[Biojava-l] (no subject)

[Thomas Down]

I'm not a Mac user -- so comments from anyone who really
is would be welcome.  However, a thought....

Are there multiple filesystems available on OSX?  For instance,
I presume there's support for the old MacOS filesystem, but
I think there's also a newer system (derived from BSD systems?).
I seem to remembder that old macs did have a filename length
limit.  So it might be that BioJava will only work on partitions
that have been newly formated with OSX...

In any case, a binary .jar file distribution ought to work,
regarless of filename length.

Could somepone who knows more confirm this?

       Thomas.

On Thu, Sep 13, 2001 at 03:42:10PM +1000, Tim Salmon wrote:
> hi biojava'ers, 
> 
> i have discovered a small potential problem with the biojava 1.10 
> distribution that i thought you might like to have brought to your 
> attention. 
> i have biojava installed on an imac running os-x. os-x apparently 
> limits the filename sizes to shorter than those of a number of the 
> files in biojava.  this is not critical in all cases as i have 
> successfully run the demo suggested on the web-page.  however, when i 
> tested the potential problem by doing a build as suggested i got this. 
> 
> tim: biojava [3:04:52pm]: java build.Builder all 
> Running complete build... 
> Compiling... 
> 
> /Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistributionFactory.java:68: 
> cannot resolve symbol 
> symbol  : class IndexedNthOrderDistribution   
> location: class org.biojava.bio.dist.OrderNDistributionFactory 
>             return new IndexedNthOrderDistribution(alpha, df); 
>                        ^ 
> 
> /Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistributionFactory.java:70: 
> cannot resolve symbol 
> symbol  : class GeneralNthOrderDistribution   
> location: class org.biojava.bio.dist.OrderNDistributionFactory 
>             return new GeneralNthOrderDistribution(alpha, df); 
>                        ^ 
> 
> /Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/TranslatedDistribution.java:59: 
> cannot resolve symbol 
> symbol  : class SimpleReversibleTranslationTable   
> location: class org.biojava.bio.dist.TranslatedDistribution 
>       new SimpleReversibleTranslationTable( 
>           ^ 
> src/org/biojava/bio/symbol/AlphabetManager.java:458: cannot resolve 
> symbol 
> symbol  : class InfiniteCrossProductAlphabet   
> location: class org.biojava.bio.symbol.AlphabetManager 
>           cpa =  new InfiniteCrossProductAlphabet(aList); 
>                      ^ 
> src/org/biojava/bio/symbol/SimpleCrossProductAlphabet.java:143: cannot 
> resolve symbol 
> symbol  : class CrossProductSymbolNameParser   
> location: class org.biojava.bio.symbol.SimpleCrossProductAlphabet 
>         return new CrossProductSymbolNameParser(this); 
>                    ^ 
> src/org/biojava/bio/symbol/SparseCrossProductAlphabet.java:104: cannot 
> resolve symbol 
> symbol  : class CrossProductSymbolNameParser   
> location: class org.biojava.bio.symbol.SparseCrossProductAlphabet 
>         return new CrossProductSymbolNameParser(this); 
>                    ^ 
> 6 errors 
> Exception in thread "main" java.io.IOException: Couldn't build! 
>         at build.Builder.buildAll(Builder.java:223) 
>         at build.Builder.main(Builder.java:175) 
>  
> As you can see, the longer file names have caused this to fail. 
> I hope this is not too much of an issue for you.  If I can be of any 
> assisatance with this matter, please let me know. 
> 
> cheers, 
> tim 
> 
> 
> ____________________________________ 
> 
> tim salmon 
> 
> tim@unsw.edu.au 
> 
>    work 
> school of civil and environmental engineering 
> unsw         
> 2053               
> australia       
> 02 9385 1595   
>                   
>    home             
> 29 margaret st   
> newtown     
> 2042        
> australia 
> 02 9517 3894 
> 
>    play 
> m: 0410 607 645
> 

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