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I would like to install Circos. I followed the instructions on Circos website. In particular, I checked for missing perl modules. I'm missing several of them:

missing            Font::TTF::Font
missing            GD
missing            GD::Polyline
missing            SVG
missing            Statistics::Basic
missing            Text::Format

So I followed again the instructions about Installing Perl Modules on Mac OS X on Circos website. Specifically, I followed the detailed instructions in Paulo Nuin's blog post. Freetype and Fontconfig were missing and I installed them.

Now, when I run the configuration for libgd-2.2.1, I get this configuration summary:

Support for Zlib: yes
Support for PNG library: yes
Support for JPEG library: yes
Support for WebP library: no
Support for TIFF library: no
Support for Freetype 2.x library: yes
Support for Fontconfig library: yes
Support for Xpm library: no
Support for liq library: no
Support for pthreads: yes

It looks good enough to me. But when I run the make, I get errors:

clang: warning: argument unused during compilation: '-pthread'
ld: malformed 64-bit a.b.c.d.e version number: 4.20201
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libgd.la] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

Since it was not working, I followed this recommendation on Stackoverflow and I ran

brew install gd

(I had to update brew by doing

cd /usr/local/Library
git pull origin master

following this answer on Stackoverflow.)

But I get an error:

Error: You must `brew link libpng freetype` before gd can be installed

And when I run 'brew link libpng freetype', I get another error:

Linking /usr/local/Cellar/libpng/1.6.21... 
Error: Could not symlink bin/libpng-config
Target /usr/local/bin/libpng-config
already exists. You may want to remove it:
  rm '/usr/local/bin/libpng-config'

To force the link and overwrite all conflicting files:
  brew link --overwrite libpng

To list all files that would be deleted:
  brew link --overwrite --dry-run libpng

Any solution to finally be able to run Circos?

Thanks in advance for your help!

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Antonin
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1 Answers1

-1

Finally, I solved the problem by changing the permissions in /usr/local:

sudo chown -R $(whoami) /usr/local

Following the recommendations on brew webpage.

Once this was solved, I just installed GD in Perl, as described in the last step in Paulo Nuin's post.

Antonin
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