[med-svn] [Git][med-team/biojava4-live][master] 5 commits: Removing obsolete patches
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Wed Oct 13 19:15:25 BST 2021
Pierre Gruet pushed to branch master at Debian Med / biojava4-live
Commits:
edd0b3c9 by Pierre Gruet at 2021-10-13T17:58:54+02:00
Removing obsolete patches
- - - - -
cf559b21 by Pierre Gruet at 2021-10-13T18:00:00+02:00
Stopping symlinking jquery-* files as it causes broken symlinks
- - - - -
e3226224 by Pierre Gruet at 2021-10-13T18:00:33+02:00
Adding a Lintian override for the resulting warning about embedded JS copies
- - - - -
bc7351de by Pierre Gruet at 2021-10-13T18:00:43+02:00
Updating changelog
- - - - -
6ea5ecb2 by Pierre Gruet at 2021-10-13T20:14:56+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/libbiojava4-java-doc.lintian-overrides
- − debian/patches/fix_code_to_support_latest_jmol
- − debian/patches/fix_uselog4j1
- − debian/patches/java8_compatibility.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+biojava4-live (4.2.12+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * Stopping symlinking jquery* files from default-jdk-doc to the ones we
+ package as symlinks break each time default-jdk-doc evolves
+ (Closes: #988846)
+ * Adding a Lintian override for the resulting warning on embedded JS copies
+ * Removing obsolete patches
+
+ -- Pierre Gruet <pgt at debian.org> Wed, 13 Oct 2021 18:00:50 +0200
+
biojava4-live (4.2.12+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -31,8 +31,7 @@ Build-Depends-Indep: libcommons-dbcp-java,
libjaxb-api-java,
libjaxb-java,
libnetx-java,
- default-jdk-doc,
- rdfind
+ default-jdk-doc
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/biojava4-live
Vcs-Git: https://salsa.debian.org/med-team/biojava4-live.git
=====================================
debian/libbiojava4-java-doc.lintian-overrides
=====================================
@@ -0,0 +1,5 @@
+# It would be too complicated to remove the javascript that is included in
+# 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/*
=====================================
debian/patches/fix_code_to_support_latest_jmol deleted
=====================================
@@ -1,26 +0,0 @@
-Subject: Latest JMOL library requires mode method definition
-Author: Olivier Sallou <osallou at irisa.fr>
-Description: Add required interface method from latest JMOL library definition
-Last--Updated: 2012-05-29
-
---- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-+++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -42,7 +42,17 @@
- public void setTextField (JTextField statusField) {
- status = statusField;
- }
--
-+
-+ public void resizeInnerPanel(java.lang.String arg0) {
-+ }
-+
-+ public boolean notifyEnabled(org.jmol.constant.EnumCallback callback) {
-+ return false;
-+ }
-+
-+ public void notifyCallback(EnumCallback type, Object[] data) {
-+ }
-+
- public String createImage(String arg0, String arg1, Object arg2, int arg3) {
- // TODO Auto-generated method stub
- return null;
=====================================
debian/patches/fix_uselog4j1 deleted
=====================================
@@ -1,74 +0,0 @@
-Subject: use log4j v1.X
-Description: upstream use log4j v2.X which is not yet available in Debian.
-There is no specific v2 API usage, so applying a patch to use the log4j
-version available in Debian waiting for new version availability.
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2014-02-01
-Forwarded: no
---- a/biojava3-structure/pom.xml
-+++ b/biojava3-structure/pom.xml
-@@ -29,9 +29,9 @@
- </dependency>
-
- <dependency>
-- <groupId>org.apache.logging.log4j</groupId>
-- <artifactId>log4j-core</artifactId>
-- <version>2.0-beta7</version>
-+ <groupId>log4j</groupId>
-+ <artifactId>log4j</artifactId>
-+ <version>1.2.17</version>
- </dependency>
-
- <!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId>
---- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
-@@ -23,8 +23,8 @@
- import java.io.InputStream;
- import java.net.URL;
-
--import org.apache.logging.log4j.LogManager;
--import org.apache.logging.log4j.Logger;
-+import org.apache.log4j.LogManager;
-+import org.apache.log4j.Logger;
- import org.w3c.dom.Element;
- import org.w3c.dom.NodeList;
-
---- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
-@@ -25,8 +25,8 @@
- import java.util.ArrayList;
- import java.util.List;
-
--import org.apache.logging.log4j.LogManager;
--import org.apache.logging.log4j.Logger;
-+import org.apache.log4j.LogManager;
-+import org.apache.log4j.Logger;
- import org.w3c.dom.Element;
- import org.w3c.dom.NodeList;
-
---- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
-@@ -31,8 +31,8 @@
- import javax.xml.parsers.DocumentBuilderFactory;
- import javax.xml.parsers.ParserConfigurationException;
-
--import org.apache.logging.log4j.LogManager;
--import org.apache.logging.log4j.Logger;
-+import org.apache.log4j.LogManager;
-+import org.apache.log4j.Logger;
- import org.w3c.dom.Document;
- import org.w3c.dom.Node;
- import org.w3c.dom.NodeList;
---- a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
-@@ -28,8 +28,8 @@
- import java.util.Set;
- import java.util.TreeSet;
-
--import org.apache.logging.log4j.LogManager;
--import org.apache.logging.log4j.Logger;
-+import org.apache.log4j.LogManager;
-+import org.apache.log4j.Logger;
-
- /**
- * Provides programmatic access to ASTRAL representative sets. See the paper by <a
=====================================
debian/patches/java8_compatibility.patch deleted
=====================================
@@ -1,13 +0,0 @@
-Description: Fix a test failure with Java 8
-Author: Emmanuel Bourg <ebourg at apache.org>
-Forwarded: no
---- a/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
-+++ b/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
-@@ -108,7 +108,7 @@
- this.circular = circular;
- this.betweenCompounds = betweenCompounds;
- this.accession = accession;
-- this.subLocations = Collections.unmodifiableList(subLocations);
-+ this.subLocations = subLocations != null ? Collections.unmodifiableList(subLocations) : Collections.<Location>emptyList();
- assertLocation();
- }
=====================================
debian/rules
=====================================
@@ -67,17 +67,6 @@ override_dh_auto_build:
cd biojavadoc && ant javadocs
# rm -rf biojavadoc
-override_jh_installjavadoc:
- jh_installjavadoc
- rdfind -makesymlinks true -followsymlinks true \
- $$(dpkg -L $$(apt-cache show default-jdk-doc | grep Depends \
- | awk '{print $$2}') | grep /usr/share/doc/ \
- | head -n1) \
- debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/
-ifeq ($(DH_VERBOSE),1)
- cat results.txt || /bin/true; rm -f results.txt
-endif
-
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo '*********************************************************************************'
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3
--
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3
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