[med-svn] r13784 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Sat Jun 1 07:37:37 UTC 2013
Author: osallou
Date: 2013-06-01 07:37:36 +0000 (Sat, 01 Jun 2013)
New Revision: 13784
Added:
trunk/packages/ncbi-blast+/trunk/debian/patches/enable_clean_after_failed_compile
trunk/packages/ncbi-blast+/trunk/debian/patches/skip_services_unit_test
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/compat
trunk/packages/ncbi-blast+/trunk/debian/control
trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/trunk/debian/patches/series
trunk/packages/ncbi-blast+/trunk/debian/rules
Log:
new upstream 2.2.28, include updates from T. Booth from Ubuntu to compile this release
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2013-06-01 07:37:36 UTC (rev 13784)
@@ -1,3 +1,10 @@
+ncbi-blast+ (2.2.28-1) unstable; urgency=low
+
+ * New upstream release
+ - Thanks to Tim Booth for package update help.
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 01 Jun 2013 08:40:51 +0200
+
ncbi-blast+ (2.2.27-3) unstable; urgency=low
* debian/series: active patch fix_arm_mips_build (Closes: #688661).
Modified: trunk/packages/ncbi-blast+/trunk/debian/compat
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/compat 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/compat 2013-06-01 07:37:36 UTC (rev 13784)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/ncbi-blast+/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/control 2013-06-01 07:37:36 UTC (rev 13784)
@@ -3,7 +3,7 @@
Priority: optional
Build-Depends: autotools-dev (>= 20100122),
debhelper (>= 7.0.50~),
- dpkg-dev (>= 1.16.1),
+ dpkg-dev (>= 1.16.1),
libboost-test-dev,
libbz2-dev,
libc0.3-dev (>= 2.13-9~) [hurd-i386],
Added: trunk/packages/ncbi-blast+/trunk/debian/patches/enable_clean_after_failed_compile
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/enable_clean_after_failed_compile (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/enable_clean_after_failed_compile 2013-06-01 07:37:36 UTC (rev 13784)
@@ -0,0 +1,11 @@
+--- a/c++/src/build-system/new_module.sh.in
++++ b/c++/src/build-system/new_module.sh.in
+@@ -178,7 +178,7 @@
+ if test -x "$bindir/datatool"; then
+ datatool=$bindir/datatool
+ COMMON_AddRunpath "$libdir"
+- else
++ elif [ "$1" != "purge_sources" ] ; then
+ echo "Unable to find datatool." >&2
+ exit 2
+ fi
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2013-06-01 07:37:36 UTC (rev 13784)
@@ -37,7 +37,7 @@
CPPFLAGS = $(ORIG_CPPFLAGS)
--DLL_LIB = blastxml xhtml xcgi
+-DLL_LIB = align_format blastxml xhtml xcgi
+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
+ seq general xser tables xncbi
@@ -79,7 +79,7 @@
+DLL_LIB = xnetblast xser xconnect xutil xncbi
--- a/c++/src/objtools/align_format/Makefile.align_format.lib
+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -10,6 +10,10 @@
+@@ -13,6 +13,10 @@
CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -88,8 +88,8 @@
+ xcgi xhtml tables xncbi
+
### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
# CFLAGS = $(FAST_CFLAGS)
+ # CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
@@ -12,3 +12,5 @@
@@ -109,7 +109,7 @@
--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -11,6 +11,6 @@
+@@ -12,6 +12,6 @@
mask_writer_blastdb_maskinfo
ASN_DEP = seqset
@@ -169,7 +169,7 @@
+DLL_LIB = xncbi
--- a/c++/src/algo/blast/api/Makefile.xblast.lib
+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,11 +74,14 @@
+@@ -74,14 +74,15 @@
deltablast_options \
deltablast
@@ -178,11 +178,12 @@
LIB = xblast
--DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
-+ xalgodustmask seqdb xobjread xobjutil xobjmgr \
-+ xnetblastcli xnetblast scoremat seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
+ DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
+ xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
+ blastdb xnetblastcli xnetblast scoremat xconnect tables \
+- $(SOBJMGR_LIBS)
++ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
++ xser xconnect sequtil tables xutil xncbi
CFLAGS = $(FAST_CFLAGS)
# Strict gcc flags
@@ -192,10 +193,10 @@
LIB = blastinput
--DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
-+ ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
-+ xobjmgr scoremat seqset seq xser xutil xncbi
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread $(OBJMGR_LIBS) xutil
++ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
++ $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
++ scoremat seqset seq xser xutil xncbi
# should be redundant, given the above :-/
ASN_DEP = seqset xnetblast
@@ -303,7 +304,7 @@
+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+ # CFLAGS = $(FAST_CFLAGS)
--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
@@ -8,6 +8,8 @@
@@ -327,9 +328,9 @@
WATCHERS = vasilche
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -14,4 +14,7 @@
- # Dependencies for shared library
+@@ -15,4 +15,7 @@
DLL_LIB =
+ DLL_DLIB = $(GENBANK_READER_LDEP)
+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
+ xser xconnect xcompress xutil xncbi
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2013-06-01 07:37:36 UTC (rev 13784)
@@ -9,7 +9,7 @@
Last-Update: 2011-06-10
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -5817,7 +5817,7 @@
+@@ -5860,7 +5860,7 @@
solaris* )
CONF_f_runpath="-R"
;;
@@ -20,7 +20,7 @@
linux*:ICC )
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1535,7 +1535,7 @@
+@@ -1558,7 +1558,7 @@
solaris* )
CONF_f_runpath="-R"
;;
@@ -42,12 +42,14 @@
--- a/c++/src/connect/ext/ncbi_localnet.c
+++ b/c++/src/connect/ext/ncbi_localnet.c
-@@ -64,6 +64,8 @@
+@@ -62,6 +62,10 @@
+ # endif /*_MAX_PATH*/
+ #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
- #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
- # define PATH_MAX _MAX_PATH
-+#elif !defined(PATH_MAX)
++#if !defined(PATH_MAX)
+# define PATH_MAX 4096
- #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
-
++#endif /*Patch added for Ubuntu build*/
++
#if PATH_MAX < 256
+ # define BUFSIZE 256
+ #else
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2013-06-01 07:37:36 UTC (rev 13784)
@@ -10,7 +10,7 @@
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -5880,7 +5880,7 @@
+@@ -5923,7 +5923,7 @@
break
;;
/* )
@@ -21,7 +21,7 @@
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1597,7 +1597,7 @@
+@@ -1620,7 +1620,7 @@
break
;;
/* )
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series 2013-06-01 07:37:36 UTC (rev 13784)
@@ -1,3 +1,4 @@
+enable_clean_after_failed_compile
hurd_fixes
legacy_rename_rpsblast
fix_lib_deps
@@ -3,3 +4,3 @@
no_multiarch_rpath
use_pie_for_apps
-fix_arm_mips_build
+skip_services_unit_test
Added: trunk/packages/ncbi-blast+/trunk/debian/patches/skip_services_unit_test
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/skip_services_unit_test (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/skip_services_unit_test 2013-06-01 07:37:36 UTC (rev 13784)
@@ -0,0 +1,11 @@
+--- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
++++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
+@@ -11,6 +11,7 @@
+
+ LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
+-CHECK_CMD = blast_services_unit_test
++# This test requires an internet connection, shouldn't be run on a build server
++# CHECK_CMD = blast_services_unit_test
+
+ WATCHERS = madden camacho
Modified: trunk/packages/ncbi-blast+/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/trunk/debian/rules 2013-06-01 07:37:36 UTC (rev 13784)
@@ -69,14 +69,22 @@
override_dh_clean:
dh_clean
- -for x in c++/src/objects/*/*.files; do \
- if [ -d $$x ]; then \
- (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \
- `basename $$x .files`.module purge_sources); \
- fi \
+ #Tricky - for each module directory there may be several module files
+ #or there may be none but then there is still a module named after the
+ #directory. Clean everything!
+ -for x in c++/src/objects/* ; do \
+ (cd "$$x" && ( \
+ mods="`echo *.module`" ; \
+ [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
+ for mod in $$mods ; do \
+ ../../../BUILD/build/new_module.sh $$mod purge_sources ; \
+ done ) ; \
+ ) ; \
done
- rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile
+ 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
%:
dh $@ -Dc++ --with autotools_dev --with quilt
More information about the debian-med-commit
mailing list