From: Olivier Sallou Date: Sat, 1 Jun 2013 07:37:36 +0000 (+0000) Subject: new upstream 2.2.28, include updates from T. Booth from Ubuntu to compile this release X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~278 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=379ea986792b061156bc91c2a75da4d2d2eeb5d2;p=ncbi-blast%2B.git new upstream 2.2.28, include updates from T. Booth from Ubuntu to compile this release --- diff --git a/debian/changelog b/debian/changelog index 6bce91e9..2b27ec06 100644 --- a/debian/changelog +++ b/debian/changelog @@ -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 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). diff --git a/debian/compat b/debian/compat index 7f8f011e..ec635144 100644 --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -7 +9 diff --git a/debian/control b/debian/control index f192bffe..fe13d9a2 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Section: science 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], diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile new file mode 100644 index 00000000..bcc1bfac --- /dev/null +++ b/debian/patches/enable_clean_after_failed_compile @@ -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 diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index df0d17eb..fc310ca4 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -37,7 +37,7 @@ Last-Update: 2011-08-28 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 @@ Last-Update: 2011-08-28 +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 @@ Last-Update: 2011-08-28 + 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 @@ Last-Update: 2011-08-28 --- 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 @@ Last-Update: 2011-08-28 +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 @@ Last-Update: 2011-08-28 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 @@ Last-Update: 2011-08-28 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 @@ Last-Update: 2011-08-28 +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 @@ Last-Update: 2011-08-28 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 diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index 4486d4d7..6e8e8f6b 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -9,7 +9,7 @@ Author: Aaron M. Ucko 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 @@ Last-Update: 2011-06-10 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 @@ Last-Update: 2011-06-10 --- a/c++/src/connect/ext/ncbi_localnet.c +++ b/c++/src/connect/ext/ncbi_localnet.c -@@ -64,6 +64,8 @@ - - #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX) - # define PATH_MAX _MAX_PATH -+#elif !defined(PATH_MAX) -+# define PATH_MAX 4096 +@@ -62,6 +62,10 @@ + # endif /*_MAX_PATH*/ #endif /*NCBI_OS_MSWIN && !PATH_MAX*/ ++#if !defined(PATH_MAX) ++# define PATH_MAX 4096 ++#endif /*Patch added for Ubuntu build*/ ++ #if PATH_MAX < 256 + # define BUFSIZE 256 + #else diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index 6bf56aab..b9e30ad1 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko 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 @@ Last-Update: 2011-08-28 esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -1597,7 +1597,7 @@ +@@ -1620,7 +1620,7 @@ break ;; /* ) diff --git a/debian/patches/series b/debian/patches/series index 5a6a434d..4e450034 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,6 +1,7 @@ +enable_clean_after_failed_compile hurd_fixes legacy_rename_rpsblast fix_lib_deps no_multiarch_rpath use_pie_for_apps -fix_arm_mips_build +skip_services_unit_test diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test new file mode 100644 index 00000000..2d5249b1 --- /dev/null +++ b/debian/patches/skip_services_unit_test @@ -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 diff --git a/debian/rules b/debian/rules index e7b553b9..99f22221 100755 --- a/debian/rules +++ b/debian/rules @@ -69,14 +69,22 @@ override_dh_install: 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