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 <[email protected]> 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 <[email protected]> + Andreas Tille <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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