[med-svn] [Git][med-team/htsjdk][master] 3 commits: Updating the classpath of the built jar

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Mon Dec 30 11:10:11 GMT 2024



Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
76286573 by Pierre Gruet at 2024-12-30T10:33:00+01:00
Updating the classpath of the built jar

- - - - -
2f30530a by Pierre Gruet at 2024-12-30T10:33:29+01:00
Updating the installed POM file

- - - - -
3d2e35c2 by Pierre Gruet at 2024-12-30T10:33:58+01:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/htsjdk.pom
- debian/htsjdk.pom.asc
- debian/libhtsjdk-java.classpath


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+htsjdk (4.1.3+dfsg-2) unstable; urgency=medium
+
+  * Updating the classpath of the built jar
+  * Updating the installed POM file (Closes: #1091589)
+
+ -- Pierre Gruet <pgt at debian.org>  Mon, 30 Dec 2024 10:33:32 +0100
+
 htsjdk (4.1.3+dfsg-1) unstable; urgency=medium
 
   * New upstream version 4.1.3+dfsg


=====================================
debian/htsjdk.pom
=====================================
@@ -1,10 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <!-- This module was also published with a richer model, Gradle metadata,  -->
+  <!-- which should be used instead. Do not delete the following line which  -->
+  <!-- is to indicate to Gradle or any Gradle module metadata file consumer  -->
+  <!-- that they should prefer consuming it instead. -->
+  <!-- do_not_remove: published-with-gradle-metadata -->
   <modelVersion>4.0.0</modelVersion>
   <groupId>com.github.samtools</groupId>
   <artifactId>htsjdk</artifactId>
-  <version>3.0.2</version>
+  <version>4.1.3</version>
   <name>HTSJDK</name>
   <description>A Java API for high-throughput sequencing data (HTS) formats</description>
   <url>https://samtools.github.io/htsjdk/</url>
@@ -28,52 +33,40 @@
   </scm>
   <dependencies>
     <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-jexl</artifactId>
-      <version>2.1.1</version>
+      <groupId>gov.nih.nlm.ncbi</groupId>
+      <artifactId>ngs-java</artifactId>
+      <version>2.9.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
-      <groupId>commons-logging</groupId>
-      <artifactId>commons-logging</artifactId>
-      <version>1.1.1</version>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-jexl</artifactId>
+      <version>2.1.1</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.xerial.snappy</groupId>
       <artifactId>snappy-java</artifactId>
-      <version>1.1.8.4</version>
-      <scope>compile</scope>
+      <version>1.1.10.5</version>
+      <scope>runtime</scope>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-compress</artifactId>
-      <version>1.19</version>
-      <scope>compile</scope>
+      <version>1.25.0</version>
+      <scope>runtime</scope>
     </dependency>
     <dependency>
-      <groupId>org.tukaani</groupId>
-      <artifactId>xz</artifactId>
-      <version>1.8</version>
-      <scope>compile</scope>
+      <groupId>org.kordamp.json</groupId>
+      <artifactId>json-lib-core</artifactId>
+      <version>3.1.0</version>
+      <scope>runtime</scope>
     </dependency>
     <dependency>
-      <groupId>gov.nih.nlm.ncbi</groupId>
-      <artifactId>ngs-java</artifactId>
-      <version>2.9.0</version>
-      <scope>compile</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.sharegov</groupId>
-      <artifactId>mjson</artifactId>
-      <version>1.4.1</version>
-      <scope>compile</scope>
-      <exclusions>
-        <exclusion>
-          <artifactId>*</artifactId>
-          <groupId>junit</groupId>
-        </exclusion>
-      </exclusions>
+      <groupId>org.mozilla</groupId>
+      <artifactId>rhino</artifactId>
+      <version>1.7.14</version>
+      <scope>runtime</scope>
     </dependency>
   </dependencies>
 </project>


=====================================
debian/htsjdk.pom.asc
=====================================
@@ -1,17 +1,17 @@
 -----BEGIN PGP SIGNATURE-----
-Version: BCPG v1.60
+Version: BCPG v1.68
 
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+=79IZ
 -----END PGP SIGNATURE-----


=====================================
debian/libhtsjdk-java.classpath
=====================================
@@ -1 +1 @@
-usr/share/java/htsjdk.jar /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar
+usr/share/java/htsjdk.jar /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/json-lib.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar



View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/4a58db4251b844adac96f61ee2c8dd6d2767318d...3d2e35c2655284e59778d89ae578ba4ab989cd8b

-- 
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/4a58db4251b844adac96f61ee2c8dd6d2767318d...3d2e35c2655284e59778d89ae578ba4ab989cd8b
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