[med-svn] [biojava-live] 14/14: prepare release 1.9.2, not yet ready for upload due to failing tests
Andreas Tille
tille at debian.org
Tue Sep 26 08:17:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch 1.9.2
in repository biojava-live.
commit dfa499cc6cc82a37cbab12979f32e333ee688bd0
Author: Olivier Sallou <osallou at debian.org>
Date: Fri Aug 21 16:48:34 2015 +0000
prepare release 1.9.2, not yet ready for upload due to failing tests
---
debian/build.xml | 6 +++---
debian/changelog | 16 +++++++---------
debian/control | 6 +++---
debian/copyright | 6 ++++++
debian/get-orig-source | 2 ++
...libbiojava1.8-java.jlibs => libbiojava1.9-java.jlibs} | 1 -
debian/rules | 6 ------
debian/watch | 5 ++++-
8 files changed, 25 insertions(+), 23 deletions(-)
diff --git a/debian/build.xml b/debian/build.xml
index 87bfddb..66bd775 100644
--- a/debian/build.xml
+++ b/debian/build.xml
@@ -21,15 +21,15 @@
<property environment="env"/>
<property name="project.jarfile.name" value="BJLIB.jar"/>
- <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
+ <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
<path id="compile.classpath">
<fileset dir="${lib.dir}">
<include name="commons-cli.jar"/>
- <include name="commons-collections.jar"/>
+ <include name="commons-collections3.jar"/>
<include name="commons-dbcp.jar"/>
<include name="commons-pool.jar"/>
- <include name="junit.jar"/>
+ <include name="junit4.jar"/>
<include name="guava.jar"/>
<include name="jgrapht0.8.jar"/>
</fileset>
diff --git a/debian/changelog b/debian/changelog
index 9bfe7f1..9cbcd57 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,14 +1,12 @@
-biojava-live (1:1.8.2-1) UNRELEASED; urgency=low
+biojava-live (1:1.9.2+dfsg-1) UNRELEASED; urgency=low
* New upstream version
- Closes: #659824
-
- * TODO fix DAS compilation, check doc and lib setup in packages: missing files
- related to biojava3-structure, need to integrate in upstream all required code.
- Mail sent upstream for information.
- * TODO issue with watch to detect latest release, organized in sub directories
- * TODO: Upstream seems to have droped the habit of shiping jar files - may be
- the get-orig-source script can be dropped
+ (Closes: #659824)
+ * d/watch: get from github
+
+ [ ISSUES]
+ Several tests are failing, some randomly. I have contacted upstream for analysis.
+
-- Olivier Sallou <osallou at debian.org> Sat, 01 Feb 2014 11:28:20 +0100
diff --git a/debian/control b/debian/control
index 4190573..f38e510 100644
--- a/debian/control
+++ b/debian/control
@@ -6,9 +6,9 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Olivier Sallou <osallou at debian.org>
Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-collections3-java (>= 2.1), libcommons-pool-java (>= 1.1),
libcommons-cli-java, libguava-java (>= 11.0.1),
- default-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
+ default-jdk, junit4,javahelper (>=0.25), libjgrapht0.8-java,
ant-optional
Build-Depends: debhelper (>= 9), cdbs, ant
Standards-Version: 3.9.5
@@ -16,7 +16,7 @@ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava/trunk/
Homepage: http://www.biojava.org
-Package: libbiojava1.8-java
+Package: libbiojava1.9-java
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends},
libcommons-pool-java (>= 1.1),
diff --git a/debian/copyright b/debian/copyright
index 12f1813..4807f71 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,6 +1,12 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: BioJava
Source: http://www.biojava.org/download/source
+Files-Excluded: core/src/test/resources/org/biojava/bio/program/indexdb/*.swiss
+ core/src/test/resources/AAC4_HUMAN.sp
+
+Files: core/src/main/java/org/biojava/bio/program/phred/PhredTools.java
+Copyright: 2001 AgResearch
+License: LGPL-2.1+
Files: *
Copyright: 1999-2008 the Individual authors who contributed the code,
diff --git a/debian/get-orig-source b/debian/get-orig-source
index 07b8204..9219e48 100755
--- a/debian/get-orig-source
+++ b/debian/get-orig-source
@@ -8,6 +8,8 @@ VERSION=`uscan --verbose --force-download --no-symlink |
head -n 1 |
sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+print "VERSION="$VERSION
+
mkdir -p ../tarballs
cd ../tarballs
diff --git a/debian/libbiojava1.8-java.jlibs b/debian/libbiojava1.9-java.jlibs
similarity index 90%
rename from debian/libbiojava1.8-java.jlibs
rename to debian/libbiojava1.9-java.jlibs
index 3f2e72b..193bbd5 100644
--- a/debian/libbiojava1.8-java.jlibs
+++ b/debian/libbiojava1.9-java.jlibs
@@ -3,7 +3,6 @@ dist/biojava-biosql.jar
dist/biojava-blast.jar
dist/biojava-bytecode.jar
dist/biojava-core.jar
-dist/biojava-das.jar
dist/biojava-gui.jar
dist/biojava-phylo.jar
dist/biojava-sequencing.jar
diff --git a/debian/rules b/debian/rules
index 163685f..7bb233a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,7 +17,6 @@ override_dh_auto_configure:
sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > alignment/build.xml
sed -e 's/BJLIB/biojava-biosql/g' debian/build.xml > biosql/build.xml
sed -e 's/BJLIB/biojava-blast/g' debian/build.xml > blast/build.xml
- sed -e 's/BJLIB/biojava-das/g' debian/build.xml > das/build.xml
sed -e 's/BJLIB/biojava-gui/g' debian/build.xml > gui/build.xml
sed -e 's/BJLIB/biojava-phylo/g' debian/build.xml > phylo/build.xml
sed -e 's/BJLIB/biojava-sequencing/g' debian/build.xml > sequencing/build.xml
@@ -31,7 +30,6 @@ override_dh_auto_build:
cd phylo && ant jar
cd sequencing && ant jar
cd gui && ant jar
- cd das && ant jar
# make doc
rm -rf biojavadoc
mkdir biojavadoc
@@ -43,21 +41,17 @@ override_dh_auto_build:
cp -r phylo/* biojavadoc/
cp -r sequencing/* biojavadoc/
cp -r gui/* biojavadoc/
- cp -r das/* biojavadoc/
sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
cd biojavadoc && ant javadocs
rm -rf biojavadoc
override_dh_auto_test:
- cd bytecode && ant test
cd core && ant test
cd alignment && ant test
cd biosql && ant test
cd blast && ant test
cd phylo && ant test
cd sequencing && ant test
- cd gui && ant test
- cd das && ant test
diff --git a/debian/watch b/debian/watch
index 45f5c06..916e854 100644
--- a/debian/watch
+++ b/debian/watch
@@ -2,4 +2,7 @@ version=3
#http://biojava.org/wiki/BioJava:Download http://biojava.org/download/bj.*/biojava-([0-9.]+)-all\.tar\.gz
#http://biojava.org/wiki/BioJava:Download http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
-http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
+#http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
+
+opts=filenamemangle=s/.+\/biojava-legacy-(\d\S*)\.tar\.gz/biojava-legacy-$1\.tar\.gz/ \
+ https://github.com/biojava/biojava-legacy/tags .*/biojava-legacy-(\d\S*)\.tar\.gz
--
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