GD Freetype and Fontconfig Installation Issues

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Parnal Sinha

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Oct 20, 2020, 10:54:16 PM10/20/20

to Circos

Hello everyone,

As usual - another GD Problem except it seems that I am missing the core freetype and fontconfig.

At first, this post by Jun Inoue (https://groups.google.com/g/circos-data-visualization/c/Pgp1FSqSVRc/m/0vTMwt9TMaYJ) seems to be very promising - I was going to try basically the second link she had posted:

https://kylase.github.io/CircosAPI/os-x-installation-guide/

Didn't get me anywhere apart from having downloaded freetype - I can' seem to run install gd --with-freetype. A lot of people seem to be having this issue when they try to use Homebrew. I removed gd too but I seem to be at my wits end now - can anyone provide clarification? If not, would uninstallation and reinstallation be the best bet? I just want to get the example running.

I see everyone running this simple line and it magically downloads it for them and I'm sitting here like :(

(circos) Parnals-MacBook-Pro-2:current parnalsinha$ brew install libgd --with-freetype

Usage: brew install [options] formula|cask

Install a formula or cask. Additional options specific to a formula may be

appended to the command.

Unless HOMEBREW_NO_INSTALL_CLEANUP is set, brew cleanup will then be run for

the installed formulae or, every 30 days, for all formulae.

-d, --debug If brewing fails, open an interactive

debugging session with access to IRB or a

shell inside the temporary build directory.

-f, --force Install formulae without checking for

previously installed keg-only or

non-migrated versions. Overwrite existing

files when installing casks.

-v, --verbose Print the verification and postinstall

steps.

--formula, --formulae Treat all named arguments as formulae.

--env If std is passed, use the standard build

environment instead of superenv. If super

is passed, use superenv even if the formula

specifies the standard build environment.

--ignore-dependencies An unsupported Homebrew development flag to

skip installing any dependencies of any

kind. If the dependencies are not already

present, the formula will have issues. If

you're not developing Homebrew, consider

adjusting your PATH rather than using this

flag.

--only-dependencies Install the dependencies with specified

options but do not install the formula

itself.

--cc Attempt to compile using the specified

compiler, which should be the name of the

compiler's executable, e.g. gcc-7 for GCC

7. In order to use LLVM's clang, specify

llvm_clang. To use the Apple-provided

clang, specify clang. This option will

only accept compilers that are provided by

Homebrew or bundled with macOS. Please do

not file issues if you encounter errors

while using this option.

-s, --build-from-source Compile formula from source even if a

bottle is provided. Dependencies will still

be installed from bottles if they are

available.

--force-bottle Install from a bottle if it exists for the

current or newest version of macOS, even if

it would not normally be used for

installation.

--include-test Install testing dependencies required to

run brew test formula.

--HEAD If formula defines it, install the HEAD

version, aka. master, trunk, unstable.

--fetch-HEAD Fetch the upstream repository to detect if

the HEAD installation of the formula is

outdated. Otherwise, the repository's HEAD

will only be checked for updates when a new

stable or development version has been

released.

--keep-tmp Retain the temporary files created during

installation.

--build-bottle Prepare the formula for eventual bottling

during installation, skipping any

post-install steps.

--bottle-arch Optimise bottles for the specified

architecture rather than the oldest

architecture supported by the version of

macOS the bottles are built on.

--display-times Print install times for each formula at the

end of the run.

-i, --interactive Download and patch formula, then open a

shell. This allows the user to run

./configure --help and otherwise

determine how to turn the software package

into a Homebrew package.

-g, --git Create a Git repository, useful for

creating patches to the software.

--cask, --casks Treat all named arguments as casks.

--[no-]binaries Disable/enable linking of helper

executables. Default: enabled

--require-sha Require all casks to have a checksum.

--[no-]quarantine Disable/enable quarantining of downloads.

Default: enabled

--skip-cask-deps Skip installing cask dependencies.

--appdir Target location for Applications. Default:

/Applications

--colorpickerdir Target location for Color Pickers. Default:

~/Library/ColorPickers

--prefpanedir Target location for Preference Panes.

Default: ~/Library/PreferencePanes

--qlplugindir Target location for QuickLook Plugins.

Default: ~/Library/QuickLook

--mdimporterdir Target location for Spotlight Plugins.

Default: ~/Library/Spotlight

--dictionarydir Target location for Dictionaries. Default:

~/Library/Dictionaries

--fontdir Target location for Fonts. Default:

~/Library/Fonts

--servicedir Target location for Services. Default:

~/Library/Services

--input_methoddir Target location for Input Methods. Default:

~/Library/Input Methods

--internet_plugindir Target location for Internet Plugins.

Default: ~/Library/Internet Plug-Ins

--audio_unit_plugindir Target location for Audio Unit Plugins.

Default:

~/Library/Audio/Plug-Ins/Components

--vst_plugindir Target location for VST Plugins. Default:

~/Library/Audio/Plug-Ins/VST

--vst3_plugindir Target location for VST3 Plugins. Default:

~/Library/Audio/Plug-Ins/VST3

--screen_saverdir Target location for Screen Savers. Default:

~/Library/Screen Savers

--language Set language of the Cask to install. The

first matching language is used, otherwise

the default language on the Cask. The

default value is the language of your

system

-q, --quiet Suppress any warnings.

-h, --help Show this message.

Error: invalid option: --with-freetype

How does one fix this issue? I tried removing my gd and reinstalling and it doesn't seem to do much.

Here is the code when I run a couple of important flags:

(circos) Parnals-MacBook-Pro-2:~ parnalsinha$ cd Applications/circos/current

(circos) Parnals-MacBook-Pro-2:current parnalsinha$ which gdlib-config

/usr/local/bin/gdlib-config

(circos) Parnals-MacBook-Pro-2:current parnalsinha$ gdlib-config --all

GD library 2.0.33

includedir: /usr/local/include

cflags: -I/usr/local/include

ldflags: -L/usr/local/lib

libs: -ljpeg -lpng -lz -liconv

libdir: /usr/local/lib

features: GD_JPEG GD_PNG GD_GIF

(circos) Parnals-MacBook-Pro-2:current parnalsinha$ circos -modules

ok 1.29 Carp

ok 0.36 Clone

ok 2.63 Config::General

ok 3.40 Cwd

ok 2.145 Data::Dumper

ok 2.52 Digest::MD5

ok 2.84 File::Basename

ok 3.40 File::Spec::Functions

ok 0.23 File::Temp

ok 1.51 FindBin

ok 0.39 Font::TTF::Font

ok 2.46 GD

ok 0.2 GD::Polyline

ok 2.39 Getopt::Long

ok 1.16 IO::File

ok 0.33 List::MoreUtils

ok 1.38 List::Util

ok 0.01 Math::Bezier

ok 1.998 Math::BigFloat

ok 0.06 Math::Round

ok 0.08 Math::VecStat

ok 1.03 Memoize

ok 1.32 POSIX

ok 1.08 Params::Validate

ok 1.61 Pod::Usage

ok 2.05 Readonly

ok 2013031301 Regexp::Common

ok 2.85 SVG

ok 1.19 Set::IntSpan

ok 1.6611 Statistics::Basic

ok 2.41 Storable

ok 1.17 Sys::Hostname

ok 2.02 Text::Balanced

ok 0.61 Text::Format

ok 1.9725 Time::HiRes

Parnal Sinha

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Oct 26, 2020, 4:59:36 PM10/26/20

to Circos

Hello,

For many who have this problem, this is my solution which is honestly the easiest method but also the most tedious method:

1. Delete all compiled files; most of the perl modules can stay perfectly intact - I used:

$ > rm ~/software/circos

BE CAREFUL USING RM - I always had the -i flag on because it pretty much deletes the file completely and pretty much it's a goodbye. It doesn't go to trash either so proceed with caution.

2. Delete the environment for Circos (if you had a conda env)

3. Delete any extra files you had downloaded like libpng, freetype, etc.

4. Download circos as specified exactly from the website and ensure you link to the specified root path correctly - follow the instructions under 0.2 of the tutorials with the heading

INSTALLING CIRCOS ON UNIX

5. DO NOT USE THE HOMEBREW METHOD TO DOWNLOAD GD - Obviously, if circos download worked for you via homebrew then you wouldn't be here anyways.

6. Under 0.6, there is a whole section as to how to download GD - follow the steps mentioned exactly - I think the hardest thing for me was the multitude methods presented and honestly the tedious and long path was worth it because it compiled exactly how I wanted it to.

A lot of this seems like basic knowledge and should be tried initially, but I tried to skirt installation and use a shortcut. Moral of the story - the method presented in the website is full-proof - no errors should pop up and installation shouldn't take more than an hour utilizing this method.

TIPS: Be careful for paths and naming - they should be exactly the SAME as the one which Martin had specified.