[Biojava-l] build problems

[Schreiber, Mark]

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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