[med-svn] [Git][med-team/picard-tools][master] Support non-amd64

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / picard-tools


Commits:
a6e95fb1 by Michael R. Crusoe at 2020-11-17T23:49:22+01:00
Support non-amd64

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/non-intel-skip-intel-tests
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,17 @@
-picard-tools (2.23.8+dfsg-1) UNRELEASED; urgency=medium
+picard-tools (2.23.8+dfsg-1~0local) UNRELEASED; urgency=medium
 
+  [ Steffen Moeller ]
   * New upstream version
   * Added link from /usr/lib/debian-med/bin/picard to PicardCommandLine
     only temporarily for now for presumed compatibility with what conda
     is offering and what bcbio is apparently expecting.
   * Added reference to d/u/metadata as suggested by upstream.
 
+  [ Michael R. Crusoe ]
+  * debian/patches/non-intel-skip-intel-tests: Skip two "Intel" specific tests
+    on non-amd64 systems.
+  * Switch to Architecture: all to match libgkl-java
+
  -- Steffen Moeller <moeller at debian.org>  Sat, 14 Nov 2020 17:50:50 +0100
 
 picard-tools (2.23.7+dfsg-1) unstable; urgency=medium


=====================================
debian/control
=====================================
@@ -18,7 +18,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
                libcommons-lang3-java,
                libcommons-math3-java,
                libbarclay-java,
-               libgkl-java,
+               libgkl-java (>= 0.8.6+dfsg-2)
                libgatk-native-bindings-java,
 # htsjdk and picard-tools are relased nearly together
                libhtsjdk-java (>= 2.22.0~),
@@ -36,7 +36,7 @@ Homepage: http://broadinstitute.github.io/picard/
 Rules-Requires-Root: no
 
 Package: picard-tools
-Architecture: amd64
+Architecture: any
 Depends: default-jre | java6-runtime,
          ${misc:Depends},
          libpicard-java (= ${binary:Version})
@@ -85,7 +85,7 @@ Description: Command line tools to manipulate SAM and BAM files
   FastqToSam                        ViewSam
 
 Package: libpicard-java
-Architecture: amd64
+Architecture: any
 Section: java
 Depends: ${misc:Depends},
 # Getting versionned depends from Build-Depends


=====================================
debian/patches/non-intel-skip-intel-tests
=====================================
@@ -0,0 +1,15 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Skip Intel tests on non-Intel
+--- picard-tools.orig/src/test/java/picard/IntelInflaterDeflaterLoadTest.java
++++ picard-tools/src/test/java/picard/IntelInflaterDeflaterLoadTest.java
+@@ -30,6 +30,10 @@
+             throw new SkipException(componentName + " is not available on this platform");
+         }
+ 
++	if (SystemUtils.OS_ARCH != null && !SystemUtils.OS_ARCH.equals("amd64")) {
++            throw new SkipException(componentName + " is not available for this architecture");
++        }
++
+         if (SystemUtils.OS_ARCH != null && SystemUtils.OS_ARCH.equals("ppc64le")) {
+             throw new SkipException(componentName + " is not available for this architecture");
+         }


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ remove_google_nio.patch
 fix_unreadabletests.patch
 60-tests-exclude-network.patch
 #fix_javadoc_ascii.patch
+non-intel-skip-intel-tests



View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/a6e95fb137e4293491b84e04b780bd6ebd5cfe34

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/a6e95fb137e4293491b84e04b780bd6ebd5cfe34
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