Package: biojava4-live / 4.2.5+dfsg-1

Metadata

Package Version Patches format
biojava4-live 4.2.5+dfsg-1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
fix_itext_class_updates | (download)

biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 one of the class from itext moved to an other package.
 Upstream code needs to refer to this new package and depends on
 newer release if iText5
use_simple_json | (download)

biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java | 20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-)

 json.org library is not "free", use simple_json
 library and update according to API
Last-Updated: 2012-12-02


fix_import | (download)

biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java | 7 7 + 0 - 0 !
1 file changed, 7 insertions(+)

 some classes are not imported
faketest | (download)

biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java | 7 7 + 0 - 0 !
1 file changed, 7 insertions(+)

 empty test creates failure at compilate, add fake test
 to allow compilation and global test success
fix_ascii_characters_mapping | (download)

biojava-forester/src/main/java/org/forester/test/Test.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 unmappable character for encoding ascii
skip_network_related_tests | (download)

biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java | 15 0 + 15 - 0 !
biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java | 79 0 + 79 - 0 !
biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java | 14 0 + 14 - 0 !
3 files changed, 108 deletions(-)

 debian builds expects to run with no network
remove_openchart_use | (download)

biojava-forester/src/main/java/org/forester/application/msa_compactor.java | 3 1 + 2 - 0 !
biojava-forester/src/main/java/org/forester/msa_compactor/Chart.java | 179 4 + 175 - 0 !
2 files changed, 5 insertions(+), 177 deletions(-)

 biojava makes use of a limited set of forester
 As openchart is not available in Debian, remove openchart related calls
 to make forester compilation OK in biojava context
ignore_fake_tests | (download)

biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java | 5 4 + 1 - 0 !
biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java | 5 4 + 1 - 0 !
2 files changed, 8 insertions(+), 2 deletions(-)

 some class tests do not have tests inside, but junit tries to execute them.
 Simple skip those classes with no real test to avoid errors during build.