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 another package.
 Upstream code needs to refer to this new package and depends on
 newer release if iText5

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
 .
 [ Gilles Filippini <pini@debian.org> ]
 Patche updated to migrate away from deprecated json-simple 1.x classes
 See json-simple 2.0.0 changelog:
 > * Deprecated JSONParse and JSONValue in favor of Jsoner.
 > * Deprecated JSONStreamAware and JSONAware in favor of Jsonable.
 > * Deprecated JSONObject in favor of JsonObject.
 > * Deprecated JSONArray in favor of JsonArray.
 .
 This patch now uses the new json-simple Json* classes. It is compatible
 with both 2.x and 3.x json-simple releases, with a few ajustments
 regarding backward incompatible changes in json-simple 3.x:
 - The package name, changed to com.github.cliftonlabs.json_simple
 This change is handled using place-holders @JSON_SIMPLE_PACKAGE@ which
 are substituted at build time by debian/rules.
 .
 With this trick the package is compatible with json-simple 2.x and 3.x.
Last-Updated: 2020-05-15

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

 some classes are not imported

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

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

biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java | 3 3 + 0 - 0 !
biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java | 2 2 + 0 - 0 !
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 !
5 files changed, 5 insertions(+), 108 deletions(-)

 debian builds expects to run with no network

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

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.

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 add explicit cast to fix ambiguos method call error

Taken from upstream to match expected method call 
https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java