| fix_itext_class_updates.patch | (download) |
forester/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
|
| use_simple_json.patch | (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
.
[ 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
|
| remove_openchart_use.patch | (download) |
forester/org/forester/application/msa_compactor.java |
3 1 + 2 - 0 !
forester/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
|
