Public bug reported:

pdfannotextractor is a script that is part of the pax package that is
part of texlive-latex-extra : https://packages.ubuntu.com/focal/texlive-
latex-extra

The default installation throws this error:

$ pdfannotextractor --debug submission.pdf

PDFAnnotExtractor 0.1l, 2012/04/18 - Copyright (c) 2008, 2011, 2012 by Heiko 
Oberdiek.
* CLASSPATH: []
* is_win: [0]
* Which kpsewhich: [/usr/bin/kpsewhich]
* Backticks: [kpsewhich --progname pdfannotextractor --format texmfscripts 
pax.jar]
* Exit code: [0/success]
* pax.jar: [/usr/share/texlive/texmf-dist/scripts/pax/pax.jar]
* pdfbox.jar: [/usr/share/java/pdfbox.jar]
* Which java: [/usr/bin/java]
* System: [java /usr/share/texlive/texmf-dist/scripts/pax/pax.jar 
submission.pdf]
Error: Could not find or load main class 
.usr.share.texlive.texmf-dist.scripts.pax.pax.jar
Caused by: java.lang.ClassNotFoundException: 
/usr/share/texlive/texmf-dist/scripts/pax/pax/jar
* Exit code: [1]

The problem is that the classpath is not properly configured to use the
jar. Simply adding the "-jar" flag solves the problem:

$ java -jar /usr/share/texlive/texmf-dist/scripts/pax/pax.jar submission.pdf
* Processing file `submission.pdf' ...

In the code, pdfannotextractor.pl, the change would be located here:

sub launch_pax () {
    check_prg $prg_java, 1;
    my @cmd = ($prg_java);
    push @cmd, $path_jar_pax;
    push @cmd, @ARGV;
    debug 'System', "@cmd";

Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal

** Affects: texlive-extra (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1892600

Title:
  pdfannotextractor launch script is missing "-jar" flag

Status in texlive-extra package in Ubuntu:
  New

Bug description:
  pdfannotextractor is a script that is part of the pax package that is
  part of texlive-latex-extra : https://packages.ubuntu.com/focal
  /texlive-latex-extra

  The default installation throws this error:

  $ pdfannotextractor --debug submission.pdf

  PDFAnnotExtractor 0.1l, 2012/04/18 - Copyright (c) 2008, 2011, 2012 by Heiko 
Oberdiek.
  * CLASSPATH: []
  * is_win: [0]
  * Which kpsewhich: [/usr/bin/kpsewhich]
  * Backticks: [kpsewhich --progname pdfannotextractor --format texmfscripts 
pax.jar]
  * Exit code: [0/success]
  * pax.jar: [/usr/share/texlive/texmf-dist/scripts/pax/pax.jar]
  * pdfbox.jar: [/usr/share/java/pdfbox.jar]
  * Which java: [/usr/bin/java]
  * System: [java /usr/share/texlive/texmf-dist/scripts/pax/pax.jar 
submission.pdf]
  Error: Could not find or load main class 
.usr.share.texlive.texmf-dist.scripts.pax.pax.jar
  Caused by: java.lang.ClassNotFoundException: 
/usr/share/texlive/texmf-dist/scripts/pax/pax/jar
  * Exit code: [1]

  The problem is that the classpath is not properly configured to use
  the jar. Simply adding the "-jar" flag solves the problem:

  $ java -jar /usr/share/texlive/texmf-dist/scripts/pax/pax.jar submission.pdf
  * Processing file `submission.pdf' ...

  In the code, pdfannotextractor.pl, the change would be located here:

  sub launch_pax () {
      check_prg $prg_java, 1;
      my @cmd = ($prg_java);
      push @cmd, $path_jar_pax;
      push @cmd, @ARGV;
      debug 'System', "@cmd";

  Description:  Ubuntu 20.04.1 LTS
  Release:      20.04
  Codename:     focal

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https://bugs.launchpad.net/ubuntu/+source/texlive-extra/+bug/1892600/+subscriptions

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