<div dir="ltr"><div>Hi,<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 5 Jun 2020 at 14:30, Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Dario,<br>
<br>
thanks a lot for your bug report. To bad that nobody reported before<br>
this issue which seems pretty obvious. May be everybody is using circos<br>
with the --conf option (as our autopkgtest is doing it as well) and thus<br>
the issue was hidden.<br>
<br>
On Fri, Jun 05, 2020 at 02:00:13AM +0000, Dario Strbenac wrote:<br>
> Package: circos<br>
> Version: 0.69.6<br>
> <br>
> I think this software has not been correctly packaged. Running the circos command with no parameters results in <br>
> <br>
> The Config::General module reported the error<br>
> Config::General The file "etc/colors_fonts_patterns.conf" does not exist<br>
> within ConfigPath:<br>
> /etc/circos.circos.circos/etc./usr/bin/etc./usr/bin/../etc./usr/bin/.../usr/bin!<br>
> at /usr/share/perl5/Circos/Configuration.pm line 820<br>
> <br>
> 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)."<br>
<br>
I've patched the code and moved some additional config files from<br>
examples to /etc/circos which helped to solve all these issues.<br>
Unfortunately there is a remaining one. @Nilesh or @Pranav: Do you<br>
have time to fix this one:<br>
<br>
/tmp $ circos<br>
debuggroup summary 0.17s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.030002<br>
debuggroup summary 0.17s current working directory /tmp<br>
debuggroup summary 0.17s command /usr/bin/circos [no flags]<br>
debuggroup summary 0.17s guessing configuration file<br>
debuggroup summary 0.17s found conf file /usr/share/circos/etc/circos.conf<br>
<br>
*** CIRCOS ERROR ***<br>
<br>
cwd: /tmp<br>
<br>
command: /usr/bin/circos<br>
<br>
CONFIGURATION FILE ERROR<br>
<br>
Error parsing the configuration file. You used an <<include FILE>> directive,<br>
but the FILE could not be found. This FILE is interpreted relative to the<br>
configuration file in which the <<include>> directive is used. Circos lookd<br>
for the file in these directories<br>
<br>
/usr/share/circos/etc<br>
<br>
/etc/circos<br>
<br>
/usr/share/circos/etc<br>
<br>
/usr/share/circos/etc/etc<br>
<br>
/usr/bin/etc<br>
<br>
/usr/bin/../etc<br>
<br>
/usr/bin/..<br>
<br>
/usr/bin<br>
<br>
The Config::General module reported the error<br>
<br>
Config::General The file "/usr/share/circos/fonts.conf" does not exist within<br>
ConfigPath:<br>
/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!<br>
at /usr/share/perl5/Circos/Configuration.pm line 820.<br>
<br>
If you are having trouble debugging this error, first read the best practices<br>
tutorial for helpful tips that address many common problems<br>
<br>
<a href="http://www.circos.ca/documentation/tutorials/reference/best_practices" rel="noreferrer" target="_blank">http://www.circos.ca/documentation/tutorials/reference/best_practices</a><br>
<br>
The debugging facility is helpful to figure out what's happening under the<br>
hood<br>
<br>
<a href="http://www.circos.ca/documentation/tutorials/configuration/debugging" rel="noreferrer" target="_blank">http://www.circos.ca/documentation/tutorials/configuration/debugging</a><br>
<br>
If you're still stumped, get support in the Circos Google Group.<br>
<br>
<a href="http://groups.google.com/group/circos-data-visualization" rel="noreferrer" target="_blank">http://groups.google.com/group/circos-data-visualization</a><br>
<br>
Please include this error, all your configuration, data files and the version<br>
of Circos you're running (circos -v). Do not email me directly -- please use<br>
the group.<br>
<br>
Stack trace:<br>
at /usr/share/perl5/Circos/Error.pm line 425.<br>
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<br>
Circos::Configuration::loadconfiguration("/usr/share/circos/etc/circos.conf") called at /usr/share/perl5/Circos.pm line 148<br>
Circos::run("Circos", "_cwd", "/tmp", "_argv", "") called at /usr/bin/circos line 538<br>
<br>
<br>
I admit I'm running out of ideas why the file<br>
<br>
Config::General The file "/usr/share/circos/fonts.conf" does not exist within<br>
<br>
is seeked instead of "/usr/share/circos/etc/fonts.conf" - may be that's<br>
a cause of the patches I did in debian/patches/fix_config_path.patch.<br>
<br>
Unfortunately I'm a bit running out of time to hunt this down finally. <br></blockquote><div><br></div><div>This was so because the config files are full of (relative) hardcoded paths. <br></div><div>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.</div><div>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.</div><div>I've pushed a patch, please take a look if it looks right to you.</div><div><br></div><div>Kind Regards,</div><div>Nilesh<br></div></div></div>