ncbi-blast+ (2.9.0-2) UNRELEASED; urgency=medium
* NOT RELEASED YET.
- * debian/rules: Delegate dpkg-{architecture,buildflags} calls to
- /usr/share/dpkg/{architecture,buildflags}.mk respectively.
-
- -- Aaron M. Ucko <ucko@debian.org> Sun, 29 Sep 2019 15:40:25 -0400
+ * debian/rules:
+ - Delegate dpkg-{architecture,buildflags} calls to
+ /usr/share/dpkg/{architecture,buildflags}.mk respectively.
+ - Allow for cross-building (Closes: #930240):
+ -- Factor a DEB_CONFIGURE_COMMON_FLAGS macro out of
+ DEB_CONFIGURE_EXTRA_FLAGS for flags that also make sense for native
+ builds of internal helpers.
+ -- Conditionally supply --build=... and --host= to the main
+ (historically, only) configure run per Helmut Grohne's suggestion.
+ (dh_auto_configure would take care of this, but insists on passing
+ a --runstatedir=... flag this configure script doesn't accept.)
+ -- Conditionally add a rule for building native datatool and
+ project_tree_builder binaries (in a parallel build tree established
+ via another configure invocation), make it a dependency of
+ override_dh_auto_configure-arch, and arrange for everything else to
+ use these binaries as needed.
+ -- Honor DEB_BUILD_OPTIONS="... nocheck ...", also per Helmut.
+ -- Rework logic to install (possibly indirect) local library
+ dependencies to use readelf rather than ldd, making as many passes
+ as necessary (four at present, but no hardcoded count).
+
+ -- Aaron M. Ucko <ucko@debian.org> Sun, 29 Sep 2019 21:50:14 -0400
ncbi-blast+ (2.9.0-1) unstable; urgency=medium
NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
endif
+DEB_CONFIGURE_COMMON_FLAGS=--without-autodep --without-makefile-auto-update \
+ --with-flat-makefile --without-caution --without-dbapi --without-lzo \
+ --without-debug --without-downloaded-vdb
+DEB_CONFIGURE_EXTRA_FLAGS=$(DEB_CONFIGURE_COMMON_FLAGS) --with-dll --with-mt \
+ --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD --with-mbedtls
-DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
- --without-makefile-auto-update --with-flat-makefile --without-caution \
- --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \
- --with-build-root=BUILD --without-debug --without-downloaded-vdb \
- --with-mbedtls
proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
#ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
# used for run_with_lock
-DEB_CONFIGURE_EXTRA_FLAGS += CFLAGS_FOR_BUILD="$(CFLAGS) -fPIE"
-DEB_CONFIGURE_EXTRA_FLAGS += LDFLAGS_FOR_BUILD="$(LDFLAGS)"
+DEB_CONFIGURE_COMMON_FLAGS += CFLAGS_FOR_BUILD="$(CFLAGS) -fPIE"
+DEB_CONFIGURE_COMMON_FLAGS += LDFLAGS_FOR_BUILD="$(LDFLAGS)"
BLAST2_VERSION=1:$(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
-llp=LD_LIBRARY_PATH
+ifneq ($(DEB_BUILD_ARCH),$(DEB_HOST_ARCH))
+NATIVE=.native
+DEB_CONFIGURE_EXTRA_FLAGS += --build=$(DEB_BUILD_GNU_TYPE) \
+ --host=$(DEB_HOST_GNU_TYPE)
+NATIVE_BINDIR=$(CURDIR)/c++/BUILD$(NATIVE)/bin
+PREBUILT_DATATOOL_EXE=$(NATIVE_BINDIR)/datatool
+PREBUILT_PTB_EXE=$(NATIVE_BINDIR)/project_tree_builder
+export PREBUILT_DATATOOL_EXE PREBUILT_PTB_EXE
+
+$(PREBUILT_DATATOOL_EXE):
+ cd c++ && PREBUILT_PTB_EXE=bootstrap \
+ ./configure $(DEB_CONFIGURE_COMMON_FLAGS) --without-objects \
+ --without-algo --without-app --with-build-root=BUILD.native || \
+ (tail -v -n +0 config.log BUILD.native/status/config.log; exit 1)
+ make -j$(NUMJOBS) -C c++/BUILD$(NATIVE)/build -f Makefile.flat \
+ datatool.exe
+endif
+
override_dh_auto_configure-indep:;
-override_dh_auto_configure-arch:
- cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
- CONFIG_SHELL=/bin/bash ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
+override_dh_auto_configure-arch: $(PREBUILT_DATATOOL_EXE)
+ cd c++ && CONFIG_SHELL=/bin/bash \
+ ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
|| (tail -v -n +0 config.log BUILD/status/config.log; exit 1)
override_dh_auto_build-arch:
echo "Save time and do nothing for architecture independent builds"
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-dh_auto_test
-c++/BUILD/build/check.sh concat_err
-cat c++/BUILD/build/check.sh.out_err
+endif
instroot = debian/ncbi-blast+/usr
leg_bin = debian/ncbi-blast+-legacy/usr/bin
rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
$(instroot)/bin/datatool $(instroot)/bin/run_with_lock \
$(instroot)/bin/project_tree_builder
- for x in $(instroot)/bin/*; do \
- LD_LIBRARY_PATH=c++/BUILD/lib ldd $$x; \
- done 2>/dev/null | awk '/BUILD/ { print $$3 }' | sort -u | \
- xargs cp -v -t $(instroot)/lib/ncbi-blast+
+ mkdir c++/BUILD/lib.observed
+ d=$(instroot)/bin; \
+ while :; do \
+ (for x in $$d/*; do \
+ readelf -d $$x 2>/dev/null \
+ | sed -ne 's/.*NEEDED.* \[\(.*\)]$$/\1/p'; \
+ done; rm -f c++/BUILD/lib.observed/*) | sort -u | while read l; do \
+ [ -f $(instroot)/lib/ncbi-blast+/$$l \
+ -o \! -f c++/BUILD/lib/$$l ] || \
+ cp -av c++/BUILD/lib/$$l c++/BUILD/lib.observed/; \
+ done; \
+ [ -n "$$(ls c++/BUILD/lib.observed)" ] || break; \
+ echo ------------------------------------------------------------; \
+ cp -a c++/BUILD/lib.observed/* $(instroot)/lib/ncbi-blast+; \
+ d=c++/BUILD/lib.observed; \
+ done
override_dh_install-indep:
#if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
mods="`echo *.module`" ; \
[ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
for mod in $$mods ; do \
- ../../../BUILD/build/new_module.sh $$mod purge_sources ; \
+ ../../../BUILD$(NATIVE)/build/new_module.sh $$mod \
+ purge_sources ; \
done ) ; \
) ; \
done
rm -rf c++/compilers/dll c++/config.log c++/Makefile
rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
find -name check_exec.pid -delete
- rm -rf c++/BUILD
+ rm -rf c++/BUILD c++/BUILD.native
mv configure.orig.save c++/configure.orig
mv c++/src/util/lmdb/Makefile.orig.save c++/src/util/lmdb/Makefile.orig
mv c++/src/util/lmdbxx/Makefile.orig.save c++/src/util/lmdbxx/Makefile.orig
projects / ncbi-blast+.git / commitdiff