[med-svn] r6958 - in trunk/packages/ncbi-blast+/tags: . 2.2.25-2/debian 2.2.25-2/debian/patches
Aaron M. Ucko
ucko at alioth.debian.org
Thu Jun 9 02:16:57 UTC 2011
Author: ucko
Date: 2011-06-09 02:16:57 +0000 (Thu, 09 Jun 2011)
New Revision: 6958
Added:
trunk/packages/ncbi-blast+/tags/2.2.25-2/
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/support_other_cpus
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules
Removed:
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series
trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.25-2
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2011-06-07 18:14:13 UTC (rev 6931)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog 2011-06-09 02:16:57 UTC (rev 6958)
@@ -1,5 +0,0 @@
-ncbi-blast+ (2.2.25-1) unstable; urgency=low
-
- * Initial release (Closes: #624394)
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 27 Apr 2011 15:19:59 +0200
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog (from rev 6957, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/changelog 2011-06-09 02:16:57 UTC (rev 6958)
@@ -0,0 +1,23 @@
+ncbi-blast+ (2.2.25-2) unstable; urgency=low
+
+ * Team upload.
+ * Fix several sources of build failures (closes: #629656):
+ - debian/rules (override_dh_install): Correctly support building only
+ architecture-dependent packages.
+ (DEB_CONFIGURE_EXTRA_FLAGS): Add --without-caution to override the
+ upstream build system's reluctance to build shared libraries on the
+ Hurd or kFreeBSD, which it doesn't specifically recognize. Limit C++
+ optimization level to -O (rather than the default -O2) on mips(el),
+ on which g++ otherwise crashes. :-/
+ - debian/patches/support_other_cpus (new; committed upstream too):
+ build correctly on architectures that wound up defining
+ NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
+ whose detection the patch fixes as well).
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 08 Jun 2011 21:42:52 -0400
+
+ncbi-blast+ (2.2.25-1) unstable; urgency=low
+
+ * Initial release (Closes: #624394)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2011-06-07 18:14:13 UTC (rev 6931)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series 2011-06-09 02:16:57 UTC (rev 6958)
@@ -1,3 +0,0 @@
-legacy_rename_rpsblast
-fix_checks
-fix_gcc46_errors
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series (from rev 6953, trunk/packages/ncbi-blast+/trunk/debian/patches/series)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/series 2011-06-09 02:16:57 UTC (rev 6958)
@@ -0,0 +1,4 @@
+legacy_rename_rpsblast
+fix_checks
+fix_gcc46_errors
+support_other_cpus
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/support_other_cpus (from rev 6953, trunk/packages/ncbi-blast+/trunk/debian/patches/support_other_cpus)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/support_other_cpus (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/patches/support_other_cpus 2011-06-09 02:16:57 UTC (rev 6958)
@@ -0,0 +1,66 @@
+Index: b/c++/include/corelib/impl/ncbi_atomic_defs.h
+===================================================================
+--- a/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:26:07.000000000 -0400
++++ b/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:29:25.000000000 -0400
+@@ -259,7 +259,7 @@
+ # endif
+ #endif
+
+-#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
++#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__powerpc__) && !defined(__powerpc64__) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
+ # define NCBI_SWAP_POINTERS_EXTERN 1
+ # define NCBI_SLOW_ATOMIC_SWAP 1
+ #endif
+Index: b/c++/include/corelib/ncbiatomic.h
+===================================================================
+--- a/c++/include/corelib/ncbiatomic.h 2011-06-08 20:26:00.000000000 -0400
++++ b/c++/include/corelib/ncbiatomic.h 2011-06-08 20:30:34.000000000 -0400
+@@ -121,14 +121,14 @@
+ asm volatile("swap [%2], %1" : "=m" (*nv_loc), "=r" (old_value)
+ : "r" (nv_loc), "1" (new_value), "m" (*nv_loc));
+ return old_value;
+-# elif defined(__ppc__) || defined(__ppc64__)
++# elif defined(__powerpc__) || defined(__powerpc64__) || defined(__ppc__) || defined(__ppc64__)
+ void* old_value;
+ int swapped = 0;
+ NCBI_SCHED_SPIN_INIT();
+ while ( !swapped ) {
+ swapped = 0;
+ asm volatile(
+-#ifdef __ppc64__
++#if defined(__powerpc64__) || defined(__ppc64__)
+ "ldarx %1,0,%4\n\tstdcx. %3,0,%4"
+ #else
+ "lwarx %1,0,%4\n\tstwcx. %3,0,%4"
+Index: b/c++/src/objects/seq/seq_id_handle.cpp
+===================================================================
+--- a/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:26:34.000000000 -0400
++++ b/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:28:43.000000000 -0400
+@@ -47,11 +47,6 @@
+ // CSeq_id_Info
+ //
+
+-//#define NCBI_SLOW_ATOMIC_SWAP
+-#ifdef NCBI_SLOW_ATOMIC_SWAP
+-DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
+-#endif
+-
+
+ CSeq_id_Info::CSeq_id_Info(CSeq_id::E_Choice type,
+ CSeq_id_Mapper* mapper)
+Index: b/c++/src/objects/seq/seq_id_tree.cpp
+===================================================================
+--- a/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:26:34.000000000 -0400
++++ b/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:28:53.000000000 -0400
+@@ -42,6 +42,11 @@
+ BEGIN_NCBI_SCOPE
+ BEGIN_SCOPE(objects)
+
++//#define NCBI_SLOW_ATOMIC_SWAP
++#ifdef NCBI_SLOW_ATOMIC_SWAP
++DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
++#endif
++
+ ////////////////////////////////////////////////////////////////////
+ //
+ // CSeq_id_***_Tree::
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules 2011-06-07 18:14:13 UTC (rev 6931)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules 2011-06-09 02:16:57 UTC (rev 6958)
@@ -1,67 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
- --without-makefile-auto-update --with-flat-makefile --without-dbapi \
- --without-lzo --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD
-proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
-
-# XXX - not quite right, as we get -DNDEBUG vs. -D_DEBUG
-ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
-DEB_CONFIGURE_EXTRA_FLAGS += --without-debug
-else
-DEB_CONFIGURE_EXTRA_FLAGS += --with-optimization
-endif
-
-llp=LD_LIBRARY_PATH
-override_dh_auto_configure:
- cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
- ./configure $(DEB_CONFIGURE_EXTRA_FLAGS)
-
-override_dh_auto_build:
- cd c++/BUILD/build && make -f Makefile.flat \
- all_projects="$(proj)" DLL_LDFLAGS=-Wl,--as-needed
-
-override_dh_auto_test:
- -dh_auto_test
- -c++/BUILD/build/check.sh concat_err
- -cat c++/BUILD/build/check.sh.out_err
-
-instroot = debian/ncbi-blast+/usr
-override_dh_auto_install:
- cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
- cp c++/BUILD/bin/* $(instroot)/bin/
-
-override_dh_install:
- # dh_install
- mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
- mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
- mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
- mv $(instroot)/bin/windowmasker_2.2.22_adapter.py \
- $(instroot)/bin/windowmasker_2.2.22_adapter
-# Clean up tests, demos, and internal build tools
- rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
- $(instroot)/bin/gene_info_reader $(instroot)/bin/datatool \
- $(instroot)/bin/project_tree_builder \
- $(instroot)/lib/ncbi-blast+/libtest_*.so
-
- cp debian/legacy/legacy.sh \
- debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin/
-
-override_dh_clean:
- dh_clean
- -for x in c++/src/objects/*/*.files; do \
- (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \
- `basename $$x .files`.module purge_sources); \
- done
- rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile
- rm -f c++/src/objects/blastxml/blastxml.module
-
-%:
- dh $@ -Dc++ --with autotools_dev --with quilt
-
-get-orig-source:
- . debian/get-orig-source
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules (from rev 6956, trunk/packages/ncbi-blast+/trunk/debian/rules)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-2/debian/rules 2011-06-09 02:16:57 UTC (rev 6958)
@@ -0,0 +1,73 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
+ --without-makefile-auto-update --with-flat-makefile --without-caution \
+ --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \
+ --with-build-root=BUILD
+proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
+
+# XXX - not quite right, as we get -DNDEBUG vs. -D_DEBUG
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+DEB_CONFIGURE_EXTRA_FLAGS += --without-debug
+else
+DEB_CONFIGURE_EXTRA_FLAGS += --with-optimization
+endif
+
+DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
+DEB_CONFIGURE_EXTRA_FLAGS += CXXFLAGS=-O FAST_CXXFLAGS=-O
+endif
+
+llp=LD_LIBRARY_PATH
+override_dh_auto_configure:
+ cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
+ ./configure $(DEB_CONFIGURE_EXTRA_FLAGS)
+
+override_dh_auto_build:
+ cd c++/BUILD/build && make -f Makefile.flat \
+ all_projects="$(proj)" DLL_LDFLAGS=-Wl,--as-needed
+
+override_dh_auto_test:
+ -dh_auto_test
+ -c++/BUILD/build/check.sh concat_err
+ -cat c++/BUILD/build/check.sh.out_err
+
+instroot = debian/ncbi-blast+/usr
+leg_bin = debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin
+override_dh_auto_install:
+ cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
+ cp c++/BUILD/bin/* $(instroot)/bin/
+
+override_dh_install:
+ # dh_install
+ mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
+ mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
+ mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
+ mv $(instroot)/bin/windowmasker_2.2.22_adapter.py \
+ $(instroot)/bin/windowmasker_2.2.22_adapter
+# Clean up tests, demos, and internal build tools
+ rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
+ $(instroot)/bin/gene_info_reader $(instroot)/bin/datatool \
+ $(instroot)/bin/project_tree_builder \
+ $(instroot)/lib/ncbi-blast+/libtest_*.so
+
+ if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
+
+override_dh_clean:
+ dh_clean
+ -for x in c++/src/objects/*/*.files; do \
+ (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \
+ `basename $$x .files`.module purge_sources); \
+ done
+ rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile
+ rm -f c++/src/objects/blastxml/blastxml.module
+
+%:
+ dh $@ -Dc++ --with autotools_dev --with quilt
+
+get-orig-source:
+ . debian/get-orig-source
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