diff -Nru emboss-6.6.0+dfsg/debian/changelog emboss-6.6.0+dfsg/debian/changelog --- emboss-6.6.0+dfsg/debian/changelog 2022-02-20 23:51:27.000000000 +0000 +++ emboss-6.6.0+dfsg/debian/changelog 2023-01-22 03:26:29.000000000 +0000 @@ -1,3 +1,21 @@ +emboss (6.6.0+dfsg-12ubuntu1) lunar; urgency=medium + + * Merge from Debian unstable. Remaining changes: + - d/p/mysql-8.0: Fix build against MySQL 8.0 by making it compatible + with stdbool.h. + + -- Logan Rosen Sat, 21 Jan 2023 22:26:29 -0500 + +emboss (6.6.0+dfsg-12) unstable; urgency=medium + + * Enable building on hppa by disabling java support which is missing there + Closes: #1021440 + * Standards-Version: 4.6.1 (routine-update) + * Use secure URI in Homepage field. + * Lintian-overrides (See lintian bug #1017966) + + -- Andreas Tille Mon, 10 Oct 2022 16:30:48 +0200 + emboss (6.6.0+dfsg-11ubuntu1) jammy; urgency=medium * Merge from Debian unstable. Remaining changes: diff -Nru emboss-6.6.0+dfsg/debian/control emboss-6.6.0+dfsg/debian/control --- emboss-6.6.0+dfsg/debian/control 2022-02-19 09:16:45.000000000 +0000 +++ emboss-6.6.0+dfsg/debian/control 2022-10-10 22:18:57.000000000 +0000 @@ -6,7 +6,7 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), -# javahelper, +# javahelper [!hppa] , libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, @@ -20,13 +20,13 @@ sharutils, tcsh | csh | c-shell, # Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031 - default-jdk, - ant + default-jdk [!hppa] , + ant [!hppa] # #Build-Depends-Indep: default-jdk -Standards-Version: 4.5.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/emboss Vcs-Git: https://salsa.debian.org/med-team/emboss.git -Homepage: http://emboss.sourceforge.net +Homepage: https://emboss.sourceforge.net Rules-Requires-Root: no Package: emboss @@ -55,6 +55,7 @@ Package: emboss-data Architecture: all Depends: ${misc:Depends} +Multi-Arch: foreign Description: data files for the EMBOSS package EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software @@ -74,6 +75,7 @@ Section: doc Depends: ${misc:Depends} Suggests: evince | pdf-viewer | postscript-viewer +Multi-Arch: foreign Description: documentation for EMBOSS EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software @@ -94,6 +96,7 @@ Depends: ${misc:Depends} Recommends: tcsh | csh | c-shell Suggests: valgrind +Multi-Arch: foreign Description: test files for the EMBOSS package EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software @@ -143,6 +146,7 @@ Package: jemboss Architecture: all +Build-Profiles: Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, diff -Nru emboss-6.6.0+dfsg/debian/rules emboss-6.6.0+dfsg/debian/rules --- emboss-6.6.0+dfsg/debian/rules 2022-02-19 09:16:45.000000000 +0000 +++ emboss-6.6.0+dfsg/debian/rules 2022-10-10 22:18:57.000000000 +0000 @@ -16,6 +16,13 @@ VERSION=$(DEB_VERSION_UPSTREAM) RENAMED := cons pscan +# Disable java packages on architecture that don't have +# an openjdk port. +nojava_archs = hppa +ifneq (,$(filter $(DEB_HOST_ARCH), $(nojava_archs))) +export DEB_BUILD_PROFILES += nojava +endif + EMBOSS-TMP = $(CURDIR)/debian/emboss_tmp EMBOSS = $(CURDIR)/debian/emboss EMBOSS-TEST = $(CURDIR)/debian/emboss-test @@ -25,8 +32,11 @@ CONFFLAGS += --libdir=/usr/lib/emboss/lib CONFFLAGS += --includedir=/usr/lib/emboss/include CONFFLAGS += --enable-systemlibs + +ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),) CONFFLAGS += --with-java=/usr/lib/jvm/default-java/include CONFFLAGS += --with-javaos=/usr/lib/jvm/default-java/include/linux +endif CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) @@ -42,9 +52,11 @@ override_dh_auto_build: dh_auto_build -- AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(DEB_LDFLAGS)" +ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),) # Add 2 extra files wanted in jemboss.jar cd jemboss/lib && make jemboss.jar cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties +endif override_dh_clean: rm -rf debian/emboss_tmp @@ -88,6 +100,7 @@ ### While the next call repeats a statement from install-arch it is needed to get the ### data dir right into place. Make should be clever enough to not duplicate the process $(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP) +ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),) $(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss bindir=/usr/bin # install target seems to remove executable flag which is claimed by lintian find debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \; @@ -95,6 +108,7 @@ rm debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE # resources.jar not needed as we use the data files in /usr/share/EMBOSS/data/ rm -f debian/jemboss/usr/share/EMBOSS/jemboss/resources/resources.jar +endif ### Installation of the test suite cp -a test debian/emboss-test/usr/share/EMBOSS/ diff -Nru emboss-6.6.0+dfsg/debian/source/lintian-overrides emboss-6.6.0+dfsg/debian/source/lintian-overrides --- emboss-6.6.0+dfsg/debian/source/lintian-overrides 1970-01-01 00:00:00.000000000 +0000 +++ emboss-6.6.0+dfsg/debian/source/lintian-overrides 2022-10-10 14:30:48.000000000 +0000 @@ -0,0 +1,2 @@ +# See lintian bug #1017966 +emboss source: source-is-missing