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

Davide Rambaldi davide.rambaldi at ifom-ieo-campus.it
Mon Oct 13 14:34:49 UTC 2008 

On 13 Oct 2008, at 16:07, Adam Kraut wrote:

> 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


Yeah something similar (note the final lib) do the job:


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


BUT note the I have to specify also lib (or it will install in /System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/ an the library in  
unreachable)


NOW:


wst433:bioruby default$ irb
 >> require 'bio'
=> true


But (cause I have added the prefix /System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/lib/)

I have now the bin into:

/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/


terrible! :(

sigh

I hate MAC frameworks.....

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

I am agree with you, and I have personally compiled my 1.8.7 ruby in / 
usr/local/bin

but may be is important to report the bug: automatic installation of  
bio.rb and bio directory in / (root) is painful for the general user

(imagine someone that see the error, want to remove /bio and for  
mistake type: sudo rm -rf / .... and the HD is gone! )



> -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  
> <%20http://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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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 < 
%20http://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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