ports/110621: [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data.

[Martin Wilke]

Synopsis: [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data.

State-Changed-From-To: open->feedback
State-Changed-By: miwi
State-Changed-When: Fri Mar 23 08:56:14 UTC 2007
State-Changed-Why: 
Hi

Can you please check the patch? ... It gives an error..

    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioFlatIndex.java:329: cannot find symbol
    [javac] symbol  : class HelpFormatter
    [javac] location: class org.biojava.app.BioFlatIndex
    [javac]         HelpFormatter help = new HelpFormatter();
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioFlatIndex.java:329: cannot find symbol
    [javac] symbol  : class HelpFormatter
    [javac] location: class org.biojava.app.BioFlatIndex
    [javac]         HelpFormatter help = new HelpFormatter();
    [javac]                                  ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:66: cannot find symbol
    [javac] symbol  : class Options
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Options opts = createOptions();
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:70: cannot find symbol
    [javac] symbol  : class CommandLine
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]             CommandLine cmd = new GnuParser().parse(opts, argv);
    [javac]             ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:70: cannot find symbol
    [javac] symbol  : class GnuParser
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]             CommandLine cmd = new GnuParser().parse(opts, argv);
    [javac]                                   ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:112: cannot find symbol
    [javac] symbol  : class MissingOptionException
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         catch (MissingOptionException moe)
    [javac]                ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:116: cannot find symbol
    [javac] symbol  : class MissingArgumentException
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         catch (MissingArgumentException mae)
    [javac]                ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:120: cannot find symbol
    [javac] symbol  : class UnrecognizedOptionException
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         catch (UnrecognizedOptionException uoe)
    [javac]                ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:132: cannot find symbol
    [javac] symbol  : class Options
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Options opts = new Options();
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:132: cannot find symbol
    [javac] symbol  : class Options
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Options opts = new Options();
    [javac]                            ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:135: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option dbname = new Option("d", "dbname", hasArg,
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:135: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option dbname = new Option("d", "dbname", hasArg,
    [javac]                             ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:139: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option format = new Option("f", "format", hasArg,
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:139: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option format = new Option("f", "format", hasArg,
    [javac]                             ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:144: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option help = new Option("h", "help", ! hasArg,
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:144: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option help = new Option("h", "help", ! hasArg,
    [javac]                           ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:148: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option namespace = new Option("n", "namespace", hasArg,
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:148: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         Option namespace = new Option("n", "namespace", hasArg,
    [javac]                                ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:163: cannot find symbol
    [javac] symbol  : class HelpFormatter
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         HelpFormatter help = new HelpFormatter();
    [javac]         ^
    [javac] /usr/home/miwi/dev/ports/biology/biojava/work/apps/org/biojava/app/BioGetSeq.java:163: cannot find symbol
    [javac] symbol  : class HelpFormatter
    [javac] location: class org.biojava.app.BioGetSeq
    [javac]         HelpFormatter help = new HelpFormatter();
    [javac]                                  ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] 64 errors

BUILD FAILED
/usr/home/miwi/dev/ports/biology/biojava/work/build.xml:322: Compile failed; see the compiler error output for details.

Total time: 17 seconds
*** Error code 1

Stop in /usr/home/miwi/dev/ports/biology/biojava.




Responsible-Changed-From-To: freebsd-ports-bugs->miwi
Responsible-Changed-By: miwi
Responsible-Changed-When: Fri Mar 23 08:56:14 UTC 2007
Responsible-Changed-Why: 
take


http://www.freebsd.org/cgi/query-pr.cgi?pr=110621