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
Taverna upstream link
EnsJ
- Fix ensj-doc
Get java2html to work from 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
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, MartJ upstream link
BioJava
- Documentation
- Has two lintian warnings
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.
freefluo upstream link
uddi4j
- Separation of documentation in separate Jar
- Proper description of documentation in debian/doc-base
- Compilation with free compiler
uddi4j upstream link
icu4j
- Seems fine, test with free Java for full DFSG compliance still pending
- Incorporate documentation
icu4j upstream link
Someone else's ITP is on this one (#333120)
wsdl4j
- Done
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 340307)
jastor
- Compile time error because of apparent version conflict with Jena
jastor upstream link
jena
- Requires some more jars to be eliminates from binary distribution
jena upstream link
ARQ
- Requires some more jars to be eliminates from binary distribution
ARQ upstream link
JSON
- Done
JSON upstream link
JEditSyntax
- Should have used CVS version of sourceforge instead.
JEditSyntax upstream link
Jmol
- Not yet tested at all
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?