[Debian-med-packaging] Bug#962247: Required Configuration Files Not Found

[Andreas Tille]

Hi Dario,

thanks a lot for your bug report.  To bad that nobody reported before
this issue which seems pretty obvious.  May be everybody is using circos
with the --conf option (as our autopkgtest is doing it as well) and thus
the issue was hidden.

On Fri, Jun 05, 2020 at 02:00:13AM +0000, Dario Strbenac wrote:
> Package: circos
> Version: 0.69.6
> 
> I think this software has not been correctly packaged. Running the circos command with no parameters results in 
> 
>   The Config::General module reported the error
>   Config::General The file "etc/colors_fonts_patterns.conf" does not exist
>   within ConfigPath:
>   /etc/circos.circos.circos/etc./usr/bin/etc./usr/bin/../etc./usr/bin/.../usr/bin!
>   at /usr/share/perl5/Circos/Configuration.pm line 820
> 
> The server administrator at university investigated the c and explains "The issue is that it looked for file etc/colors_fonts_patterns.conf in various places including current directory and in /etc/circos, when that file was present as /etc/circos/colors_fonts_patterns.conf (while circos tried the name /etc/circos/etc/colors_fonts_patterns.conf with an extra or bogus /etc/ in the middle)."

I've patched the code and moved some additional config files from
examples to /etc/circos which helped to solve all these issues.
Unfortunately there is a remaining one.  @Nilesh or @Pranav:  Do you
have time to fix this one:

/tmp $ circos
debuggroup summary 0.17s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.030002
debuggroup summary 0.17s current working directory /tmp
debuggroup summary 0.17s command /usr/bin/circos [no flags]
debuggroup summary 0.17s guessing configuration file
debuggroup summary 0.17s found conf file /usr/share/circos/etc/circos.conf

  *** CIRCOS ERROR ***

      cwd: /tmp

      command: /usr/bin/circos

  CONFIGURATION FILE ERROR

  Error parsing the configuration file. You used an <<include FILE>> directive,
  but the FILE could not be found. This FILE is interpreted relative to the
  configuration file in which the <<include>> directive is used. Circos lookd
  for the file in these directories

  /usr/share/circos/etc

  /etc/circos

  /usr/share/circos/etc

  /usr/share/circos/etc/etc

  /usr/bin/etc

  /usr/bin/../etc

  /usr/bin/..

  /usr/bin

  The Config::General module reported the error

  Config::General The file "/usr/share/circos/fonts.conf" does not exist within
  ConfigPath:
  /usr/share/circos/etc./etc/circos./usr/share/circos/etc./usr/share/circos/etc/etc./usr/bin/etc./usr/bin/../etc./usr/bin/.../usr/bin!
  at /usr/share/perl5/Circos/Configuration.pm line 820.

  If you are having trouble debugging this error, first read the best practices
  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the
  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group.

      http://groups.google.com/group/circos-data-visualization

  Please include this error, all your configuration, data files and the version
  of Circos you're running (circos -v). Do not email me directly -- please use
  the group.

  Stack trace:
 at /usr/share/perl5/Circos/Error.pm line 425.
        Circos::Error::fatal_error("configuration", "cannot_find_include", "/usr/share/circos/etc\x{a}/etc/circos\x{a}/usr/share/circos/etc\x{a}/usr/"..., "Config::General The file \"/usr/share/circos/fonts.conf\" does "...) called at /usr/share/perl5/Circos/Configuration.pm line 826
        Circos::Configuration::loadconfiguration("/usr/share/circos/etc/circos.conf") called at /usr/share/perl5/Circos.pm line 148
        Circos::run("Circos", "_cwd", "/tmp", "_argv", "") called at /usr/bin/circos line 538


I admit I'm running out of ideas why the file

      Config::General The file "/usr/share/circos/fonts.conf" does not exist within

is seeked instead of  "/usr/share/circos/etc/fonts.conf" - may be that's
a cause of the patches I did in debian/patches/fix_config_path.patch.

Unfortunately I'm a bit running out of time to hunt this down finally.


Question to the bug reporter Dario since you was talking about some
server installation:  Assumed we would solve the issue which should be
not that hard finally - would it help if we would create a backport of
the fixed package?  Please let us know.

Kind regards

     Andreas.

-- 
http://fam-tille.de