Error running Circos 0.48 on Windows XP

[encleadus]

Hi, I am trying to get Circos 0.48 working on Windows XP. I have
installed ActiveState Perl 5.10.0 and installed all of the required
additional modules using ActiveState's PPM via the CPAN repository.
Thanks for any help!

#####

Lines that I changed in the bin\circos file are:

line 1 - to my perl, #!c:\perl\bin\perl.exe
line 285 - to perl library, c:\perl\lib
line 298 - to perl library, c:\perl\lib

Lines that I changed in the tutorials\2\2\circos.conf file are:

line 23 - to new output directory, d:\programs\circos\tmp

The error I am receiving is:

D:\programs\circos\circos-0.48>perl bin\circos -conf tutorials
\2\2\circos.conf

zoomregion ideogram 0 chr hs1 0 247249719 scale 1.00
absolutescale 1.00
zoomregion ideogram 1 chr hs2 0 242951149 scale 1.00
absolutescale 1.00
zoomregion ideogram 2 chr hs3 0 199501827 scale 1.00
absolutescale 1.00
zoomregion ideogram 3 chr hs4 0 191273063 scale 1.00
absolutescale 1.00
zoomregion ideogram 4 chr hs5 0 180857866 scale 1.00
absolutescale 1.00
zoomregion ideogram 5 chr hs6 0 170899992 scale 1.00
absolutescale 1.00
zoomregion ideogram 6 chr hs7 0 158821424 scale 1.00
absolutescale 1.00
zoomregion ideogram 7 chr hs8 0 146274826 scale 1.00
absolutescale 1.00
zoomregion ideogram 8 chr hs9 0 140273252 scale 1.00
absolutescale 1.00
zoomregion ideogram 9 chr hs10 0 135374737 scale 1.00
absolutescale 1.00
zoomregion ideogram 10 chr hs11 0 134452384 scale 1.00
absolutescale 1.00
zoomregion ideogram 11 chr hs12 0 132349534 scale 1.00
absolutescale 1.00
zoomregion ideogram 12 chr hs13 0 114142980 scale 1.00
absolutescale 1.00
zoomregion ideogram 13 chr hs14 0 106368585 scale 1.00
absolutescale 1.00
zoomregion ideogram 14 chr hs15 0 100338915 scale 1.00
absolutescale 1.00
zoomregion ideogram 15 chr hs16 0 88827254 scale 1.00
absolutescale 1.00
zoomregion ideogram 16 chr hs17 0 78774742 scale 1.00
absolutescale 1.00
zoomregion ideogram 17 chr hs18 0 76117153 scale 1.00
absolutescale 1.00
zoomregion ideogram 18 chr hs19 0 63811651 scale 1.00
absolutescale 1.00
zoomregion ideogram 19 chr hs20 0 62435964 scale 1.00
absolutescale 1.00
zoomregion ideogram 20 chr hs21 0 46944323 scale 1.00
absolutescale 1.00
zoomregion ideogram 21 chr hs22 0 49691432 scale 1.00
absolutescale 1.00
zoomregion ideogram 22 chr hsX 0 154913754 scale 1.00
absolutescale 1.00
zoomregion ideogram 23 chr hsY 0 57772954 scale 1.00
absolutescale 1.00
registering tag hs1
registering tag hs2
registering tag hs3
registering tag hs4
registering tag hs5
registering tag hs6
registering tag hs7
registering tag hs8
registering tag hs9
registering tag hs10
registering tag hs11
registering tag hs12
registering tag hs13
registering tag hs14
registering tag hs15
registering tag hs16
registering tag hs17
registering tag hs18
registering tag hs19
registering tag hs20
registering tag hs21
registering tag hs22
registering tag hsX
registering tag hsY
ideogramspacing hs1 hs1 hs2 hs2 10000000
ideogramspacing hs2 hs2 hs3 hs3 10000000
ideogramspacing hs3 hs3 hs4 hs4 10000000
ideogramspacing hs4 hs4 hs5 hs5 10000000
ideogramspacing hs5 hs5 hs6 hs6 10000000
ideogramspacing hs6 hs6 hs7 hs7 10000000
ideogramspacing hs7 hs7 hs8 hs8 10000000
ideogramspacing hs8 hs8 hs9 hs9 10000000
ideogramspacing hs9 hs9 hs10 hs10 10000000
ideogramspacing hs10 hs10 hs11 hs11 10000000
ideogramspacing hs11 hs11 hs12 hs12 10000000
ideogramspacing hs12 hs12 hs13 hs13 10000000
ideogramspacing hs13 hs13 hs14 hs14 10000000
ideogramspacing hs14 hs14 hs15 hs15 10000000
ideogramspacing hs15 hs15 hs16 hs16 10000000
ideogramspacing hs16 hs16 hs17 hs17 10000000
ideogramspacing hs17 hs17 hs18 hs18 10000000
ideogramspacing hs18 hs18 hs19 hs19 10000000
ideogramspacing hs19 hs19 hs20 hs20 10000000
ideogramspacing hs20 hs20 hs21 hs21 10000000
ideogramspacing hs21 hs21 hs22 hs22 10000000
ideogramspacing hs22 hs22 hsX hsX 10000000
ideogramspacing hsX hsX hsY hsY 10000000
ideogramspacing hsY hsY hs1 hs1 10000000
ideogramreport 0 hs1 0 hs1 0.000 247249.719
247249.720 0.000 0.000 r 1275 1175 1275 100
ideogramreport 1 hs2 1 hs2 0.000 242951.149 242951.150
247249.719 247249.719 r 1275 1175 1275 100
ideogramreport 2 hs3 2 hs3 0.000 199501.827 199501.828
490200.868 490200.868 r 1275 1175 1275 100
ideogramreport 3 hs4 3 hs4 0.000 191273.063 191273.064
689702.695 689702.695 r 1275 1175 1275 100
ideogramreport 4 hs5 4 hs5 0.000 180857.866 180857.867
880975.758 880975.758 r 1275 1175 1275 100
ideogramreport 5 hs6 5 hs6 0.000 170899.992 170899.993
1061833.624 1061833.624 r 1275 1175 1275 100
ideogramreport 6 hs7 6 hs7 0.000 158821.424 158821.425
1232733.616 1232733.616 r 1275 1175 1275 100
ideogramreport 7 hs8 7 hs8 0.000 146274.826 146274.827
1391555.040 1391555.040 r 1275 1175 1275 100
ideogramreport 8 hs9 8 hs9 0.000 140273.252 140273.253
1537829.866 1537829.866 r 1275 1175 1275 100
ideogramreport 9 hs10 9 hs10 0.000 135374.737 135374.738
1678103.118 1678103.118 r 1275 1175 1275 100
ideogramreport 10 hs11 10 hs11 0.000 134452.384 134452.385
1813477.855 1813477.855 r 1275 1175 1275 100
ideogramreport 11 hs12 11 hs12 0.000 132349.534 132349.535
1947930.239 1947930.239 r 1275 1175 1275 100
ideogramreport 12 hs13 12 hs13 0.000 114142.980 114142.981
2080279.773 2080279.773 r 1275 1175 1275 100
ideogramreport 13 hs14 13 hs14 0.000 106368.585 106368.586
2194422.753 2194422.753 r 1275 1175 1275 100
ideogramreport 14 hs15 14 hs15 0.000 100338.915 100338.916
2300791.338 2300791.338 r 1275 1175 1275 100
ideogramreport 15 hs16 15 hs16 0.000 88827.254 88827.255
2401130.253 2401130.253 r 1275 1175 1275 100
ideogramreport 16 hs17 16 hs17 0.000 78774.742 78774.743
2489957.507 2489957.507 r 1275 1175 1275 100
ideogramreport 17 hs18 17 hs18 0.000 76117.153 76117.154
2568732.249 2568732.249 r 1275 1175 1275 100
ideogramreport 18 hs19 18 hs19 0.000 63811.651 63811.652
2644849.402 2644849.402 r 1275 1175 1275 100
ideogramreport 19 hs20 19 hs20 0.000 62435.964 62435.965
2708661.053 2708661.053 r 1275 1175 1275 100
ideogramreport 20 hs21 20 hs21 0.000 46944.323 46944.324
2771097.017 2771097.017 r 1275 1175 1275 100
ideogramreport 21 hs22 21 hs22 0.000 49691.432 49691.433
2818041.340 2818041.340 r 1275 1175 1275 100
ideogramreport 22 hsX 22 hsX 0.000 154913.754 154913.755
2867732.772 2867732.772 r 1275 1175 1275 100
ideogramreport 23 hsY 23 hsY 0.000 57772.954 57772.955
3022646.526 3022646.526 r 1275 1175 1275 100
drawing ticks hs1 radius 1275 type absolute spacing 10000000
Set::IntSpan::_copy_run_list: Bad order: -2002--2003
at bin\circos line 4202

[Martin]

> drawing ticks hs1 radius 1275 type absolute spacing 10000000
> Set::IntSpan::_copy_run_list: Bad order: -2002--2003
> at bin\circos line 4202

This problem is due to a font issue - your GD module (Perl's interface
to gd, the graphics library) does not have TTF (provided by the
freetype library) support. This could be because you didn't install GD
with TTF support, or gd isn't compiled with TTF support on your
machine.

To verify this, run bin/gddiag as follows

> cd circos-x.xx/bin
> ./gddiag -conf ../tutorials/2/2/circos.conf -output_file ~/tmp/gddiag.png -colsize 50 -labelsie 14

Now take a look at gddiag.png - do you see text labels? I've attached
what this file should look like.

To fix this problem, make sure that GD is being installed with
freetype option on.

[encleadus]

I'm not able to see your attachment, but I ran the command and I get
an image of colored squares on a white background with no text. Now I
need to figure out how to get GD compiled with freetype support.

[mario ruggier]

Hello!

I have just attempted to get circos-0.49 up on a windows XP machine,
and I also get the same identical error as noted above when I try to
run the same tutorial.

I have installed activeperl 5.10.0 natively on windows, and cygwin
1.5.25-15.
Doing (under cygwin):
cd circos-0.49

./install
$ dos2unix install
$ ./install
This script sets the location of the Perl binary in Circos scripts,
and sets the output directory for tutorial image files.
What is the full path to your perl binary? (/bin/env perl)
/cygdrive/c/Perl/bin/perl
Setting Perl binary to /cygdrive/c/Perl/bin/perl
Can't do inplace edit without backup.
xargs: perl: exited with status 255; aborting
What is the directory to which tutorial images should be written? (/
tmp)
/cygdrive/c/circos-work/tmp
Setting output directory for tutorial files to /cygdrive/c/circos-work/
tmp
Can't do inplace edit without backup.
xargs: perl: exited with status 255; aborting
Done. You can run this script at any time to change these values.

So, I then just modified the files by hand... and running

bin\circos -conf tutorials \2\2\circos.conf

gives identical error as above.

Any tips appreciated!

Thanks, mario

[Jordan Atlas]

Hello,

I am also having the "Set::IntSpan::_copy_run_list: Bad order:
-2002--2003" error described in the original post.

Can anyone provide a starting place for installing gd with TTF
support under windows?

Thank you, and apologies for the repeated mailings today.

--Jordan

On Apr 6, 9:18 am, mario ruggier <mario.rugg...@gmail.com> wrote:
> Hello!
>

> I have just attempted to get circos-0.49 up on awindowsXP machine,

> and I also get the same identical error as noted above when I try to
> run the same tutorial.
>

> I have installed activeperl 5.10.0 natively onwindows, and cygwin

> > togd, the graphics library) does not have TTF (provided by the
> >freetypelibrary) support. This could be because you didn't installGD
> > with TTF support, orgdisn't compiled with TTF support on your

[Lee]

Hi -
I had the same issue running on WindowsXP with active perl 5.8.8 and
PPM version 4.03. I can correct this problem & get text labels by
installing the GD-Text package through PPM. Simple install and then it
worked perfectly. Hope this helps someone....

--Lee

[Lee]

Ooops, sorry, thats supposed to be GD-Text and GD-Text-Arc. I needed
them both.
apologies

[Sophie]

Hi
I am really new at Perl under windows. I am just trying to install
Circos to interface with our C# software. I apologize in advance if
the question is very trivial.
I have Active Perl 5.10. something installed and I was going to
install GD-Text-Arc but could not find it under the PPM list.
I did a quick google search and found it http://search.cpan.org/~dallen/GD-Text-Arc-0.02/
I downloaded it and followed the README installation directive under
cygwin. It doesn't work. I think it has to do with a discrepancy
between cygwin path notation and windows path notation. How should I
install this package which seems to be crucial to the execution of
circos?
Thanks for any information
Best regards
Sophie

> > > > >freetypeoption on.- Hide quoted text -
>
> - Show quoted text -

[stoyan]

Adding this to Repository will make GD-Text-Arc appear at PPM:
http://www.bribes.org/perl/ppm/package.xml

Anyway, I still get the error:

drawing ticks hs1 radius 1275 type absolute spacing 10000000
Set::IntSpan::_copy_run_list: Bad order: -2002--2003

at circos-0.49.pl line 4153

On May 27, 7:52 am, Sophie <sophiec...@gmail.com> wrote:
> Hi
> I am really new at Perl under windows. I am just trying to install
> Circos to interface with our C# software. I apologize in advance if
> the question is very trivial.
> I have Active Perl 5.10. something installed and I was going to
> install GD-Text-Arc but could not find it under the PPM list.

> I did a quick google search and found ithttp://search.cpan.org/~dallen/GD-Text-Arc-0.02/

> I downloaded it and followed the README installation directive under
> cygwin. It doesn't work. I think it has to do with a discrepancy
> between cygwin path notation and windows path notation. How should I
> install this package which seems to be crucial to the execution of
> circos?
> Thanks for any information
> Best regards
> Sophie
>

[stoyan]

Actually reinstalling GD from PPM made it work afterwords!