Debian Patches

Status for biojava6-live/6.1.0+dfsg-4

Patch Description Author Forwarded Bugs Origin Last update
fix_itext_class_updates.patch 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
Olivier Sallou <> not-needed
use_simple_json.patch library is not "free", use simple_json library and update according to API
[ Gilles Filippini <> ]
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.
Olivier Sallou <> no
fix_import.patch some classes are not imported Olivier Sallou not-needed
fix_ascii_characters_mapping.patch unmappable character for encoding ASCII Olivier Sallou <> yes upstream
skip_network_related_tests.patch debian builds expects to run with no network Pierre Gruet <> Olivier Sallou <> not-needed
remove_openchart_use.patch 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
Olivier Sallou <> not-needed
ignore_fake_tests.patch 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. Olivier Sallou <> not-needed
poms.patch Including forester and jcolorbrewer into the Maven build Pierre Gruet <> not-needed 2021-10-19
jmol_path_in_pom.patch currently jmol does not ship Maven artifacts Pierre Gruet <> not-needed 2021-10-19
remove_tests_needing_junitx.patch omitting tests needing junitx.framework.FileAssert as junitx is not packaged in Debian Pierre Gruet <> not-needed 2021-10-19

All known versions for source package 'biojava6-live'