[med-svn] [Git][med-team/fastqc][master] 5 commits: Patching files to avoid importing the sis-jhdf5 classes

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / fastqc


Commits:
c26a05c1 by Pierre Gruet at 2024-09-08T13:15:39+02:00
Patching files to avoid importing the sis-jhdf5 classes

- - - - -
908360d4 by Pierre Gruet at 2024-09-08T13:16:14+02:00
Raising Standards version to 4.7.0 (no change)

- - - - -
e16cac57 by Pierre Gruet at 2024-09-08T13:18:31+02:00
Adding header to patch

- - - - -
4b683b48 by Pierre Gruet at 2024-09-08T15:15:49+02:00
Refreshing patches

- - - - -
e8d195ba by Pierre Gruet at 2024-09-08T15:18:26+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/build_xml.patch
- + debian/patches/no_hdf5.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+fastqc (0.12.1+dfsg-4) unstable; urgency=medium
+
+  * Stopping (build-)depending on libsis-jhdf5-java:
+    - Patching files to avoid importing the sis-jhdf5 classes
+    - Refreshing patches
+  * Raising Standards version to 4.7.0 (no change)
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 08 Sep 2024 15:15:52 +0200
+
 fastqc (0.12.1+dfsg-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -11,9 +11,8 @@ Build-Depends: debhelper-compat (= 13),
                ant,
                libhtsjdk-java,
                libjbzip2-java,
-               libcommons-math3-java,
-               libsis-jhdf5-java
-Standards-Version: 4.6.2
+               libcommons-math3-java
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/fastqc
 Vcs-Git: https://salsa.debian.org/med-team/fastqc.git
 Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
@@ -27,7 +26,6 @@ Depends: ${misc:Depends},
          libjbzip2-java,
          libcommons-math3-java,
          libfindbin-libs-perl,
-         libsis-jhdf5-java,
          default-jre
 Description: quality control for high throughput sequence data
  FastQC aims to provide a simple way to do some quality control checks on


=====================================
debian/patches/build_xml.patch
=====================================
@@ -5,7 +5,7 @@ Description: Use Debian packaged JARs
 
 --- a/build.xml
 +++ b/build.xml
-@@ -11,9 +11,10 @@
+@@ -11,9 +11,9 @@
      <property name="source" value="11"/>
      <path id="FastQC.classpath">
          <pathelement location="bin"/>
@@ -14,7 +14,6 @@ Description: Use Debian packaged JARs
 -        <pathelement location="cisd-jhdf5.jar"/>
 +        <pathelement location="/usr/share/java/jbzip2.jar"/>
 +        <pathelement location="/usr/share/java/htsjdk.jar"/>
-+        <pathelement location="/usr/share/java/sis-jhdf5.jar"/>
 +        <pathelement location="/usr/share/java/commons-math3.jar"/>
      </path>
      <target name="init">


=====================================
debian/patches/no_hdf5.patch
=====================================
@@ -0,0 +1,29 @@
+Description: skipping the imports from classes of sis-jhdf5
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-09-07
+
+--- a/build.xml
++++ b/build.xml
+@@ -35,6 +35,7 @@
+         <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
+             <src path="."/>
+             <exclude name=".pc/**"/>
++            <exclude name="**/Fast5File.java"/>
+             <classpath refid="FastQC.classpath"/>
+         </javac>
+     </target>
+--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
++++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+@@ -99,9 +99,9 @@
+ 			// We default to using all reads
+ 			return new BAMFile(file,false);
+ 		}
+-		else if (file.getName().toLowerCase().endsWith(".fast5")) {
++		/*else if (file.getName().toLowerCase().endsWith(".fast5")) {
+ 			return new Fast5File(file);
+-		}
++		}*/
+ 		else {
+ 			return new FastQFile(config,file);
+ 		}


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ build_xml.patch
 fastqc.patch
 fix-help-call.patch
 set_configuration_path.patch
+no_hdf5.patch



View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/fa262229a9dce7765e66e67cdc49a06fa39970f8...e8d195ba4da629c773abb72f33aa08f80fef8d5e

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/fa262229a9dce7765e66e67cdc49a06fa39970f8...e8d195ba4da629c773abb72f33aa08f80fef8d5e
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