Yet another GD problem : )

[Thomas Dybdal Pedersen]

Hi

As the title shows this is another GD problem, but probably of my own doing. I had circos set up and running fine on my mac but did not use it for a while. Now when I try to run it, it gives the following error:

Can't load '/opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/auto/GD/GD.bundle' for module GD: dlopen(/opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/auto/GD/GD.bundle, 1): Library not loaded: /opt/local/lib/libpng14.14.dylib

  Referenced from: /opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/auto/GD/GD.bundle

  Reason: image not found at /opt/local/lib/perl5/5.12.4/darwin-thread-multi-2level/DynaLoader.pm line 204.

 at /opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/GD/Polyline.pm line 45

Compilation failed in require at /opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/GD/Polyline.pm line 45.

BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.12.4/darwin-thread-multi-2level/GD/Polyline.pm line 45.

Compilation failed in require at /usr/local/circos-0.62-1/bin/../lib/Circos.pm line 59.

BEGIN failed--compilation aborted at /usr/local/circos-0.62-1/bin/../lib/Circos.pm line 59.

Compilation failed in require at /usr/bin/circos line 184.

BEGIN failed--compilation aborted at /usr/bin/circos line 184.

I have searched around on my computer and have found that the libpng14.14 it is referring to does not exist but instead there is libpng15.15. I gathered that I had updated the libpng library in the time where I had not used circos and that I just needed to reinstall GD to sort this out. After trying this the problem persists though.

Anyone having some informed idea on which things I need to reinstall/uninstall to make GD and circos play nicely?

best wishes

Thomas

[Martin Krzywinski]

I think you'll need to recompile libgd and then GD, if your original library is no longer there.

You could try to fake it by linking libpng15.15.dylib to libpng14.14.dylib. This is almost certainly going to not work, but it's worth trying.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

Thomas

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[Duleep Samuel]

Sir, I run tableviewer online and make good charts Thanks
I want to run the same download circos.conf on my PC, but it refuses
to run, what modifications I must make in the conf file to run on my
win desktop perl
thanks, Samuel
This will help me to learn slowly at my own speed


================
C:\Users\dksam_000\Circos\bin>perl
"C:\Users\dksam_000\Circos\bin\circos" -conf
"C:\Users\dksam_000\Circos\2\etc\circos.conf"
debuggroup conf 0.58s welcome to circos v0.62-1 25 Jun 2012
debuggroup conf 0.58s loading configuration from file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.58s looking for conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.58s found conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf

*** CIRCOS ERROR ***

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

C:\Users\dksam_000\Circos\2\etc\

C:\Users\dksam_000\Circos\2\etc

C:\Users\dksam_000\Circos\2\etc/etc

C:/Users/dksam_000/Circos/bin/etc

C:/Users/dksam_000/Circos/bin/../etc

C:/Users/dksam_000/Circos/bin/..

C:/Users/dksam_000/Circos/bin

The Config::General module reported the error

Config::General The file "data/colors.conf" does not exist within ConfigPath:
C:\Users\dksam_000\Circos\2\etc\.C:\Users\dksam_000\Circos\2\etc.C:\Users\dksam_000\Circos\2\etc/etc.C:/Users/dksam_000/Circos/bin/etc.C:/Users/dksam_000/Circos/bin/../etc.C:/Users/dksam_000/Circos/bi
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Configuration.pm line 605.

If you are having trouble debugging this error, use this tutorial to learn how
to use the debugging facility

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

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

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

Stack trace:
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Error.pm line 332.
Circos::Error::fatal_error('configuration',
'cannot_find_include',
'C:\Users\dksam_000\Circos\2\etc\\x{a}C:\Users\dksam_000\Circos\2\...',
'Config::General The file "data/colors.conf" does not e
Circos::Configuration::loadconfiguration('C:\Users\dksam_000\Circos\2\etc\circos.conf')
called at C:/Users/dksam_000/Circos/bin/../lib/Circos.pm line 156
Circos::run('Circos', 'configfile',
'C:\Users\dksam_000\Circos\2\etc\circos.conf') called at
C:\Users\dksam_000\Circos\bin\circos line 233

C:\Users\dksam_000\Circos\bin>cd ..

C:\Users\dksam_000\Circos>cd 2

C:\Users\dksam_000\Circos\2>dir
Volume in drive C has no label.
Volume Serial Number is 6EDA-D28E

Directory of C:\Users\dksam_000\Circos\2

11/12/2012 12:20 <DIR> .
11/12/2012 12:20 <DIR> ..
11/12/2012 12:20 <DIR> batch
11/12/2012 12:20 <DIR> data
11/12/2012 12:20 <DIR> etc
11/12/2012 12:20 <DIR> results
11/12/2012 12:20 <DIR> uploads
0 File(s) 0 bytes
7 Dir(s) 780,197,933,056 bytes free

C:\Users\dksam_000\Circos\2>cd data

C:\Users\dksam_000\Circos\2\data>dir
Volume in drive C has no label.
Volume Serial Number is 6EDA-D28E

Directory of C:\Users\dksam_000\Circos\2\data

11/12/2012 12:20 <DIR> .
11/12/2012 12:20 <DIR> ..
07/12/2012 09:34 1,411 all.txt
07/12/2012 09:34 698 cap.col.txt
07/12/2012 09:34 703 cap.row.txt
07/12/2012 09:34 1,805 cells.txt
07/12/2012 09:34 704 col.txt
07/12/2012 09:34 227 colors.conf
07/12/2012 09:34 577 colors_percentile.conf
07/12/2012 09:34 391 karyotype.txt
07/12/2012 09:34 14,339 parsed.txt
07/12/2012 09:34 707 row.txt
07/12/2012 09:34 162 scaling.conf
07/12/2012 09:34 217 segmentlabel.txt
07/12/2012 09:34 0 stderr.txt
13 File(s) 21,941 bytes
2 Dir(s) 780,197,933,056 bytes free

C:\Users\dksam_000\Circos\2\data>perl
"C:\Users\dksam_000\Circos\bin\circos" -conf
"C:\Users\dksam_000\Circos\2\etc\circos.conf"
debuggroup conf 0.18s welcome to circos v0.62-1 25 Jun 2012
debuggroup conf 0.18s loading configuration from file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.18s looking for conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.18s found conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf

*** CIRCOS ERROR ***

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

C:\Users\dksam_000\Circos\2\etc\

C:\Users\dksam_000\Circos\2\etc

C:\Users\dksam_000\Circos\2\etc/etc

C:/Users/dksam_000/Circos/bin/etc

C:/Users/dksam_000/Circos/bin/../etc

C:/Users/dksam_000/Circos/bin/..

C:/Users/dksam_000/Circos/bin

The Config::General module reported the error

Config::General The file "data/colors.conf" does not exist within ConfigPath:
C:\Users\dksam_000\Circos\2\etc\.C:\Users\dksam_000\Circos\2\etc.C:\Users\dksam_000\Circos\2\etc/etc.C:/Users/dksam_000/Circos/bin/etc.C:/Users/dksam_000/Circos/bin/../etc.C:/Users/dksam_000/Circos/bi
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Configuration.pm line 605.

If you are having trouble debugging this error, use this tutorial to learn how
to use the debugging facility

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

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

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

Stack trace:
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Error.pm line 332.
Circos::Error::fatal_error('configuration',
'cannot_find_include',
'C:\Users\dksam_000\Circos\2\etc\\x{a}C:\Users\dksam_000\Circos\2\...',
'Config::General The file "data/colors.conf" does not e
Circos::Configuration::loadconfiguration('C:\Users\dksam_000\Circos\2\etc\circos.conf')
called at C:/Users/dksam_000/Circos/bin/../lib/Circos.pm line 156
Circos::run('Circos', 'configfile',
'C:\Users\dksam_000\Circos\2\etc\circos.conf') called at
C:\Users\dksam_000\Circos\bin\circos line 233

C:\Users\dksam_000\Circos\2\data>cd..

C:\Users\dksam_000\Circos\2>cd etc

C:\Users\dksam_000\Circos\2\etc>perl
"C:\Users\dksam_000\Circos\bin\circos" -conf
"C:\Users\dksam_000\Circos\2\etc\circos.conf"
debuggroup conf 0.18s welcome to circos v0.62-1 25 Jun 2012
debuggroup conf 0.18s loading configuration from file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.18s looking for conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf
debuggroup conf 0.18s found conf file
C:\Users\dksam_000\Circos\2\etc\circos.conf

*** CIRCOS ERROR ***

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

C:\Users\dksam_000\Circos\2\etc\

C:\Users\dksam_000\Circos\2\etc

C:\Users\dksam_000\Circos\2\etc/etc

C:/Users/dksam_000/Circos/bin/etc

C:/Users/dksam_000/Circos/bin/../etc

C:/Users/dksam_000/Circos/bin/..

C:/Users/dksam_000/Circos/bin

The Config::General module reported the error

Config::General The file "data/colors.conf" does not exist within ConfigPath:
C:\Users\dksam_000\Circos\2\etc\.C:\Users\dksam_000\Circos\2\etc.C:\Users\dksam_000\Circos\2\etc/etc.C:/Users/dksam_000/Circos/bin/etc.C:/Users/dksam_000/Circos/bin/../etc.C:/Users/dksam_000/Circos/bi
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Configuration.pm line 605.

If you are having trouble debugging this error, use this tutorial to learn how
to use the debugging facility

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

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

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

Stack trace:
at C:/Users/dksam_000/Circos/bin/../lib/Circos/Error.pm line 332.
Circos::Error::fatal_error('configuration',
'cannot_find_include',
'C:\Users\dksam_000\Circos\2\etc\\x{a}C:\Users\dksam_000\Circos\2\...',
'Config::General The file "data/colors.conf" does not e
Circos::Configuration::loadconfiguration('C:\Users\dksam_000\Circos\2\etc\circos.conf')
called at C:/Users/dksam_000/Circos/bin/../lib/Circos.pm line 156
Circos::run('Circos', 'configfile',
'C:\Users\dksam_000\Circos\2\etc\circos.conf') called at
C:\Users\dksam_000\Circos\bin\circos line 233

C:\Users\dksam_000\Circos\2\etc>

[Martin Krzywinski]

When you use a relative path in your configuration file (e.g. data/colors.conf), Circos will search for this file relative to your current directory.

If you're running Circos from Circos/bin, then Circos will look for Circos/bin/data/colors.conf, which doesn't exist. Hence the error.

You want to run Circos from where the path can be resolved. For example

cd C:\Users\dksam_000\Circos\2

C:\Users\dksam_000\Circos\2>perl C:\Users\dksam_000\Circos\bin\circos -conf etc\circos.conf

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Amrita Yadav]

Hello Martin Sir,
I run Homer and got circos error in between -

 *** CIRCOS ERROR ***

  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

  /etc/circos

  .

  ./etc

  /usr/bin/etc

  /usr/bin/../etc

  /usr/bin/..

  /usr/bin

  The Config::General module reported the error

  Config::General The file "etc/colors.conf" does not exist within ConfigPath:
  /etc/circos..../etc./usr/bin/etc./usr/bin/../etc./usr/bin/.../usr/bin! at
  /usr/share/perl5/Circos/Configuration.pm line 721.

  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/tutorials/lessons/configuration/debugging

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

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

  Stack trace:

 at /usr/share/perl5/Circos/Error.pm line 362.
    Circos::Error::fatal_error("configuration", "cannot_find_include", "/etc/circos\x{a}.\x{a}./etc\x{a}/usr/bin/etc\x{a}/usr/bin/../etc\x{a}/usr/bin/..\x{a}"..., "Config::General The file \"etc/colors.conf\" does not exist wit"...) called at /usr/share/perl5/Circos/Configuration.pm line 733
    Circos::Configuration::loadconfiguration("-HeatInt.circos.conf") called at /usr/share/perl5/Circos.pm line 197
    Circos::run("Circos", "configfile", "-HeatInt.circos.conf") called at /usr/bin/circos line 300
    !!! Problem running circos.  Command:
        circos -conf -HeatInt.circos.conf.




Thank you :)

[Martin Krzywinski]

This is not a GD problem. 

There is something wrong with your installation paths -- Circos cannot find the etc/colors.conf file in its installation directory. 

Please include in your bug report

- exact command you ran

- directory from which the command was executed

- location of the Circos installation

- contents of circos.conf

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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