[med-svn] [Git][med-team/artemis][master] 3 commits: Update patch that prevents copying of non-existing files; d/rules: Use…
Andreas Tille
gitlab at salsa.debian.org
Sun Aug 5 15:24:02 BST 2018
Andreas Tille pushed to branch master at Debian Med / artemis
Commits:
9cd5f4dc by Andreas Tille at 2018-08-05T12:49:51Z
Update patch that prevents copying of non-existing files; d/rules: Use dh_auto_build instead of $(MAKE)
- - - - -
2a678f55 by Andreas Tille at 2018-08-05T14:10:25Z
Do not try to install non-existing files.
- - - - -
551ab850 by Andreas Tille at 2018-08-05T14:23:36Z
Do not mention non-existing test target
- - - - -
3 changed files:
- debian/changelog
- debian/patches/jar-rules.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,8 @@ artemis (17.0.1+dfsg-1) UNRELEASED; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.0
* Class FTPSeekableStream should not be excluded
+ * Update patch that prevents copying of non-existing files
+ * d/rules: Use dh_auto_build instead of $(MAKE)
-- Andreas Tille <tille at debian.org> Sat, 17 Mar 2018 11:41:38 +0100
=====================================
debian/patches/jar-rules.patch
=====================================
--- a/debian/patches/jar-rules.patch
+++ b/debian/patches/jar-rules.patch
@@ -4,48 +4,61 @@ Description: Leave out removed files when building jar files
Their absence causes "can not stat" errors, so any reference to
them is removed here.
Author: Afif Elghraoui <afif at ghraoui.name>
+ Andreas Tille <tille at debian.org>
Forwarded: not-needed
-Last-Update: 2015-10-22
+Last-Update: Sun, 05 Aug 2018 07:16:40 +0200
+
--- a/Makefile
+++ b/Makefile
-@@ -75,6 +75,7 @@ artemis.jar : $(CLASSES)
+@@ -75,27 +75,7 @@ artemis.jar : $(CLASSES)
mkdir -p jar_build/build
rm -f *.jar
cd jar_build/build; \
-+ if [ "$$BUILDSYSEM" = "not-Debian" ] ; then \
- for fileJar in ../../lib/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
-@@ -96,7 +97,11 @@ artemis.jar : $(CLASSES)
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
-- ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
-+ ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap . \
-+ else \
-+ cp -R ../uk ../org ../nsdb ../type ../seqdb ../etc ../images \
-+ ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap . ; \
-+ fi
+- for fileJar in ../../lib/*.jar; do \
+- jar xvf $$fileJar; \
+- rm -rf META-INF/MANIFEST.MF; \
+- done; \
+- for fileJar in ../../lib/j2ssh/*.jar; do \
+- jar xvf $$fileJar; \
+- rm -rf META-INF/MANIFEST.MF; \
+- done; \
+- for fileJar in ../../lib/ibatis/*.jar; do \
+- jar xvf $$fileJar; \
+- rm -rf META-INF/MANIFEST.MF; \
+- done; \
+- for fileJar in ../../lib/batik/*.jar; do \
+- jar xvf $$fileJar; \
+- rm -rf META-INF/MANIFEST.MF; \
+- done; \
+- for fileJar in ../../lib/picard/*.jar; do \
+- jar xvf $$fileJar; \
+- rm -rf META-INF/MANIFEST.MF; \
+- done; \
+- cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
++ cp -R ../../uk ../../org ../../etc ../../images \
+ ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
find jar_build/build -name '*.java' -print | xargs rm -f
find jar_build/build -name '.svn' -print | xargs rm -rf
- find jar_build/build -name '*.DS_Store' -print | xargs rm -rf
-@@ -104,15 +109,15 @@ artemis.jar : $(CLASSES)
+@@ -103,16 +83,16 @@ artemis.jar : $(CLASSES)
+ cd jar_build/build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
- jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
+- jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
-+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
++ jar cmf manifest-art ../artemis.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
++ artemis_sqlmap org uk ; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
- org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
-+ org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
++ org uk joptsimple ngs freemarker ; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
- jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \
-+ jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
++ jar cmf manifest-bamview ../bamview.jar etc org uk ; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
- jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
+- jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
-+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
++ jar cmf manifest-act ../act.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
++ artemis_sqlmap org uk ; \
rm -rf jar_build/build;
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -38,14 +38,13 @@ export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))
dh $@ --with javahelper
override_dh_auto_build:
- $(MAKE) jar
- # dh_auto_build -- jar # does not work since the build does not find all plain files that should be include in jar since it cds to subdir first
+ dh_auto_build -- jar
sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \
debian/artemis.manifest
convert images/helix.gif -resize 96x96\! images/helix.png
override_dh_auto_test:
- cd test && ant -f build-test.xml test-headless -DEMBOSS_ROOT=/usr
+ cd test && ant -f build-test.xml -DEMBOSS_ROOT=/usr
override_dh_auto_clean:
dh_auto_clean
View it on GitLab: https://salsa.debian.org/med-team/artemis/compare/b62d032ad478158c5a9117a603827869e0c2bbb0...551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8
--
View it on GitLab: https://salsa.debian.org/med-team/artemis/compare/b62d032ad478158c5a9117a603827869e0c2bbb0...551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8
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