[med-svn] [genometools] 04/08: remove PDF trailer IDs

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository genometools.

commit 0134f03ccb12d21231b96157540e2c66a2014872
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Sep 2 15:56:33 2016 +0000

    remove PDF trailer IDs
---
 debian/changelog             |   1 +
 debian/patches/reproducible  | 139 +++++++++++++++++++++++++++++++++++++++++--
 debian/patches/split-manuals |  14 ++---
 3 files changed, 142 insertions(+), 12 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a0f5719..1b11f26 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ genometools (1.5.9+ds-3) unstable; urgency=medium
     Closes: #836283
   * Make build reproducible.
     - Remove absolute include path to make __FILE__ use relative paths.
+    - Remove PDF trailer IDs.
 
  -- Sascha Steinbiss <satta at debian.org>  Thu, 01 Sep 2016 17:16:40 +0000
 
diff --git a/debian/patches/reproducible b/debian/patches/reproducible
index 7b7f40a..686a8f5 100644
--- a/debian/patches/reproducible
+++ b/debian/patches/reproducible
@@ -23,7 +23,15 @@ Author: Sascha Steinbiss <satta at debian.org>
            sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
 --- a/doc/manuals/annotationsketch.tex
 +++ b/doc/manuals/annotationsketch.tex
-@@ -241,7 +241,7 @@
+@@ -51,6 +51,7 @@
+ \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
+ 
+ \date{11/07/2012}
++\pdftrailerid{}
+ \begin{document}
+ 
+ \maketitle
+@@ -241,7 +242,7 @@
  We will call the second part (after the ``\texttt{|}'') of these track titles \emph{track identifier strings} in the rest of this document.
  
  \begin{figure}[ht]
@@ -32,7 +40,7 @@ Author: Sascha Steinbiss <satta at debian.org>
  \caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
  \label{tsexample1}
  \end{figure}
-@@ -271,7 +271,7 @@
+@@ -271,7 +272,7 @@
  Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
  
  \begin{figure}[ht]
@@ -41,7 +49,7 @@ Author: Sascha Steinbiss <satta at debian.org>
  \caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
  \label{tsexample2}
  \end{figure}
-@@ -313,7 +313,7 @@
+@@ -313,7 +314,7 @@
  This code results in the image shown in Fig.~\ref{tsexample3} :
  
  \begin{figure}[ht]
@@ -50,7 +58,7 @@ Author: Sascha Steinbiss <satta at debian.org>
  \caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
  \label{tsexample3}
  \end{figure}
-@@ -322,7 +322,7 @@
+@@ -322,7 +323,7 @@
  There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ct [...]
  
  \begin{figure}[ht]
@@ -59,7 +67,7 @@ Author: Sascha Steinbiss <satta at debian.org>
  \caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
  \label{ctexample1}
  \end{figure}
-@@ -415,7 +415,7 @@
+@@ -415,7 +416,7 @@
  Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
  
  \begin{figure}[ht]
@@ -68,3 +76,124 @@ Author: Sascha Steinbiss <satta at debian.org>
  \caption{The example insertion site custom track (at the bottom), displaying three sample data points.}
  \label{ctexample2}
  \end{figure}
+--- a/doc/manuals/genomediff.tex
++++ b/doc/manuals/genomediff.tex
+@@ -60,6 +60,7 @@
+ \end{tabular}}
+ 
+ \date{02/10/2012}
++\pdftrailerid{}
+ \begin{document}
+ %\tsuhhfamily
+ \maketitle
+--- a/doc/manuals/hop.tex
++++ b/doc/manuals/hop.tex
+@@ -33,6 +33,7 @@
+         \end{tabular}}
+ 
+ \date{15/05/2014}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/ltrdigest.tex
++++ b/doc/manuals/ltrdigest.tex
+@@ -42,6 +42,7 @@
+         \end{tabular}}
+ 
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/ltrharvest.tex
++++ b/doc/manuals/ltrharvest.tex
+@@ -42,6 +42,7 @@
+         \end{tabular}
+         \end{tabular}}
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/mgth.tex
++++ b/doc/manuals/mgth.tex
+@@ -38,6 +38,7 @@
+          Germany\\[1cm]
+         \end{tabular}}
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/packedindex.tex
++++ b/doc/manuals/packedindex.tex
+@@ -39,6 +39,7 @@
+         \end{tabular}
+         \end{tabular}}
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/readjoiner.tex
++++ b/doc/manuals/readjoiner.tex
+@@ -46,6 +46,7 @@
+         \end{tabular}}
+ 
+ \date{18/02/2014}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/repfind.tex
++++ b/doc/manuals/repfind.tex
+@@ -29,6 +29,7 @@
+         \end{tabular}}
+ 
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ This manual describes the options of the program \Repfind. It also gives
+--- a/doc/manuals/tagerator.tex
++++ b/doc/manuals/tagerator.tex
+@@ -23,6 +23,7 @@
+         \end{tabular}}
+ 
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/manuals/tallymer.tex
++++ b/doc/manuals/tallymer.tex
+@@ -96,6 +96,7 @@
+         \end{tabular}}
+ 
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ This manual describes the \textit{Tallymer}-software, a collection of programs
+--- a/doc/manuals/uniquesub.tex
++++ b/doc/manuals/uniquesub.tex
+@@ -48,6 +48,7 @@
+         \end{tabular}}
+ 
+ \date{26/08/2013}
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ 
+--- a/doc/devguide/devguide.tex
++++ b/doc/devguide/devguide.tex
+@@ -38,7 +38,7 @@
+         \texttt{sascha at steinbiss.name}}}
+ \date{18/02/2016}
+ 
+-
++\pdftrailerid{}
+ \begin{document}
+ \maketitle
+ \tableofcontents
diff --git a/debian/patches/split-manuals b/debian/patches/split-manuals
index efc6e35..55af3ea 100644
--- a/debian/patches/split-manuals
+++ b/debian/patches/split-manuals
@@ -207,7 +207,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  
  \author{\begin{tabular}{c}
           \textit{Stefan Kurtz}\\
-@@ -65,7 +42,6 @@
+@@ -66,7 +43,6 @@
  which specify to use a packed index or an enhanced suffix array for 
  a given set of subject sequences.
  
@@ -215,7 +215,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  \Program computes for all positions \(i\) in each unit, say \(s\) of length
  \(n\), the length \(\Mup{i}\) of the minimum unique prefix 
  at position \(i\), if it exists. Uniqueness always refers to all substrings
-@@ -85,17 +61,6 @@
+@@ -86,17 +62,6 @@
  substring. In this case, the program reports nothing for the corresponding
  unit. The program was developed for designing whole genome tiling arrays.
  The corresponding publication is \cite{GRAE:NIE:KUR:HUY:BIR:STU:FLI:2007}.
@@ -233,7 +233,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  
  The following options are available in \Program:
  
-@@ -122,7 +87,6 @@
+@@ -123,7 +88,6 @@
  gzipped format, in which case they have to end with the suffix \texttt{.gz}.
  }
  
@@ -241,7 +241,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  \Option{min}{$\ell$}{
  Specify the minimum length $\ell$ of the minimum unique prefixes.
  That is, for each unit \(s\) and each positions \(i\) in \(s\), the program 
-@@ -142,34 +106,6 @@
+@@ -143,34 +107,6 @@
  Using the keyword $\Showoptionkey{sequence}$ shows the sequence content
  of the match.
  }
@@ -276,7 +276,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  
  \Helpoption
  
-@@ -213,7 +149,6 @@
+@@ -214,7 +150,6 @@
  
  This is used in the following call to the program \Program:
  
@@ -284,7 +284,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  \begin{Output}
  gt uniquesub -output querypos -min 20 -max 30 -query queryfile.fna 
               -pck human-all
-@@ -249,27 +184,7 @@
+@@ -250,27 +185,7 @@
  1013 21 gttttttttttttactttata
  ...
  \end{Output}
@@ -312,7 +312,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  %\bibliographystyle{plain}
  %\bibliography{defines,kurtz}
  \begin{thebibliography}{1}
-@@ -281,5 +196,4 @@
+@@ -282,5 +197,4 @@
  \newblock {\em {Bioinformatics}}, {23 ISMB/ECCB 2007}:{i195--i204}, 2007.
  
  \end{thebibliography}

-- 
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