[med-svn] [Git][med-team/biojava4-live][master] 3 commits: Fixing ambiguous call to newFileSystem

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / biojava4-live


Commits:
080b624d by Pierre Gruet at 2022-12-11T21:52:11+01:00
Fixing ambiguous call to newFileSystem

- - - - -
51dcbc97 by Pierre Gruet at 2022-12-11T22:19:07+01:00
Corrrecting the Lintian override for embedded JS after a change in Lintian syntax

- - - - -
f519396c by Pierre Gruet at 2022-12-11T22:19:35+01:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/libbiojava4-java-doc.lintian-overrides
- + debian/patches/fix_ambiguous_method_call.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+biojava4-live (4.2.12+dfsg-8) unstable; urgency=medium
+
+  * Fixing ambiguous method call to newFileSystem, thanks to Hans Joachim
+    Desserud! (Closes: #1025887)
+  * Correcting the Lintian override for embedded JS after a change in Lintian
+    syntax
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 11 Dec 2022 22:19:23 +0100
+
 biojava4-live (4.2.12+dfsg-7) unstable; urgency=medium
 
   * Moving javahelper from B-D-Indep to B-D to avoid clean failure in source


=====================================
debian/libbiojava4-java-doc.lintian-overrides
=====================================
@@ -2,4 +2,4 @@
 # javadocs, see the discussion on Debian Java mailing list starting at 
 # https://lists.debian.org/debian-java/2018/06/msg00020.html.
 # See also https://bugs.debian.org/988846
-embedded-javascript-library usr/share/doc/libbiojava4-java/api/jquery/*
+embedded-javascript-library please use * [usr/share/doc/libbiojava4-java/api/script-dir/*s]


=====================================
debian/patches/fix_ambiguous_method_call.patch
=====================================
@@ -0,0 +1,31 @@
+Description: 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
+
+---
+
+Origin: upstream
+Forwarded: not-needed
+Last-Update: 2022-12-11
+
+--- biojava4-live-4.2.12+dfsg.orig/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
++++ biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+@@ -236,7 +236,7 @@ public class ZipChemCompProvider impleme
+ 		final String filename = "chemcomp/" + recordName+".cif.gz";
+ 
+ 		// try with resources block to read from the filesystem.
+-		try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, null)) {
++		try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, (ClassLoader)null)) {
+ 			Path cif = fs.getPath(filename);
+ 
+ 			if (Files.exists(cif)) {
+@@ -293,7 +293,7 @@ public class ZipChemCompProvider impleme
+ 		*/
+ 
+ 		// Copy in each file.
+-		try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, null)) {
++		try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, (ClassLoader)null)) {
+ 			Files.createDirectories(pathWithinArchive);
+ 			for (File f : files) {
+ 				if (!f.isDirectory() && f.exists()) {


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ fix_ascii_characters_mapping
 skip_network_related_tests
 remove_openchart_use
 ignore_fake_tests
+fix_ambiguous_method_call.patch



View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/459bfd75d783d68ebfadc0b6115e1d21c4c06160...f519396c8de49b2a6b219203554df7d1b2d02396

-- 
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/459bfd75d783d68ebfadc0b6115e1d21c4c06160...f519396c8de49b2a6b219203554df7d1b2d02396
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