Hi, On Fri, 5 Jun 2020 at 14:30, Andreas Tille <andr...@an3as.eu> 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 +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. > 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, Nilesh
