Bug#962247: Required Configuration Files Not Found
Hi,
On Fri, 5 Jun 2020 at 14:30, Andreas Tille wrote:
> 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 +, 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 <>
> directive,
> but the FILE could not be found. This FILE is interpreted relative to the
> configuration file in which the <> 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.
>
This was so because the config files are full of (relative) hardcoded
paths.
I read up the documentation, only to realise that the code just works that
way i.e. with hardcoded relative paths: the only way to prevent this is to
add an absolute hard-coded path.
Hence, I replaced all the hardcoded paths with the installation paths
(which is also, in a way hard-coded). But this will likely work on all(most
of) GNU/Linux distributions and I suppose that's what we care about.
I've pushed a patch, please take a look if it looks right to you.
Kind Regards,
Bug#962247: Required Configuration Files Not Found
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 +, 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 <> directive,
but the FILE could not be found. This FILE is interpreted relative to the
configuration file in which the <> 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
Bug#962247: Required Configuration Files Not Found
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)." -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia
