Back to [[pkg-escience]] == Package-specific Issues == ==== Taverna ==== * reinvestigate elimination of jdom.jar - it apparently worked with MartJ * Upload fix for missing dependency to /usr/share/java/libicu4j-java and the respective entry in the classpath (svn is down at the moment) * Prepare script for automated testing * [[http://taverna.sf.net|Taverna]] upstream link ==== EnsJ ==== * Fix ensj-doc * Get java2html to work from [[http://www.java2html.de|www.java2html.de]] * Fix debian/ensj-doc.docs * Test compatibility with Taverna * Fix debian/watch * Fix [[Teams/Lintian]] warnings {{{ W: ensj: binary-without-manpage id_mapping_cleanup.sql W: ensj: binary-without-manpage run_idmapping.sh W: ensj: binary-without-manpage run_idmapping_gui.sh W: ensj: binary-without-manpage run_probeset_2_transcript_mapping.sh W: ensj: executable-not-elf-or-script ./usr/bin/id_mapping_cleanup.sql }}} * [[http://www.ensembl.org/software/java|EnsJ]] upstream link ==== MartJ ==== * Fix classpath settings for applications other than MartShell * Integrate with Taverna package and test compatibility * Adds dependencies on novel jars * Incompatibility of Taverna with latest release {{{ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartProcessor.java:182: cannot find symbol [javac] symbol : method setAdaptor(org.ensembl.mart.lib.config.RegistryDSConfigAdaptor) [javac] location: class org.ensembl.mart.lib.Query [javac] query.setAdaptor(ra); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartProcessor.java:220: cannot find symbol [javac] symbol : constructor DatabaseDSConfigAdaptor(org.ensembl.mart.lib.DetailedDataSource,java.lang.String,boolean,boolean,boolean) [javac] location: class org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor [javac] DSConfigAdaptor adaptor = new DatabaseDSConfigAdaptor(ds, ds.getUser(), [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartProcessor.java:291: cannot find symbol [javac] symbol : method getUniqueName() [javac] location: class org.ensembl.mart.lib.FieldAttribute [javac] String fieldName = ((FieldAttribute)attributes[i]).getUniqueName(); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartScavenger.java:36: cannot find symbol [javac] symbol : constructor DatabaseDSConfigAdaptor(org.ensembl.mart.lib.DetailedDataSource,java.lang.String,boolean,boolean,boolean) [javac] location: class org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor [javac] DSConfigAdaptor adaptor = new DatabaseDSConfigAdaptor(ds, ds.getUser(), true, false, false); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartTask.java:92: cannot find symbol [javac] symbol : method getUniqueName() [javac] location: class org.ensembl.mart.lib.FieldAttribute [javac] String portName = ((FieldAttribute)attributes[i]).getUniqueName(); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartXMLHandler.java:260: cannot find symbol [javac] symbol : method getUniqueName() [javac] location: class org.ensembl.mart.lib.FieldAttribute [javac] if (f.getUniqueName() != null) { [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartXMLHandler.java:261: cannot find symbol [javac] symbol : method getUniqueName() [javac] location: class org.ensembl.mart.lib.FieldAttribute [javac] e.setAttribute("uniquename", f.getUniqueName()); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/BiomartXMLHandler.java:272: cannot find symbol [javac] symbol : method setUniqueName(java.lang.String) [javac] location: class org.ensembl.mart.lib.FieldAttribute [javac] fa.setUniqueName(e.getAttributeValue("uniquename")); [javac] ^ [javac] /home/moeller/debian/taverna/build-area/taverna-1.3/build/src/org/embl/ebi/escience/scuflworkers/biomart/TestQuerySerializer.java:50: cannot find symbol [javac] symbol : constructor DatabaseDSConfigAdaptor(org.ensembl.mart.lib.DetailedDataSource,java.lang.String,boolean,boolean,boolean) [javac] location: class org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor [javac] DSConfigAdaptor adaptor = new DatabaseDSConfigAdaptor(ds, }}} * [[http://www.biomart.org|MartJ]] upstream link ==== BioJava ==== * Documentation * Has two lintian warnings * [[http://www.biojava.org|BioJava]] upstream link ==== freefluo ==== * Source tree is wrong. * Separation of documentation in separate Jar * Proper description of documentation in debian/doc-base * Lacking tests and proof of working integration with Taverna * The freefluo-ext-taverna separate jar is still missing. * [[http://freefluo.sf.net|freefluo]] upstream link ==== uddi4j ==== * Separation of documentation in separate Jar * Proper description of documentation in debian/doc-base * Compilation with free compiler * [[http://uddi4j.sf.net|uddi4j]] upstream link ==== icu4j ==== * Seems fine, test with free Java for full DFSG compliance still pending * Incorporate documentation * [[http://icu.sf.net|icu4j]] upstream link * Someone else's ITP is on this one ([[DebianBug:333120|#333120]]) ==== wsdl4j ==== * Done * [[http://sourceforge.net/projects/wsdl4j/|wsdl4j]] upstream link ==== axis ==== * Said to be patched by Taverna developers, trying 1.4 anyway * The compilation of axis requires a more recent commons-httpclient (version 3 * rather than version 2 that ships with Debian - BTS bug [[DebianBug:340307]]) ==== jastor ==== * Compile time error because of apparent version conflict with Jena * [[http://jastor.sf.net|jastor]] upstream link ==== jena ==== * Requires some more jars to be eliminates from binary distribution * [[http://jena.sf.net|jena]] upstream link ==== ARQ ==== * Requires some more jars to be eliminates from binary distribution * [[http://jena.sourceforge.net/ARQ/|ARQ]] upstream link ==== JSON ==== * Done * [[http://www.json.org|JSON]] upstream link ==== JEditSyntax ==== * Should have used CVS version of sourceforge instead. * [[http://syntax.jedit.org|JEditSyntax]] upstream link ==== Jmol ==== * Not yet tested at all * [[http://www.jmol.org|Jmol]] upstream link ==== Talisman ==== * Last upstream edit in the year 2003 * Requires older library of EnsJ * Has tons of errors like {{{ prepare-src: [ajc] Compiling 126 source and 0 arg files [ajc] public volatile Writer StringWriter.append(char) conflicts with public StringWriter StringWriter.append(char): defined in same type [ajc] public volatile Writer StringWriter.append(CharSequence, int, int) conflicts with public StringWriter StringWriter.append(CharSequence, int, int): defined in same type [ajc] public volatile Writer StringWriter.append(CharSequence) conflicts with public StringWriter StringWriter.append(CharSequence): defined in same type [ajc] public volatile Appendable StringWriter.append(char) conflicts with public StringWriter StringWriter.append(char): defined in same type [ajc] public volatile Appendable StringWriter.append(CharSequence, int, int) conflicts with public StringWriter StringWriter.append(CharSequence, int, int): defined in same type [ajc] public volatile Appendable StringWriter.append(CharSequence) conflicts with public StringWriter StringWriter.append(CharSequence): defined in same type [ajc] public volatile Appendable Writer.append(char) conflicts with public Writer Writer.append(char): defined in same type [ajc] public volatile Appendable Writer.append(CharSequence, int, int) conflicts with public Writer Writer.append(CharSequence, int, int): defined in same type .... }}} Any idea?