[Biojava-l] (no subject)
Tim Salmon
tim@unsw.edu.au
Thu, 13 Sep 2001 15:42:10 +1000
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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
--Apple-Mail-592024533-3
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charset=us-ascii
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.
<fontfamily><param>Courier</param>tim: biojava [3:04:52pm]: java
build.Builder all
Running complete build...
Compiling...
=
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistribut=
ionFactory.java:68:
cannot resolve symbol
symbol : class IndexedNthOrderDistribution =20
location: class org.biojava.bio.dist.OrderNDistributionFactory
return new IndexedNthOrderDistribution(alpha, df);
^
=
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistribut=
ionFactory.java:70:
cannot resolve symbol
symbol : class GeneralNthOrderDistribution =20
location: class org.biojava.bio.dist.OrderNDistributionFactory
return new GeneralNthOrderDistribution(alpha, df);
^
=
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/TranslatedDistr=
ibution.java:59:
cannot resolve symbol
symbol : class SimpleReversibleTranslationTable =20
location: class org.biojava.bio.dist.TranslatedDistribution
new SimpleReversibleTranslationTable(
^
src/org/biojava/bio/symbol/AlphabetManager.java:458: cannot resolve
symbol
symbol : class InfiniteCrossProductAlphabet =20
location: class org.biojava.bio.symbol.AlphabetManager
cpa =3D new InfiniteCrossProductAlphabet(aList);
^
src/org/biojava/bio/symbol/SimpleCrossProductAlphabet.java:143: cannot
resolve symbol
symbol : class CrossProductSymbolNameParser =20
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 =20
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)
</fontfamily>
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 =20
2053 =20
australia =20
02 9385 1595 =20
=20
home =20
29 margaret st =20
newtown =20
2042 =20
australia
02 9517 3894
play
m: 0410 607 645=
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