#!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export LC_ALL=C.UTF-8 JAVA_HOME=/usr/lib/jvm/default-java JSON_SIMPLE_VERSION = $(shell dpkg -l libjson-simple-java | grep '^ii' | awk '{print $$3}') JSON_SIMPLE_3 = $(shell dpkg --compare-versions '$(JSON_SIMPLE_VERSION)' '>' '3.1.1-1~' && echo yes || echo no) ifeq (yes,$(JSON_SIMPLE_3)) JSON_SIMPLE_PACKAGE = com.github.cliftonlabs.json_simple else JSON_SIMPLE_PACKAGE = org.json.simple endif %: dh $@ --with javahelper override_dh_auto_configure: dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml sed -e 's/BJLIB/biojava4-sequencing/g' debian/build.xml > biojava-sequencing/build.xml sed -e 's/BJLIB/biojava4-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml sed -e 's/BJLIB/biojava4-structure/g' debian/build.xml > biojava-structure/build.xml sed -e 's/BJLIB/biojava4-ws/g' debian/build.xml > biojava-ws/build.xml sed -e 's/BJLIB/biojava4-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml override_dh_auto_build: find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,$(JSON_SIMPLE_PACKAGE),' \ {} \; -print cd biojava-jcolorbrewer && ant jar cd biojava-forester && ant jar cd biojava-core && ant jar cd biojava-phylo && ant jar cd biojava-alignment && ant jar cd biojava-aa-prop && ant jar cd biojava-genome && ant jar cd biojava-sequencing && ant jar cd biojava-structure && ant jar cd biojava-structure-gui && ant jar cd biojava-modfinder && ant jar cd biojava-ontology && ant jar cd biojava-protein-disorder && ant jar cd biojava-protein-comparison-tool && ant jar cd biojava-ws && ant jar cd biojava-survival && ant jar # make doc rm -rf biojavadoc mkdir biojavadoc cp -r biojava-*/src biojavadoc/ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml cd biojavadoc && ant javadocs # rm -rf biojavadoc override_jh_installjavadoc: jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ $$(dpkg -L $$(apt-cache show default-jdk-doc | grep Depends \ | awk '{print $$2}') | grep /usr/share/doc/ \ | head -n1) \ debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/ ifeq ($(DH_VERBOSE),1) cat results.txt || /bin/true; rm -f results.txt endif override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) echo '*********************************************************************************' echo '* The following test is ignored since under certain circumstances it might fail *' echo '* Please check the result! *' echo '* More information can be found in the Debian BTS at *' echo '* https://bugs.debian.org/843712 *' echo '*********************************************************************************' cd biojava-core && (ant test || true) cd biojava-alignment && ant test # Investigate test failure cd biojava-aa-prop && ant test # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure #cd biojava-protein-disorder && ant test # Requires remote access and tmp directory write access #cd biojava-structure && ant test cd biojava-structure-gui && ant test cd biojava-ontology && ant test endif override_dh_clean: dh_clean rm -rf build rm -rf dist rm -rf javadoc rm -rf test rm -f biojava-*/build.xml rm -rf biojavadoc rm -rf doc find . -name "*.class" -delete rm -rf buildtest find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $$file $${file%.json-simple}' \; -print get-orig-source: debian/get-orig-source