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

[Davide Rambaldi]

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.
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