update biojava to 1.5beta2. BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit. BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. Fix: Patch attached with submission follows:
State Changed From-To: open->feedback 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 take
I had make a mistake of BUILD_DEPNEDS. I fix it now. The attachment is the new patch. On 3/23/07, nemo <nemoliu@gmail.com> wrote: > ok,I will check it now. > > > On 3/23/07, Martin Wilke <miwi@freebsd.org> wrote: > > 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 > > > >
State Changed From-To: feedback->closed Committed. Thanks!
miwi 2007-03-27 08:01:54 UTC FreeBSD ports repository Modified files: biology/biojava Makefile distinfo biology/biojava/files patch-build.xml Log: - Update to 1.5-beta2 - Pass maintainership to submitter PR: 110621 Submitted by: Nemo Liu<nemoliu@gmail.com> Revision Changes Path 1.13 +9 -8 ports/biology/biojava/Makefile 1.6 +3 -3 ports/biology/biojava/distinfo 1.2 +2 -2 ports/biology/biojava/files/patch-build.xml _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"