Installing Circos using Homebrew

[Shaun Jackman]

I created a Homebrew formula to install Circos. Due to the trickiness of installing GD, it's not as simple as brew install circos, but hopefully we'll get there. Here's the instructions:

Install Homebrew on Mac OS or Linuxbrew on Linux.

Run the following commands to install GD and Circos.

brew tap homebrew/science
brew remove gd
brew install gd --with-freetype
brew install cpanminus
sudo chown "$USER":admin /Library/Perl/5.16 # on Mac OS
cpanm Config::General Font::TTF::Font Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format
cpanm --force GD::Polyline
brew install circos
brew test circos

Cheers,
Shaun

[Martin Krzywinski]

Thanks Shaun. A lot of people have trouble getting freetype into gd -- this should help.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Harry Osoff]

Shaun,

What ever magic you know - it is strong.

Those simple steps solved my issue with getting circos to run the example.

Now I am of in search of something else to test 

Thanks ever so much

Harry

[Jon]

I'm following the steps above exactly and still getting an error for GD::Polyline. I recently did a clean installation of Mavericks so I wonder if that might be causing problems. All the other modules installed just fine, but when I type

brew install circos

I get this error:

circos: Unsatisfied dependency: GD::Polyline

Homebrew does not provide Perl dependencies; install with:

  cpan -i GD::Polyline

Error: An unsatisfied requirement failed this build.

no matter, right? because I should just be able to type:

sudo cpanm --force GD::Polyline

But this isn't getting me anywhere.

--> Working on GD::Polyline

Fetching http://www.cpan.org/authors/id/L/LD/LDS/GD-2.52.tar.gz ... OK

Configuring GD-2.52 ... OK

Building and testing GD-2.52 ... FAIL

! Testing GD-2.52 failed but installing it anyway.

Successfully reinstalled GD-2.52

1 distribution installed

Jons-MacBook-Pro:~ Jon$ brew install circos

circos: Unsatisfied dependency: GD::Polyline

Homebrew does not provide Perl dependencies; install with:

  cpan -i GD::Polyline

Error: An unsatisfied requirement failed this build.

Any help would be greatly appreciated!

[dhess]

Hi,

Thanks for the Homebrew formula. Quick question. When I try to install gd --with-freetype I get the following error:

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

And when I try to brew link libpng freetype I get another error telling me that the target already exists. However when I try and overwrite it I get a permission denied response. How can I get around this?

Thanks,

Daisy

[austin garner]

I am attempting this installation but when I go to run cpanm --force GD::Polyline, I get the following error:

ERROR: Can't create '/Users/austingarner/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/darwin-2level/auto/GD'mkdir /Users/austingarner/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/darwin-2level/auto/GD: Permission denied at /Users/austingarner/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/ExtUtils/Install.pm line 494.

I am fairly green at this and am at a loss as to what to do, any suggestions would be much appreciated. 

Thanks, 
AG

[Martin Krzywinski]

The error is produced by 

mkdir /Users/austingarner/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/darwin-2level/auto/GD

It looks like you can't create this directory because you don't have permission to write to the directory above it.

Perhaps if the original installation was done as root, then the tree isn't owned by you.

Try running cpan with 

sudo cpan ...

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[David Cook]

Did you ever figure this out, Jon? I seem to be having the same problem.

I've been having some troubles getting GD properly installed in order to run Circos. I think everything looks okay until I run ./test.modules after installation. I was originally trying to install everything using homebrew, but came across some troubles:

DPC@Love-Machine:~$ brew install circos

circos: Unsatisfied dependency: GD::Polyline

Homebrew does not provide Perl dependencies; install with:

  cpan -i GD::Polyline

Error: An unsatisfied requirement failed this build.

DPC@Love-Machine:~$ cpan -i GD::Polyline

Reading '/Users/DPC/.cpan/Metadata'

  Database was generated on Thu, 11 Sep 2014 15:53:16 GMT

GD::Polyline is up to date (0.2).       #???

Download Circos manually and ran ./test.modules. As expected, problems with GD:

ok   Carp

ok   Clone

ok   Config::General

ok   Cwd

ok   Data::Dumper

ok   Digest::MD5

ok   File::Basename

ok   File::Spec::Functions

ok   File::Temp

ok   FindBin

ok   Font::TTF::Font

fail GD is not usable (it or a sub-module is missing)

fail GD::Image is not usable (it or a sub-module is missing)

ok   Getopt::Long

ok   IO::File

ok   List::MoreUtils

ok   List::Util

ok   Math::Round

ok   Math::VecStat

ok   Memoize

ok   POSIX

ok   Params::Validate

ok   Pod::Usage

ok   Readonly

ok   Regexp::Common

ok   Storable

ok   Sys::Hostname

ok   Text::Balanced

ok   Text::Format

ok   Time::HiRes

Tried to download and install GD and libs manually. After ./configure libgd:

** Configuration summary for libgd 2.1.0-rc2:

   Support for Zlib:                 yes

   Support for PNG library:          yes

   Support for JPEG library:         yes

   Support for VPX library:          no

   Support for TIFF library:         yes

   Support for Freetype 2.x library: yes

   Support for Fontconfig library:   yes

   Support for Xpm library:          no

   Support for pthreads:             yes

When running GD's Makefile.pl, I got a warning:

Checking for stray libgd header files...

** WARNING: found gd.h header file in /usr/local/includegd.h, but it is expected at /usr/local/Cellar/gd/2.1.0_2/include/gd.h. This may cause compile errors! **

** Possible problems found **

Included Features:          GD_TIFF GD_JPEG GD_FONTCONFIG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON

GD library used from:       /usr/local/Cellar/gd/2.1.0_2

I figured it was safe to remove the stray header file mentioned, so I did (note: also tried without removing the stray header).

During make, it had problems with some dylibs:

ld: warning: ld: warning: ignoring file /usr/local/lib/libjpeg.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libjpeg.dylibignoring file /usr/local/lib/libz.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libz.dylib

ld: warning: ignoring file /usr/local/lib/libfreetype.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libfreetype.dylib

ld: warning: ignoring file /usr/local/lib/libpng16.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libpng16.dylib

ld: warning: ignoring file /usr/local/lib/libfontconfig.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libfontconfig.dylib

ld: warning: ignoring file /usr/local/lib/libtiff.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libtiff.dylib

ld: warning: ignoring file /usr/local/lib/libgd.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libgd.dylib

But it kept running. Did sudo make install to see if it would work anyway:

DPC@Love-Machine:/srctemp/GD-2.49$ sudo make install

Manifying blib/man1/bdf2gdfont.pl.1

Files found in blib/arch: installing files in blib/lib into architecture dependent library tree

Installing /Library/Perl/5.16/darwin-thread-multi-2level/auto/GD/GD.bundle

Installing /Library/Perl/5.16/darwin-thread-multi-2level/GD.pm

Installing /Library/Perl/5.16/darwin-thread-multi-2level/GD/Simple.pm

Installing /usr/local/share/man/man3/GD.3pm

Installing /usr/local/share/man/man3/GD::Polygon.3pm

Installing /usr/local/share/man/man3/GD::Polyline.3pm

Installing /usr/local/share/man/man3/GD::Simple.3pm

Appending installation info to /Library/Perl/Updates/5.16.2/darwin-thread-multi-2level/perllocal.pod

Redid ./test.modules with no change:

fail GD is not usable (it or a sub-module is missing)

fail GD::Image is not usable (it or a sub-module is missing)

My (extremely) naive guess is that it's something to do with the "architecture being linked", but truly, I have no idea what this means or what I can do to fix it. If anyone has some insight, I would really appreciate the help!

David

[Martin Krzywinski]

If you're using both homebrew and cpan it may be that you're writing the Perl modules into different directories.

If you run CPAN as non-root, the module will be typically written under your home directory, which by default is not where Perl looks for modules. 

To guard against this, when you use CPAN pay careful attention to the scrolling output and look for the path where the module is installed. Then, look at the @INC path at the bottom of

perl -V

output to see where Perl will look for modules. It's best to run CPAN as root

> sudo perl -MCPAN -e shell

I'm also wary of the fact that you're seeing /usr/local/lib as a path in your errors rather than /usr/lib. Is it possible that you have several installations of libjpeg on your system? The stray header errors suggest that you have several installations of the libraries. Check with

locate libjpeg

These kinds of errors are hard to pin down. I would suggest that you try compiling all the requirements for libgd yourself in a fresh location. At each step, check that the compiler isn't trying to bring in files from elsewhere. 

When installing GD for Perl, check the Makefile for those paths too.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Tim Dee]

Hey guys,

Just tried following the instrictions on this page on OS X and got the following error message - anyone know how to proceed? I'm not a programmer so all this is totally new to me. Seems bizarre that the installation for Circos is such a nightmare. Thanks so much!
Tim

Homebrew does not provide Perl dependencies; install with:

cpan -i Config::General
circos: Unsatisfied dependency: Font::TTF::Font

Homebrew does not provide Perl dependencies; install with:

cpan -i Font::TTF::Font

circos: Unsatisfied dependency: GD::Polyline
Homebrew does not provide Perl dependencies; install with:
cpan -i GD::Polyline

circos: Unsatisfied dependency: Math::Bezier

Homebrew does not provide Perl dependencies; install with:

cpan -i Math::Bezier
circos: Unsatisfied dependency: Math::VecStat

Homebrew does not provide Perl dependencies; install with:

cpan -i Math::VecStat
circos: Unsatisfied dependency: Readonly

Homebrew does not provide Perl dependencies; install with:

cpan -i Readonly
circos: Unsatisfied dependency: Set::IntSpan

Homebrew does not provide Perl dependencies; install with:

cpan -i Set::IntSpan
circos: Unsatisfied dependency: Text::Format

Homebrew does not provide Perl dependencies; install with:

cpan -i Text::Format
Error: Unsatisified requirements failed this build.

[Paulo Nuin]

It just means that most Circos dependencies are not installed with homebrew. Just run each one of the commands

cpan -i


and install the Perl dependencies. Usually Circos installation with home-brew should cover the libraries.

Cheers
Paulo

[Lifang He]

Hi,

When I try to install cairo by "brew install cairo", I also get such an error:

You must `brew link libpng freetype' before cairo can be installed

Could you please tell me how to solve this problem? any suggestion is appreciated. Thanks.

在 2014年4月1日星期二 UTC-5上午9:42:52，dhess写道：

[Vikram]

I just tried using Shaun's Homebrew formula after getting stuck trying to install GD. i am copy-pasting what happened after i tried to use circos on the example file. Please note that i am on a Mac computer running on OS 10.11.6 El Capitan. And i have not disabled  the 'rootless' feature of El Capitan.

----

Vikrams-MBP:example k$ ./run

Creating image circos.png and writing report to run.out.

Example takes ~45-60 seconds to generate.

Vikrams-MBP:example k$ ls

README circos.svg etc run.out

circos.png data run

Vikrams-MBP:example k$ pwd

/Users/k/Desktop/downloads/circos-0.69/example

Vikrams-MBP:example k$ /Users/k/Desktop/downloads/circos-0.69/bin/circos -conf etc/circos.conf

*** REQUIRED MODULE(S) MISSING OR OUT-OF-DATE ***

You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial

http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules

missing GD

  error Can't locate GD.pm in @INC (you may need to install the GD module) (@INC contains: /Users/k/Desktop/downloads/circos-0.69/bin/lib /Users/k/Desktop/downloads/circos-0.69/bin/../lib /Users/k/Desktop/downloads/circos-0.69/bin /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2/darwin-thread-multi-2level /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at (eval 29) line 1.

missing GD::Polyline

  error Can't locate GD/Polyline.pm in @INC (you may need to install the GD::Polyline module) (@INC contains: /Users/k/Desktop/downloads/circos-0.69/bin/lib /Users/k/Desktop/downloads/circos-0.69/bin/../lib /Users/k/Desktop/downloads/circos-0.69/bin /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2/darwin-thread-multi-2level /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at (eval 30) line 1.

Vikrams-MBP:example k$ 

----

One more point: when i type these commands:

Vikrams-MBP:etc k$ cd

Vikrams-MBP:~ k$ vi .bash_profile

now, in the .bash_profile file i see this:

# Setting PATH for Python 2.7

# The original version is saved in .bash_profile.pysave

PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"

export PATH

what do i need to add to the file .bash_profile (to enable me to run circos  from any directory)? can i add the file named 'circos'  (in the bin folder) to my Applications on my Mac?

[Jim Guo]

Hi Shaun,

Thanks, you are my hero! I used your approach successfully installed circos on my server (OS version: Ubuntu 14.04.5 LTS (GNU/Linux 3.13.0-98-generic x86_64)). Below I share the commands with slight modifications of Shaun's original post for Linux users.

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)"

export PATH="$HOME/.linuxbrew/bin:$PATH"

export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"

export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"

brew tap linuxbrew/science

brew install gd --with-freetype

brew install cpanminus

sudo chown "$USER":admin /usr/local/lib/perl/5.18.2

# Note: depending on what modules are pre-installed with your perl pacakage, the following modules might differ among different users. 

sudo cpanm Config::General Font::TTF::Font Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format Params::Validate Math::Round Regexp::Common Clone

sudo cpanm --force GD::Polyline

brew install circos

brew test circos

## If brew test circos failed, it might indicate that some modules are missed. run "circos -modules", use sudo cpanm to install missed packages and re-test.

[Eric Stemn]

Thanks Shaun, you make the installation looked easier. I have been struggling for the past weeks to get around this but nothing seemed working till I came across your post. You are a genius!, you know that......

Can I get help on how to generating the circos example image. I am finding it difficult to locate the circos/example directory. I am a novice to command line.

Eric 

[Martin Krzywinski]

To generate the example image,

> cd /path/to/circos-v0.xx

> cd example

> ../bin/circos

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Kennith]

When I followed the installation procedure above, the following error(s) arose during the "brew test circos" step:

VPN-18-101-8-109:Applications $ brew test circos

Testing homebrew/science/circos

==> /usr/local/Cellar/circos/0.67-7/bin/circos -conf /usr/local/Cellar/circos/0.

Last 15 lines from /Users/-/Library/Logs/Homebrew/circos/test.01.circos:

2017-12-04 18:13:44 -0500

/usr/local/Cellar/circos/0.67-7/bin/circos

-conf

/usr/local/Cellar/circos/0.67-7/libexec/example/etc/circos.conf

-debug_group

summary,timer

Error: homebrew/science/circos: failed

Failed executing: /usr/local/Cellar/circos/0.67-7/bin/circos -conf /usr/local/Cellar/circos/0.67-7/libexec/example/etc/circos.conf -debug_group summary,timer

/usr/local/Homebrew/Library/Homebrew/formula.rb:1796:in `block in system'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1734:in `open'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1734:in `system'

/usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/circos.rb:87:in `block in <class:Circos>'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1640:in `block (3 levels) in run_test'

/usr/local/Homebrew/Library/Homebrew/utils.rb:554:in `with_env'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1639:in `block (2 levels) in run_test'

/usr/local/Homebrew/Library/Homebrew/formula.rb:834:in `with_logging'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1638:in `block in run_test'

/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:14:in `block in mktemp'

/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `block in run'

/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `chdir'

/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `run'

/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:13:in `mktemp'

/usr/local/Homebrew/Library/Homebrew/formula.rb:1632:in `run_test'

/usr/local/Homebrew/Library/Homebrew/test.rb:28:in `block in <main>'

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/lib/ruby/2.3.0/timeout.rb:91:in `block in timeout'

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/lib/ruby/2.3.0/timeout.rb:33:in `block in catch'

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/lib/ruby/2.3.0/timeout.rb:33:in `catch'

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/lib/ruby/2.3.0/timeout.rb:33:in `catch'

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/lib/ruby/2.3.0/timeout.rb:106:in `timeout'

/usr/local/Homebrew/Library/Homebrew/test.rb:27:in `<main>'

Do you have any recommendations on how to fix this?

Thanks,

Kendall

[hqu...@ucr.edu]

Hi Shaun,

I tried your method but cannot "brew" freetype with gd.

It showed:"Warning: gd: this formula has no --with-freetype option so it will be ignored!" Could you please help me out?

Thank you in advance!

Han

On Thursday, February 20, 2014 at 12:37:10 PM UTC-8, Shaun Jackman wrote:

[uf...@us.ibm.com]

The previous steps seemed to have worked, but still getting the error:

No available formula with the name "circos"

When I try brew install circos.  Any suggestions?

[Paulo Nuin]

Circos shouldn’t be in homebrew/science anymore, it was merged in the main tap/core. Apart from this change the other steps should be identical.

Paulo

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[Shaun Jackman]

To install Circos using Homebrew or Linuxbrew, run…

brew install brewsci/bio/circos

See https://brew.sh and http://linuxbrew.sh

Cheers,

Shaun

[crlc06]

I am very sorry, I realize this may not be the place for this, but I have been trying for hours to get Circos to work on Mac 10.13.4

Can you please give clear and concise instructions on how to install circos and make it work properly.

I have tried with circos 0.69 and 0.69-6.

After muddling through all of the issues and finally running this command, it works....but actually nothing works, I cannot use the program. It is there, and it says it is already installed, but I cannot access it, so please tell me what I am doing wrong :-(

Best regards!

[as1...@nyu.edu]

Hi, im having trouble installing Circos..

I'm following these command lines from the Circos website (http://www.circos.ca/documentation/tutorials/configuration/installation/)

brew tap homebrew/science
brew remove gd
brew install gd --with-freetype
brew install cpanminus
sudo chown "$USER":admin /Library/Perl/5.16 # on Mac OS
cpanm Config::General Font::TTF::Font Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format
cpanm --force GD::Polyline
brew install circos
brew test circos

I'm having trouble with these steps:

sudo chown "$USER":admin /Library/Perl/5.16

Cannot find path
I put my username instead of "USER" and I put the path to the perl5 module installed on my computer but I'm sure I'm doing something wrong.
This is what I type in terminal: sudo chown "$myusername":admin myusername/perl5

cpanm --force GD::Polyline
#BELOW IS THE ERROR I GET FROM RUNNING THE ABOVE COMMAND

--> Working on GD::Polyline

Fetching http://www.cpan.org/authors/id/R/RU/RURBAN/GD-2.68.tar.gz ... OK
==> Found dependencies: ExtUtils::PkgConfig
--> Working on ExtUtils::PkgConfig
Fetching http://www.cpan.org/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz ... OK
Configuring ExtUtils-PkgConfig-1.16 ... N/A
! Configure failed for ExtUtils-PkgConfig-1.16. See /Users/as11798/.cpanm/work/1526901628.13976/build.log for details.
! Installing the dependencies failed: Module 'ExtUtils::PkgConfig' is not installed
! Bailing out the installation for GD-2.68.


Any tips, links or suggestions would be helpful. Thank you.

[Shaun Jackman]

Hi. Installing Circos with Homebrew should be much easier now. Try…

brew tap brewsci/bio

brew install circos

Cheers,

Shaun

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[Ahmed Shibl]

Thanks! I feel like I made progress but still isn't able to run it...

I go into the /usr/local/Cellar directory and when I 'ls' it I get these:
circos        fontconfig    gd        libpng        webp
cpanminus    freetype    jpeg        libtiff

I then try to run circos but I get this error:

*** REQUIRED MODULE(S) MISSING OR OUT-OF-DATE ***

You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial

http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules

missing GD

  error Can't load '/usr/local/Cellar/circos/0.69-6/libexec/lib/perl5/darwin-thread-multi-2level/auto/GD/GD.bundle' for module GD: dlopen(/usr/local/Cellar/circos/0.69-6/libexec/lib/perl5/darwin-thread-multi-2level/auto/GD/GD.bundle, 1): Library not loaded: @@HOMEBREW_PREFIX@@/opt/libpng/lib/libpng16.16.dylib  Referenced from: /usr/local/Cellar/circos/0.69-6/libexec/lib/perl5/darwin-thread-multi-2level/auto/GD/GD.bundle  Reason: unsafe use of relative rpath @@HOMEBREW_PREFIX@@/opt/libpng/lib/libpng16.16.dylib in /usr/local/Cellar/circos/0.69-6/libexec/lib/perl5/darwin-thread-multi-2level/auto/GD/GD.bundle with restricted binary at /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194. at (eval 29) line 1.Compilation failed in require at (eval 29) line 1.
missing GD::Polyline
  error Attempt to reload GD.pm aborted.Compilation failed in require at /usr/local/Cellar/circos/0.69-6/libexec/lib/perl5/darwin-thread-multi-2level/GD/Polyline.pm line 45.

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[Ahmed Shibl]

In addition, when I run brew test circos, this is what I get:

Testing brewsci/bio/circos
==> /usr/local/Cellar/circos/0.69-6/bin/circos -conf /usr/local/Cellar/circos/0.69-6/libexec/example/etc/circos.con
Error: brewsci/bio/circos: failed
<#<Pathname:/tmp/circos-test-20180522-60086-epnuf8/circos.png>>.exist? is true value expected but was<false>

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[Shaun Jackman]

I've fixed the issue just now with this commit:

https://github.com/brewsci/homebrew-bio/commit/253415eff989a788b5b054f3861083b52c36eee2

Try…

brew update

brew reinstall circos

Cheers,

Shaun

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[Carolina Barrón]

Thank you! This totally works for me on MacOS!

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[abhay]

Thanks Shaun, Martin and others

unable to work 

error are as follows

Stack trace:

 at /usr/local/Cellar/circos/0.69-6_1/libexec/bin/../lib/Circos/Error.pm line 425.

Circos::Error::fatal_error('configuration', 'missing') called at /usr/local/Cellar/circos/0.69-6_1/libexec/bin/../lib/Circos.pm line 146

Circos::run('Circos', '_cwd', '/usr/local/Cellar/circos/0.69-6_1/bin', '_argv', '') called at /usr/local/Cellar/circos/0.69-6_1/libexec/bin/circos line 536

kindly help

Abhay

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[Golrokh Kiani]

It is now brewsci/bio

brew tap brewsci/bio

On Thursday, February 20, 2014 at 3:37:10 PM UTC-5, Shaun Jackman wrote:

I created a Homebrew formula to install Circos. Due to the trickiness of installing GD, it's not as simple as brew install circos, but hopefully we'll get there. Here's the instructions:

Install Homebrew on Mac OS or Linuxbrew on Linux.

Run the following commands to install GD and Circos.

brew tap homebrew/science
brew remove gd
brew install gd --with-freetype
brew install cpanminus
sudo chown "$USER":admin /Library/Perl/5.16 # on Mac OS

cpanm Config::General Font::TTF::Font Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format
cpanm --force GD::Polyline
brew install circos
brew test circos

Cheers,
Shaun

[Alicia Talavera]

Hello circos group, 

I am trying to install circos on my computer (macOS Catalina v. 10.15.7), but I am getting several problems. If I execute: 

brew tap homebrew/science

Error: homebrew/science was deprecated. This tap is now empty and all its contents were either deleted or migrated.

 brew remove gd

Error: No available formula or cask with the name "gd".

 brew install gd --with-freetype

I get several errors. I tried different options showed in the group and tutorials, but I am stuck. Could you please help me? 

Thank you, 

[Shaun Jackman]

Try…
brew install brewsci/bio/circos

Cheers,

Shaun

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[Alicia Talavera]

Hello Shaun, 

Thank you for your email. In my case, It works after run: git -C $(brew --repository homebrew/core) checkout master.

Thank you, 

Best wishes, 

Alicia 

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Alicia Talavera Júdez, Ph.D.

Department of Subtropical and mediterranean fruit crops.

Estación Experimental IHSM La Mayora (CSIC-UMA)

29750 Algarrobo-Costa, Málaga (Spain)

Find me on: 

[Beatrice Zita Passerini]

Hello everyone,

I am new to Circos and I am trying to install it on my Mac OS Ventura v 13.6.3. I am currently working with Perl v 5.38.2. 

I have followed both these guides to install Circos:

1. https://circos.ca/documentation/tutorials/configuration/installation/
2. https://kylase.github.io/CircosAPI/os-x-installation-guide/ 

I have run these commands:

• brew tap brewsci/science 
• brew remove gd
• brew install gd   ### instead of ‘brew install gd --with-freetype’ because it wasn’t working
• brew install cpanminus
• sudo chown "$USER":admin /Library/Perl/5.16     ### it didn’t work and gave me this error —> chown: /Library/Perl/5.16: No such file or directory

•  cpanm Config::General Font::TTF::Font Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format

•  cpanm --force GD::Polyline ### This also didn’t work

•  brew install circos
•  brew test circos

I ran 'circos -modules'  and the GD and GD::Polyline are missing  

circos -modules             

ok       1.50 Carp

ok       0.45 Clone

ok       2.65 Config::General

ok       3.78 Cwd

ok      2.174 Data::Dumper

ok       2.55 Digest::MD5

ok       2.85 File::Basename

ok       3.78 File::Spec::Functions

ok     0.2309 File::Temp

ok       1.51 FindBin

ok       0.39 Font::TTF::Font

missing            GD

missing            GD::Polyline

ok        2.5 Getopt::Long

ok       1.40 IO::File

ok      0.428 List::MoreUtils

ok        1.5 List::Util

ok       0.01 Math::Bezier

ok   1.999816 Math::BigFloat

ok       0.07 Math::Round

ok       0.08 Math::VecStat

ok    1.03_01 Memoize

ok       1.88 POSIX

ok       1.29 Params::Validate

ok       1.69 Pod::Usage

ok       2.05 Readonly

ok 2017060201 Regexp::Common

ok       2.87 SVG

ok       1.19 Set::IntSpan

ok     1.6611 Statistics::Basic

ok       3.15 Storable

ok       1.22 Sys::Hostname

ok       2.03 Text::Balanced

ok       0.62 Text::Format

ok      1.976 Time::HiRes

Trying to install them I end up with this message:

Building and testing ExtUtils-PkgConfig-1.16 ... FAIL

! Installing ExtUtils::PkgConfig failed. See /Users/beazita/.cpanm/work/1712564244.48608/build.log for details. Retry with --force to force install it.

! Installing the dependencies failed: Module 'ExtUtils::PkgConfig' is not installed

! Bailing out the installation for GD-2.78.

I have tried to run: 

• perl -MCPAN -e shell 
• cpan[1]> install ExtUtils::PkgConfig

And 

• cpanm --force ExtUtils::PkgConfig

To see if I could solve the problem but it also return

--> Working on ExtUtils::PkgConfig

Fetching http://www.cpan.org/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz ... OK

Configuring ExtUtils-PkgConfig-1.16 ... OK

Building and testing ExtUtils-PkgConfig-1.16 ... FAIL

! Installing ExtUtils::PkgConfig failed. See /Users/beazita/.cpanm/work/1712564610.51061/build.log for details. Retry with --force to force install it.

I don’t know how to solve this problem. Has anyone had these kind of problems? 

Any tips, links or suggestions would be helpful. Thank you.

P.S: I don’t know if this is important, but I have download GD-2.50, because I cannot decompress  GD-2.78 using the command in the tutorial (2)