Date: Fri, 23 Mar 2007 08:59:29 GMT From: Martin Wilke <miwi@FreeBSD.org> To: nemoliu@gmail.com, miwi@FreeBSD.org, freebsd-ports-bugs@FreeBSD.org, miwi@FreeBSD.org Subject: Re: ports/110621: [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data. Message-ID: <200703230859.l2N8xTo3006361@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
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
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?200703230859.l2N8xTo3006361>