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commit 75ff6ba6626f1ca49943bb8897c024c483dc1a1d Author: Emmanuel Bourg <ebo...@apache.org> Date: Wed Sep 2 13:11:05 2015 +0200 Replaced the dependency on libsnappy1.0.3-java with libsnappy-java --- debian/changelog | 7 +++++++ debian/control | 2 +- debian/patches/01-build.xml | 2 +- debian/patches/02-snappy-java-compatibility.patch | 24 +++++++++++++++++++++++ debian/patches/series | 1 + 5 files changed, 34 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index bf5e711..9ae495e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +picard-tools (1.113-2) UNRELEASED; urgency=medium + + * Team upload. + * Replaced the dependency on libsnappy1.0.3-java with libsnappy-java. + + -- Emmanuel Bourg <ebo...@apache.org> Wed, 02 Sep 2015 13:10:32 +0200 + picard-tools (1.113-1) unstable; urgency=medium * New upstream release 1.113 diff --git a/debian/control b/debian/control index fff4981..52aa451 100644 --- a/debian/control +++ b/debian/control @@ -8,7 +8,7 @@ Priority: optional Build-Depends: ant, default-jdk, testng, - libsnappy1.0.3-java, + libsnappy-java, debhelper (>= 9), libjbzip2-java, libcofoja-java, diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml index b663c6d..9031c63 100644 --- a/debian/patches/01-build.xml +++ b/debian/patches/01-build.xml @@ -30,7 +30,7 @@ Forwarded: no <include name="**/*.jar"/> </fileset> + <pathelement path="/usr/share/java/testng.jar"/> -+ <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/> ++ <pathelement path="/usr/share/java/snappy-java.jar"/> + <pathelement path="/usr/share/java/jbzip2.jar"/> + <pathelement path="/usr/share/java/cofoja.jar"/> + <pathelement path="/usr/share/java/commons-jexl2.jar"/> diff --git a/debian/patches/02-snappy-java-compatibility.patch b/debian/patches/02-snappy-java-compatibility.patch new file mode 100644 index 0000000..ebe08ab --- /dev/null +++ b/debian/patches/02-snappy-java-compatibility.patch @@ -0,0 +1,24 @@ +Description: Fix the compatibility with the latest version of snappy-java. + The fix is Debian specific and assumes the native library is always available + (which is true in Debian). +Author: Emmanuel Bourg <ebo...@apache.org> +Forwarded: not-needed +--- a/src/java/net/sf/samtools/util/SnappyLoader.java ++++ b/src/java/net/sf/samtools/util/SnappyLoader.java +@@ -24,7 +24,6 @@ + package net.sf.samtools.util; + + import net.sf.samtools.SAMException; +-import org.xerial.snappy.LoadSnappy; + import org.xerial.snappy.SnappyInputStream; + + import java.io.InputStream; +@@ -83,7 +82,7 @@ + // Don't try to call any Snappy code until classes have been found via reflection above. + boolean tmpSnappyAvailable; + try { +- if (!LoadSnappy.load()) { ++ if (false) { + if (verbose) System.err.println("Snappy dll failed to load."); + tmpSnappyAvailable = false; + } diff --git a/debian/patches/series b/debian/patches/series index 24b6ad5..ec86589 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ use_libjbzip2-java 01-build.xml +02-snappy-java-compatibility.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit