Re: Binmode () on closed filehandle PNG ; print () on closed filehandle PNG

[luoxiong...@gmail.com]

Hi, all,

 

I have solved this problem. Thanks.

 

Best

 

On Friday, January 11, 2013 4:09:44 PM UTC-5, luoxiong...@gmail.com wrote:

Hi all,

 

When i run the examples from HIGHLIGHTS:wedges, i encountered a problem. The following error appeared:

 

binmode() on closed filehandle PNG at C:/Cygwin/circos-0.62-1/bin/../lib/Circos.pm line 3306, <F> line 35019.
print() on closed filehandle PNG at C:/Cygwin/circos-0.62-1/bin/../lib/Circos.pm line 3307, <F> line 35019.

 

I don't know why this happened. Could anyone tell me how to fix this problem ? By the way, when i run other exaamples, it works quite well. Thanks so much for help.

 

XIongjian

[luoxiong...@gmail.com]

Hi,

 

I solved this problem by changing the dir in the Circos.CONF file. The default dir = /tmp (In circos.conf). This is a probelm here, the dir defines the directory of the generated PNG or SVG figures. However, since the default is /tmp, the circos don't know how to store the generated PNG or SVG file. Since there are no directory for these files, the PERL treat them as closed filehandle. Therefore, it can't write the generated file to the dir. Here is my solution: (I changed the dir)

 

<image>
dir = C:/Cygwin/circos-0.62-1/circos-tutorials-0.62/tutorials/2/33 (# you can set the directory by youself, but should remember that the file is existed, otherwiase it can't work)
file  = circos-tutorial.png

now the generated files are wrote to my defined directory.

[luoxiong...@gmail.com]

Hi,

I solved this problem by changing the dir in the Circos.CONF file. The default dir = /tmp (In circos.conf). This is a probelm here, the dir defines the directory of the generated PNG or SVG figures. However, since the default is /tmp, the circos don't know how to store the generated PNG or SVG file. Since there are no directory for these files, the PERL treat them as closed filehandle. Therefore, it can't write the generated file to the dir. Here is my solution: (I changed the dir)

<image>
dir = C:/Cygwin/circos-0.62-1/circos-tutorials-0.62/tutorials/2/33 (# you can set the directory by youself, but should remember that the file is existed, otherwiase it can't work)
file = circos-tutorial.png

now the generated files are wrote to my defined directory.

 

 

On Monday, January 14, 2013 12:17:41 PM UTC-5, Jinho Lee wrote:

Hi,

I also have encountered same error message you have.
I am using Win7 and installed StrawberryPerl and just started to use Circos.
I tried to follow the tutorials from the beginning to generate png file but I couldn't.
Could you please show us how you solve this problem?

Thanks

[Jinho Lee]

Thanks a lot!

It works greatly for me.

[Martin Krzywinski]

You can always put 

dir = .

and Circos will create the output image in your current directory.

Where possible, try not to code absolute paths in the configuration files. This creates configuration files that are not portable. 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[yjjjn...@gmail.com]

Hi,hi , I've got some wired peoblems. I set up circos well in linux server, but when I run ./bin/circos -conf ./etc/circos.conf .The result is only SVG no PNG output. What can I fix the problem. And I fixed the etc/circos.conf file like this but it doesn't work.  thanks for advance.

在 2013年1月15日星期二 UTC+8上午1:54:59，Kevin Richard写道：