,
    ] 
\end{axis}
\end{tikzpicture}
\end{minipage}
\end{document}

So, now I just remove all .AUX files before running (unless I specifically need multiple runs) and that seems to fix my problem. I do not think that this is only cause of these kind of problem, and if I can reproduce this problem with a different method I will post that here. For instance, this problem on scaling pgfplots graph did not require a re-run to produce similar behavior.

share|improve this question
    
@Peter that looks very strange. I suppose you have double checked the system driver used by pgf? pdflatex should work best, the dvips driver slightly less so - all other drivers need to be enabled explicitly. But I suppose you have that under control... –  Christian Feuersänger May 20 '11 at 17:23
    
I am using pfdlatex. –  Peter Grill May 20 '11 at 17:45
1  
@Peter, @Christian: The problem is somehow related to TikZ' remember picture option: Instead of using the todo package, the problem can also be recreated by having the command \tikz[remember picture]; (i.e. an empty tikzpicture with remember picture) before the tikzpicture containing the axis, running pdflatex, removing the \tikz command, and running pdflatex again. Furthermore, the problem seems to be caused by the current axis node (used by axis lines=middle): If the axis labels are placed using a coordinate like at={(rel axis cs:0,0)}, the problem doesn't appear. –  Jake Jun 20 '11 at 23:52
1  
@Peter, @Jake: after experimenting a little bit, I found that the todo package actually boils down to a \tikz[remember picture] statement - that explains Jake's comment. Furthermore, I found that uncommenting it screws up the internal \pgfpictureid values: the id which was reserved for the remember picture was accidentally used for current axis, leading to a wrong inter-picture shift. All technical, but: it was ok; that's expected behavior and is just due to the standard .aux-file issues. Perhaps a package (pgf?) hacks the id counter \pgf@picture@serial@count? I do not know:-( –  Christian Feuersänger Jun 24 '11 at 18:21
2  
@PeterGrill Yes, but then I did a third run and all was fine :-) –  Joseph Wright Apr 16 '12 at 14:46
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1 Answer

up vote 3 down vote accepted

It just needs to be re-run a third time to stabilize. (solved in comments by @JosephWright)

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