[med-svn] r13469 - in trunk/packages/ncbi-blast+: . branches branches/2.2.28_ubuntu branches/2.2.28_ubuntu/debian branches/2.2.28_ubuntu/debian/patches
Timothy Booth
tbooth-guest at alioth.debian.org
Thu May 2 17:09:17 UTC 2013
Author: tbooth-guest
Date: 2013-05-02 17:09:17 +0000 (Thu, 02 May 2013)
New Revision: 13469
Added:
trunk/packages/ncbi-blast+/branches/
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/skip_services_unit_test
Modified:
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/series
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/rules
Log:
I've put my updates for 2.2.28 into this new subversion branch
/packages/ncbi-blast+/branches/2.2.28_ubuntu/ because:
1) They have changed the build system and I'm not 100%
confident that my fixes to the patches are all correct.
2) Because of an oddity with the Boost libs on Ubuntu, and because
Ubuntu LTS is getting old, the build dependencies are not right
for Debian Sid, so you can't use my build unmodified in any case.
The thing I think you will find most useful is my new "override_dh_clean"
logic in rules. It took me about 8 attempts to get the package to build
and clean fully and I don't want you to waste the time repeating my mistakes!
Modified: trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog 2013-05-02 17:09:17 UTC (rev 13469)
@@ -1,3 +1,14 @@
+ncbi-blast+ (2.2.28-3ubuntu1) precise; urgency=low
+
+ * New upstream
+ * Rebuild for Ubuntu
+ * Patch to skip test that needs network connection
+ * Re-jiggle shared build patch
+ * Drop mips patch as it is now in upstream
+ * Use newer Boost 1.48
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Apr 2013 12:49:09 +0100
+
ncbi-blast+ (2.2.27-3) unstable; urgency=low
* debian/series: active patch fix_arm_mips_build (Closes: #688661).
Modified: trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control 2013-05-02 17:09:17 UTC (rev 13469)
@@ -4,7 +4,7 @@
Build-Depends: autotools-dev (>= 20100122),
debhelper (>= 7.0.50~),
dpkg-dev (>= 1.16.1),
- libboost-test-dev,
+ libboost-test1.48-dev,
libbz2-dev,
libc0.3-dev (>= 2.13-9~) [hurd-i386],
libpcre3-dev,
Added: trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
===================================================================
--- trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile (rev 0)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/hurd_fixes 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/patches/no_multiarch_rpath
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/no_multiarch_rpath 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/series 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/patches/skip_services_unit_test
===================================================================
--- trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/skip_services_unit_test (rev 0)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/skip_services_unit_test 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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+/branches/2.2.28_ubuntu/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules 2013-05-01 20:09:53 UTC (rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/rules 2013-05-02 17:09:17 UTC (rev 13469)
@@ -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
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