[med-svn] [Git][med-team/ncbi-blastplus][master] 7 commits: Start work on ncbi-blast+ 2.9.0-2, primarily for #930240.
Aaron M. Ucko
gitlab at salsa.debian.org
Mon Sep 30 04:50:06 BST 2019
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
9682d07d by Aaron M. Ucko at 2019-09-29T19:37:27Z
Start work on ncbi-blast+ 2.9.0-2, primarily for #930240.
- - - - -
de8ac77e by Aaron M. Ucko at 2019-09-29T19:40:26Z
debian/rules: Use /usr/share/dpkg/{architecture,buildflags}.mk.
Delegate dpkg-{architecture,buildflags} calls to
/usr/share/dpkg/{architecture,buildflags}.mk respectively.
- - - - -
fdbb78f4 by Aaron M. Ucko at 2019-09-30T01:50:15Z
debian/rules: 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).
- - - - -
3f95d82b by Aaron M. Ucko at 2019-09-30T01:54:40Z
debian/rules: Install get_species_taxids without the .sh suffix.
- - - - -
5ab1958e by Aaron M. Ucko at 2019-09-30T01:55:46Z
debian/copyright: Remove redundant ncbi_menu_*.js stanza.
- - - - -
67053dfe by Aaron M. Ucko at 2019-09-30T01:56:58Z
debian/control: Standards-Version: 4.4.1 (already compliant).
- - - - -
bd00a267 by Aaron M. Ucko at 2019-09-30T01:57:32Z
Finalize ncbi-blast+ 2.9.0-2 for upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,31 @@
+ncbi-blast+ (2.9.0-2) unstable; urgency=medium
+
+ * debian/control: Standards-Version: 4.4.1 (already compliant).
+ * debian/copyright: Remove redundant ncbi_menu_*.js stanza.
+ * 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).
+ - Install get_species_taxids without the .sh suffix.
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 29 Sep 2019 21:57:31 -0400
+
ncbi-blast+ (2.9.0-1) unstable; urgency=medium
* New upstream release
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends-Arch: 2to3,
libpcre3-dev,
time,
zlib1g-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
=====================================
debian/copyright
=====================================
@@ -165,14 +165,6 @@ License: GPL-2
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-Files: c++/src/html/ncbi_menu_*.js
-Copyright: 1997-1999 Netscape Communications Corp.
-License: Netscape
- Netscape grants you a royalty free license to use or modify this
- software provided that this copyright notice appears on all copies.
- This software is provided "AS IS," without a warranty of any kind.
-
-
Files: c++/include/util/bitset/*
Copyright: 2002-2003 Anatoliy Kuznetsov
License: MIT
=====================================
debian/rules
=====================================
@@ -9,12 +9,12 @@ ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
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)))
@@ -26,12 +26,10 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
-DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+include /usr/share/dpkg/architecture.mk
+include /usr/share/dpkg/buildflags.mk
-CFLAGS := $(shell dpkg-buildflags --get CFLAGS)
-CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
-CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS)
-LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -Wl,--as-needed
+LDFLAGS += -Wl,--as-needed
ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
CXXFLAGS := $(CXXFLAGS:-O%=-O)
@@ -41,16 +39,33 @@ endif
export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
# used for run_with_lock
-DEB_CONFIGURE_EXTRA_FLAGS += CFLAGS_FOR_BUILD="$(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)+:$$$(llp)} \
- CONFIG_SHELL=/bin/bash ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
+override_dh_auto_configure-arch: $(PREBUILT_DATATOOL_EXE)
+ cd c++ && CONFIG_SHELL=/bin/bash \
+ ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
|| (tail -v -n +0 config.log BUILD/status/config.log; exit 1)
override_dh_auto_build-arch:
@@ -62,9 +77,11 @@ override_dh_auto_build-indep:
echo "Save time and do nothing for architecture independent builds"
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-dh_auto_test
-c++/BUILD/build/check.sh concat_err
-cat c++/BUILD/build/check.sh.out_err
+endif
instroot = debian/ncbi-blast+/usr
leg_bin = debian/ncbi-blast+-legacy/usr/bin
@@ -79,6 +96,8 @@ override_dh_install-arch:
# dh_install
mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+
+ mv $(instroot)/bin/get_species_taxids.sh \
+ $(instroot)/bin/get_species_taxids
mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
sed -e '1s/$$/3/' $(instroot)/bin/windowmasker_2.2.22_adapter.py \
@@ -90,10 +109,22 @@ override_dh_install-arch:
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 "$$(ls c++/BUILD/lib.observed)" ] || break; \
+ echo ------------------------------------------------------------; \
+ cp -a c++/BUILD/lib.observed/* $(instroot)/lib/ncbi-blast+; \
+ d=c++/BUILD/lib.observed; \
+ done
override_dh_install-indep:
#if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
@@ -118,14 +149,15 @@ override_dh_clean:
mods="`echo *.module`" ; \
[ "$${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
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/657af60fdd491321109fc2f5e68961ea7706b07e...bd00a2671eb95cdfdd16edfe5f0f048e931a6e02
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/657af60fdd491321109fc2f5e68961ea7706b07e...bd00a2671eb95cdfdd16edfe5f0f048e931a6e02
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