Hi -
I have noticed some build problems. Seems to be a real problem as I have
checked the source files and the methods really do exist but do not
confomr to some of the class dependencies. Also I notice the getToken()
method is being called (which I thought had been scrubbed). cvs update
-d and new check out have the same problems as does the latest snapshot?
I think the cvs tree has gone a bit wonky, although I notice that there
is a binary snapshot so I'm assuming that Thomas can get things to
build.
Can anyone notice something obvious going wrong, below is the ant log
Mark
Buildfile: build.xml
init:
prepare:
prepare-src:
compile:
[javac] Compiling 546 source files to
C:\Dev\JavaLibs\biojava-live\ant-build\classes\main
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\seq\io\C
rossProductSymbolNameParser.java:154: cannot resolve symbol
[javac] symbol : method getParser (java.lang.String)
[javac] location: interface org.biojava.bio.symbol.Alphabet
[javac] parser[c++] = a.getParser("name");
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\seq\io\T
okenParser.java:55: cannot resolve symbol
[javac] symbol : method ambiguities ()
[javac] location: class org.biojava.bio.symbol.SimpleAlphabet
[javac] for (Iterator si = ((SimpleAlphabet)
alphabet).ambiguities(); si.hasNext(); ) {
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\seq\io\T
okenParser.java:64: cannot resolve symbol
[javac] symbol : method getToken ()
[javac] location: interface org.biojava.bio.symbol.Symbol
[javac] char token = sym.getToken();
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\seq\io\T
okenParser.java:71: cannot resolve symbol
[javac] symbol : method getToken ()
[javac] location: interface org.biojava.bio.symbol.Symbol
[javac] char token = sym.getToken();
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\seq\io\S
eqFormatTools.java:305: cannot resolve symbol
[javac] symbol : method getToken ()
[javac] location: interface org.biojava.bio.symbol.Symbol
[javac] sb.append(syms[i].getToken());
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\program\
das\DASGFFParser.java:98: cannot resolve symbol
[javac] symbol : method getOutputListener ()
[javac] location: class
org.biojava.bio.program.das.FeatureRequestManager.Ticket
[javac] parseSegment(echld,
t.getOutputListener());
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\program\
das\DASGFFParser.java:107: cannot resolve symbol
[javac] symbol : method getOutputListener ()
[javac] location: class
org.biojava.bio.program.das.FeatureRequestManager.Ticket
[javac] SeqIOListener siol =
t.getOutputListener();
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\symbol\C
ircularRangeLocation.java:47:
org.biojava.bio.symbol.CircularRangeLocation should be declared
abstract; it does not define
newInstance(org.biojava.bio.symbol.Location) in
org.biojava.bio.symbol.CircularRangeLocation
[javac] public class CircularRangeLocation implements Location,
java.io.Serializable{
[javac] ^
[javac]
C:\Dev\JavaLibs\biojava-live\ant-build\src\main\org\biojava\bio\symbol\A
llTokensAlphabet.java:55: cannot resolve symbol
[javac] symbol : method getToken ()
[javac] location: interface org.biojava.bio.symbol.AtomicSymbol
[javac] Character token = new Character(s.getToken());
[javac] ^
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -deprecation for details.
[javac] 9 errors
BUILD FAILED
C:\Dev\JavaLibs\biojava-live\build.xml:140: Compile failed, messages
should have been provided.
Total time: 38 seconds
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
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