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Homebrew tap for formulae to build ARB (http://www.arb-home.de) and related software.
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README.md

homebrew-arb

Homebrew tap for formulae to build ARB and related software.

Open tasks

  • extend test for successful installation to make sure PERL integration works(test block)
  • add stable version when 6.1 is released
  • configure Preview as viewer for PDF and PS files (removes GV dependency)
  • bottles
  • integration into the ARB release cycle, formula needs to be tagged, too
  • add formula for SINA
  • add SINA to ARB
  • fix cosmetic PERL bug
  • repair OpenGL build

Prerequisites

Homebrew is required to install ARB via the formula provided in this tap.

Add this tap to your Homebrew installation.

brew tap arb-project/arb

ARB requires a X11 server. It was bundled with MacOS from version 10.5 to 10.7. For all modern MacOS versions, it must be installed separately. If you have already installed XQuartz on your Mac, you are fine. Otherwise you must install it either by using the installer provided on the XQuartz website or via Homebrew:

brew cask install xquartz

Install ARB

The arb formula allows you to install three different versions of ARB on your Mac. Homebrew and ARB using different naming conventions for the builds.

ARB name Homebrew name command
release stable brew install arb
production development brew install --devel arb
n/a head brew install --HEAD arb

The stable version of ARB 6.0 does not work reliably when build with this formula. If you really need ARB 6.0 please use macports. This formula would have to apply too many changes to make ARB 6.0 work in the Homebew environment. Therefore, the stable version is not supported until ARB 6.1 is released. You can use the current ARB 6.1 beta version by using the production version (see below).

The production version of ARB is installed and used in-house at MPI for Marine Microbiology in Bremen. It is frequently updated from development changes, i.e. it contains recent bug fixes and newest features, but also may break working things. It is updated at least every few months.

If you use the production version, please file bug reports (if you encounter any bugs) via the ARB bug tracker. It helps the ARB team to make the next release version more stable.

The head version of ARB gives you the latest changes from development, including the latest bug fixes and features. However, any of the changes might break working things as the version might just be in the beginning of being tested. It is not recommended to install this version for daily, productive usage but it gives you the opportunity to test if the latest changes in development resolve any issues you might have with the release and/or production version of ARB.

Install arbitrary versions of ARB

You can install arbitrary versions of ARB by editing the Homebrew formula for ARB and specifying a revision for the head build. This requires you to be a brew expert user. If you don't know how to edit formulas you shouldn't do it.

Please keep in mind that the revision you are trying to install might contain broken features or might not even compile (on a Mac) at all. Building older revisions might even require to change the dependencies and/or build steps in the formula. Please be aware that you build these revisions on you own risk and that we cannot provide support for these builds.

Install an old release / production version

You can install an old release / production version of ARB using Homebrew. Normally this is not required as Homebrew does not delete old versions when you install a new version (see switching between versions) unless you call brew cleanup.

If you need to install an old release on a new Mac or after a cleanup you need to activate the corresponding version of the formula. The oldest versions you can install are

  • Release: n/a
  • Production 6.1-beta_r17491

Let's assume the ARB team has released version 6.2.0 and you installed it but you also want to install version 6.1.0:

# unlink the current version of ARB
brew unlink arb

# change into the directory containing your local copy of this tab
cd "$(brew --repo arb-project/arb)"

# if you do not know the exact version you need to install, you can list
# the available ones
git tag

# activate the old version of the formula
git checkout tags/v6.1.0

# install and tell Homebrew that it must not activate the newest version of the
# formula
HOMEBREW_NO_AUTO_UPDATE=1 brew install arb

After this steps version 6.1.0 of ARB will be installed and your active ARB version.

Options

OpenGL

By default all versions are build without support for the OpenGL features of ARB. To enable OpenGL support in ARB add --with-open-gl to the build command, e.g.

brew install --with-open-gl arb

to build the stable version of ARB with OpenGL support.

The OpenGL build is work in progress and currently not working due to a missing dependency. We haven't yet figured out which changes to the formula are required to fix the issue. Fixing this issue has a low priority as the missing feature is not affecting our work. Pull requests to fix this issue are welcome.

Unit tests

By default all versions are build without executing the unit tests of ARB. However, when preparing a new release for MacOS they should be executed to make sure everything is working as expected. To include the unit tests into the build run

brew install arb --with-test

This options is intended for contributors and ARB developers only. It may or may not work at any given time. No support is given for using this option.

Debug

You can add debug symbols to the binary by using the debug option:

brew install arb --with-debug

This option is intended for contributors and not for end-users. ARB shouldn't be used with debug symbols enabled for your daily work.

Switching between versions

When you install different versions of ARB you can switch between them using the switch command of Homebrew.

brew switch arb 6.1.0

will activate the release version 6.1.0 of ARB (if installed).

You can list the installed versions of ARB with

brew list --versions arb

Perl support

The versions created by this formula support all features of ARB which require perl scripts, e.g. markSpecies.pl or Import/Import fields from calc-sheet.

On MacOS versions, ARB has a cosmetic bug which results in the following error message being shown when ever a perl script is executed by ARB:

Error: 'Not inside GB_shell'
Can't continue - terminating..

-------------------- ARB-backtrace 'GBK_terminate (reason above) ':
0   ARB.bundle                          0x0000000107715836 _Z13GBK_terminatePKc + 66
1   ARB.bundle                          0x00000001077324a8 _ZN8GB_shellD1Ev + 0
2   ARB.bundle                          0x00000001077324b1 _ZN8GB_shellD1Ev + 9
3   libsystem_c.dylib                   0x00007fff9bbc9463 __cxa_finalize_ranges + 345
4   libsystem_c.dylib                   0x00007fff9bbc9767 exit + 55
5   perl                                0x000000010717de7d main + 303
6   libdyld.dylib                       0x00007fff9b51d5ad start + 1
-------------------- End of backtrace
[Terminating with signal 11]

For the perl scripts included in ARB, this error is not restricting the functionality of the script. The script has been successfully executed and the error is occurring when the script terminates.

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