I keep getting the following error with GD 2.49 for Circos on the mac

Question

[Avro]

Hi everyone,

I am having trouble compiling GD 2.49 to use Circos. Here is the error:

perl Makefile.PL
Notice: Type perl Makefile.PL -h for command-line option summary.

Configuring for libgd version 2.0.34.
Checking for stray libgd header files...

WARNING: found gd.h header file in /usr/includegd.h, but it is expected at /usr/local/include/gd.h. This may cause compile errors!
Possible problems found

Included Features:          GD_JPEG GD_FONTCONFIG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF GD_FTCIRCLE VERSION_33
GD library used from:       /usr/local
Generating a Unix-style Makefile
Writing Makefile for GD
Writing MYMETA.yml and MYMETA.json

If I compile it anyway, Circos' example doesn't run. Has anyone encountered a similar problem. GD is really tricky. Any suggestion would be greatly appreciated. Thank you!

Answer 1

[Alex Reynolds]

Perhaps try installing it via Homebrew:

$ brew install gd
...
$ ls -al /usr/local/include/gd.h
lrwxr-xr-x  1 alexpreynolds  admin  33 Sep 25 12:43 /usr/local/include/gd.h -> ../Cellar/gd/2.1.0_2/include/gd.h

Or you could perhaps try a symbolic link to the existing installation:

$ ln -s /usr/include/gd.h /usr/local/include/gd.h

[Avro]

Hi Alex

Thank you for you answer. However, when I try the first option, I get several errors. When I try the second option, I still get the same error.

[Alex Reynolds]

I'm not really sure.

Maybe before you manually compile GD, set the compilation prefix to /usr/local, i.e., ./configure --prefix=/usr/local ...

I'm not sure what the side effects would be of having two GD installations of different versions, but so long as you are not overwriting a version packaged with OS X, you should probably be fine.

You could also try to get help through the Circos site and mailing list. I see lots of questions there about getting past the installation "hump".