Error running example in .56

[Andrew Gallo]

Greetings:

Brand-new to Circos, so apologies if this is overly basic or has been covered, but I have searched :)

I installed .56 on a Debian machine, applied the .56-1 patch.  I installed all the required Perl modules (bin/test.modules had no failures).

From the online tutorials and the README in example/ ,  I thought I could run Circos based on the example data (/example/run)  however, I'm getting these errors:
about 200 lines that look like:
Use of uninitialized value in subtraction (-) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8454, <F> line 1577.
Use of uninitialized value in subtraction (-) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8455, <F> line 1577.
Use of uninitialized value in subtraction (-) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8455, <F> line 1577.
Use of uninitialized value in numeric eq (==) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8453, <F> line 1577.
Use of uninitialized value in numeric eq (==) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8453, <F> line 1577.
Use of uninitialized value in subtraction (-) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8454, <F> line 1577.
Use of uninitialized value in subtraction (-) at /usr/local/circos-0.56/bin/../lib/Circos.pm line 8454, <F> line 1577.

plus the following:
 at /usr/local/circos-0.56/bin/../lib/Circos/Error.pm line 278
        Circos::Error::fatal_error('argument', 'list_size', 'get_label_wh_from_bounds', 'Circos::Font', 8, 0) called at /usr/local/circos-0.56/bin/../lib/Circos/Font.pm line 183
        Circos::Font::get_label_wh_from_bounds() called at /usr/local/circos-0.56/bin/../lib/Circos/Font.pm line 167
        Circos::Font::get_label_size('font_file', '/usr/local/circos-0.56/example/../fonts/modern/cmunbmr.otf', 'size', 24, 'text', 'hs1') called at /usr/local/circos-0.56/bin/../lib/Circos.pm line 885
        Circos::run('Circos', 'configfile', 'etc/circos.conf', 'debug_group', 'summary,timer,textplace') called at ../bin/circos line 229


I've searched for these errors, but found nothing.

Thanks for helping a beginner.

[Martin]

I'll check these out tomorrow and get back to you.

Sorry about this first experience being so errorful.
Martin

[Martin]

It looks like this is caused by a problem with True Type font support.
I will try to add better sanity checking code to Circos so that this
is caught.

Please run

bin/gddiag

and look at the output image, which should look like this

http://www.circos.ca/documentation/tutorials/configuration/png_output/images

If you don't see any text, then your perl pipeline is lacking True
Type support. This can be due to

1. GD module was compiled without TTF support,
2. your gd library was compiled without TTF support,
2. your system lacks freetype library, so no TTF support is possible

Given that both gd and freetype are standard, it's very likely that GD
is the culprit.

You can check your gd state by

> gdlib-config --all
GD library 2.0.33
includedir: /usr/include
cflags: -I/usr/include
ldflags: -L/usr/lib64
libs: -lXpm -lX11 -ljpeg -lfontconfig -lfreetype -lpng12 -lz -
lm
libdir: /usr/lib64
features: GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE GD_PNG GD_GIF

If you have GD_FREETYPE in the features line, then it's certainly GD
that is the problem.

Others here have mentioned this error - search the message board for
it. It requires reinstallation of GD.

Martin

On Feb 16, 5:34 pm, Andrew Gallo <aga...@gmail.com> wrote:

[Andrew Gallo]

Looks like I don't have GD_FREETYPE.

I'll work on that and continue.

Thank you for the quick reply.

[Andrew Gallo]

Thanks for the quick reply, and sorry for my late response (away on
vacation)....

looks like I don't have GD_FREETYPE as a feature:
gdlib-config --all
GD library 2.0.36
includedir: /usr/local/include
cflags: -I/usr/local/include
ldflags: -L/usr/lib
libs: -ljpeg -lpng12 -lz -lm
libdir: /usr/local/lib
features: GD_JPEG GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON

I'll work on that and continue.

Thank you!

On Feb 20, 3:00 pm, Martin <martin.krzywin...@gmail.com> wrote:
> It looks like this is caused by a problem with True Type font support.
> I will try to add better sanity checking code to Circos so that this
> is caught.
>
> Please run
>
> bin/gddiag
>
> and look at the output image, which should look like this
>

> http://www.circos.ca/documentation/tutorials/configuration/png_output...

[Andrew Gallo]

Recompiled GD and it worked.

I'm running Debian 6.0.3 and the version of gd (2.0.36) installed with
apt-get. Couldn't figure out how to add GD to package (or reinstall
with GD as an option) using the package manager, so I compiled
manually and installed. I ran the example script - worked like a
champ with no errors.

Thanks for your quick help.

BTW, what I am looking to do is use Circos to visualize Washington's
Capital Bikeshare trip data (http://www.capitalbikeshare.com/trip-
history-data). I thought it would be interesting to visualize the
popular stations and where people are going to/from.

Thanks again!

On Feb 28, 2:10 pm, Andrew Gallo <aga...@gmail.com> wrote:
> Thanks for the quick reply, and sorry for my late response (away on
> vacation)....
>

> looks like I don't haveGD_FREETYPEas a feature:

> > If you haveGD_FREETYPEin the features line, then it's certainly GD