biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java | 19 9 + 10 - 0 !
1 file changed, 9 insertions(+), 10 deletions(-)

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

biojava3-forester/src/main/java/org/forester/test/Test.java | 2 1 + 1 - 0 !
biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 unmappable character for encoding ascii

biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java | 12 1 + 11 - 0 !
biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java | 15 0 + 15 - 0 !
2 files changed, 1 insertion(+), 26 deletions(-)

 remove tests requiring external
 network access

biojava3-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

biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix a test failure with java 8