debian/changelog

-infernal (1.1.3-2) UNRELEASED; urgency=medium
+infernal (1.1.3-2) unstable; urgency=medium
 
   * Team upload.
   * Add python3 build-dep for `make check`
@@ -9,8 +9,11 @@ infernal (1.1.3-2) UNRELEASED; urgency=medium
   * Enable a verbose build log
   * infernal-doc: mark Multi-Arch: foreign (thanks Multiarch hinter!)
   * debian/patches/hardening: added CPPFLAGS to easel, rmark, and hmmer/profmark
+  * Install example binaries into /usr/lib/ and symlink them into the
+    doc/infernal/examples directory (fixes a FHS violation)
+  * Added missing autopkgtest dependency on python3
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 30 Nov 2019 11:00:30 +0100
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 01 Dec 2019 16:35:34 +0100
 
 infernal (1.1.3-1) unstable; urgency=medium
 

debian/rules

@@ -6,6 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 include /usr/share/dpkg/default.mk
 pkgdata:=infernal
 sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
+sampledir_lib:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples
 
 %:
 	dh  $@
@@ -36,12 +37,15 @@ override_dh_install:
 
 override_dh_installexamples:
 	dh_installexamples
-	mkdir -p $(sampledir)/src/;
-	mkdir -p $(sampledir)/easel/miniapps/;
-	find ./src -name "*test" -exec cp \{\} $(sampledir)/src/ \;
-	cp ./src/itest_brute $(sampledir)/src/;
-	cp ./easel/miniapps/esl-reformat $(sampledir)/easel/miniapps/;
-	cp ./easel/miniapps/esl-shuffle $(sampledir)/easel/miniapps/;
-	cp ./easel/miniapps/esl-sfetch $(sampledir)/easel/miniapps/;
-	cp -aR testsuite $(sampledir)/;
-	cp ./easel/devkit/sqc $(sampledir)/;
+	mkdir -p $(sampledir)
+	mkdir -p $(sampledir_lib)/src/
+	mkdir -p $(sampledir_lib)/easel/miniapps/
+	find ./src -name "*test" -exec cp \{\} $(sampledir_lib)/src/ \;
+	cp ./src/itest_brute $(sampledir_lib)/src/
+	cp ./easel/miniapps/esl-reformat $(sampledir_lib)/easel/miniapps/
+	cp ./easel/miniapps/esl-shuffle $(sampledir_lib)/easel/miniapps/
+	cp ./easel/miniapps/esl-sfetch $(sampledir_lib)/easel/miniapps/
+	cd $(sampledir) && ln -s ../../../../lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples/easel ./easel \
+		&& ln -s ../../../../lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples/src ./src
+	cp -aR testsuite $(sampledir)/
+	cp ./easel/devkit/sqc $(sampledir)/

debian/tests/control

 Tests: run-unit-test
-Depends: @
+Depends: @, python3
 Restrictions:

debian/tests/run-unit-test

@@ -7,7 +7,7 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+cp -Lr /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
 
@@ -16,5 +16,5 @@ find . -name "*.gz" -exec gunzip \{\} \;
 chmod -R +x .
 
 echo infernal testsuite
-find /usr/bin -name "cm*" -exec ln -s \{\} src \;
+find /usr/bin -name "cm*" -exec ln -s \{\} src/ \;
 ./sqc 2 ./testsuite/testsuite.sqc . ./testsuite/..