[BioRuby] Installation from git repository on a MAC Intel 10.5.5

[Adam Kraut]

Hi Davide,

Have you tried using the --prefix option for the 'install' command?  The
prefix only applies to the install task according to the help.  This appears
to be working OK for me on 10.5.5

/usr/bin/ruby install.rb install
--prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr

Note that I personally compile my own Ruby in /usr/local and don't recommend
using the Ruby supplied by Apple.  YMMV.

-Adam

On Mon, Oct 13, 2008 at 8:34 AM, Davide Rambaldi <
davide.rambaldi at ifom-ieo-campus.it> wrote:

> Hi all,
>
> the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super desktop
> m boss give me at the lab.... (wow)
>
> MAC OS X 10.5 came with ruby embedded in Developer tools.
>
> Here is the gem env:
>
> RubyGems Environment:
>  - RUBYGEMS VERSION: 1.0.1 (1.0.1)
>  - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal-darwin9.0]
>  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
>  - RUBYGEMS PREFIX:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
>  - RUBY EXECUTABLE:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
>  - RUBYGEMS PLATFORMS:
>    - ruby
>    - universal-darwin-9
>  - GEM PATHS:
>     -
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8
>     - /Library/Ruby/Gems/1.8
>  - GEM CONFIGURATION:
>     - :update_sources => true
>     - :verbose => true
>     - :benchmark => false
>     - :backtrace => false
>     - :bulk_threshold => 1000
>  - REMOTE SOURCES:
>     - http://gems.rubyforge.org
>
>
>
> You may notice that installation directory are under
> /System/Library/Frameworks/...    (you know: mac like to make developer life
> more complicated)
>
> So now I retrieve the last bioruby from git with: git clone git://
> github.com/bioruby/bioruby.git
>
> I enter dir and I install in the canonical way:
>
> ruby install.rb config
> ruby install.rb setup
>
>
> At this point the config.save file (is the file that stoe the urrent
> configuration sure?) contains:
>
> bin-dir=$prefix/bin
> prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> make-prog=make
> rb-dir=$site-ruby
> without-ext=no
>
> ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> std-ruby=$prefix/lib/ruby/1.8
> data-dir=$prefix/share
>
>
> So all seems ok but when I try to install with:
>
> sudo ruby install.rb install
>
>
> install.rb: entering install phase...
> ---> bin
> mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install bioruby
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biofetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_bioflat.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biogetseq.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_pmfetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> <--- bin
> ---> lib
> mkdir -p /
> install bio.rb /
> ---> lib/bio
> mkdir -p /bio
>
> [...] (continue)
>
>
> ARGH!!!! after the bin install the install.rb install ALL the bio library
> in ROOT!
>
> So to summarize:
>
> - first bin are install correctly in /System/Library/.../usr/bin
> - the ENTIRE library is installed in the wrong PATH (/)
>
> Please notice that in another MAC with 10.5 really similar BUT with a
> manual installed version of ruby 1.8.7 in /url/local/bin the installation of
> bioruby is correct and all is installed in the correct path (in that case
> /usr/local/lib)
>
> To conclude seems that there is a BUG in install.rb that is unable to
> install the bioruby library in
> /System/Library/Frameworks/Ruby.framework/Version/1.8/usr/lib
>
> If you don't have a MAC for testing, I can try to fix this, just give me
> some clues.
>
> I have tried to specify the prefix with:
>
> ruby install.rb setup
> --prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> but in installation I have the same problem that is summarized by this 2
> lines of the install log!:
>
> mkdir -p /
> install bio.rb /
>
>
> Again I can help you fix this, cause I have the right MAC to make tests,
> but I have no clues of where is the bug....
>
>
> Best Regards
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:
> davide.rambaldi at ifom-ieo-campus.it>
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20
> http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>
> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
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