From 3cf28381b19ca73516ce8e4cca3edee3831eab59 Mon Sep 17 00:00:00 2001 From: Olivier Sallou Date: Sat, 22 Nov 2014 14:32:04 +0000 Subject: [PATCH] adapt patches to new release --- debian/changelog | 3 +- debian/patches/fix_lib_deps | 202 +++++++++++++++++++----------- debian/patches/no_multiarch_rpath | 4 +- debian/patches/series | 1 - debian/patches/use_pie_for_apps | 4 +- 5 files changed, 136 insertions(+), 78 deletions(-) diff --git a/debian/changelog b/debian/changelog index 96ebffcd..9ebad7c6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,7 +2,8 @@ ncbi-blast+ (2.2.30-1) UNRELEASED; urgency=medium * New upstream release * d/control: switch to Standards 3.9.6 - [TODO] updates patches to new release + [TODO] fix missing Makefile.flat + [DONE] updates patches to new release -- Olivier Sallou Fri, 21 Nov 2014 18:21:26 +0100 diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 7063fd5b..4e1a626e 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -13,13 +13,14 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/algo/blast/core/Makefile.blast.lib +++ b/c++/src/algo/blast/core/Makefile.blast.lib -@@ -21,5 +21,6 @@ +@@ -21,6 +21,7 @@ CFLAGS = $(FAST_CFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = composition_adjustment xconnect tables - WATCHERS = maning madden camacho + WATCHERS = madden camacho + --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib @@ -11,6 +11,8 @@ @@ -33,22 +34,27 @@ Last-Update: 2011-08-28 WATCHERS = morgulis --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib -@@ -7,6 +7,7 @@ +@@ -7,7 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) --DLL_LIB = align_format blastxml xhtml xcgi +-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ -+ seq general xser tables xncbi ++ seq general xser tables xncbi blastxml2 WATCHERS = jianye zaretska madden camacho fongah2 + --- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib +++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib -@@ -21,3 +21,4 @@ +@@ -21,7 +21,7 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) +- +DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi + + USES_LIBRARIES = \ + seqmasks_io --- a/c++/src/cgi/Makefile.cgi.lib +++ b/c++/src/cgi/Makefile.cgi.lib @@ -9,6 +9,8 @@ @@ -62,21 +68,25 @@ Last-Update: 2011-08-28 WATCHERS = vakatov --- a/c++/src/html/Makefile.html.lib +++ b/c++/src/html/Makefile.html.lib -@@ -7,4 +7,6 @@ +@@ -7,6 +7,8 @@ commentdiag indentstream html_exception writer_htmlenc LIB = xhtml +DLL_LIB = xncbi + WATCHERS = ivanov + + --- a/c++/src/objects/blast/Makefile.xnetblastcli.lib +++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib -@@ -2,3 +2,5 @@ - +@@ -3,6 +3,7 @@ LIB = xnetblastcli SRC = blastclient blastclient_ -+ + +DLL_LIB = xnetblast xser xconnect xutil xncbi + + USES_LIBRARIES = \ + xconnect xnetblast --- a/c++/src/objtools/align_format/Makefile.align_format.lib +++ b/c++/src/objtools/align_format/Makefile.align_format.lib @@ -13,6 +13,10 @@ @@ -92,24 +102,29 @@ Last-Update: 2011-08-28 # CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -@@ -12,3 +12,5 @@ +@@ -12,7 +12,7 @@ WATCHERS = todorov dicuccio grichenk +- +DLL_LIB = xobjmgr seqset seq xser tables xncbi -+ + + USES_LIBRARIES = \ + tables xobjutil --- a/c++/src/objtools/readers/Makefile.xobjread.lib +++ b/c++/src/objtools/readers/Makefile.xobjread.lib -@@ -20,5 +20,5 @@ +@@ -21,7 +21,7 @@ message_listener line_error -DLL_LIB = creaders +DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi + + --- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib -@@ -12,6 +12,6 @@ +@@ -12,7 +12,7 @@ mask_writer_blastdb_maskinfo ASN_DEP = seqset @@ -117,6 +132,7 @@ Last-Update: 2011-08-28 +DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi WATCHERS = morgulis camacho + --- a/c++/src/objtools/simple/Makefile.xobjsimple.lib +++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib @@ -7,6 +7,8 @@ @@ -141,13 +157,15 @@ Last-Update: 2011-08-28 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -@@ -7,4 +7,6 @@ +@@ -7,6 +7,8 @@ ASN_DEP = blastdb seqset +DLL_LIB = seqdb xobjmgr seqset seq xncbi + WATCHERS = camacho + + --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib @@ -5,6 +5,8 @@ @@ -159,14 +177,6 @@ Last-Update: 2011-08-28 ASN_DEP = blastdb xnetblast WATCHERS = camacho ---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib -+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib -@@ -5,3 +5,5 @@ - CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG_CPPFLAGS) - LIB = gene_info - SRC = gene_info gene_info_reader file_utils -+ -+DLL_LIB = xncbi --- a/c++/src/algo/blast/api/Makefile.xblast.lib +++ b/c++/src/algo/blast/api/Makefile.xblast.lib @@ -74,14 +74,15 @@ @@ -224,70 +234,73 @@ Last-Update: 2011-08-28 WATCHERS = lavr --- a/c++/src/connect/ext/Makefile.xconnext.lib +++ b/c++/src/connect/ext/Makefile.xconnext.lib -@@ -6,4 +6,6 @@ +@@ -6,6 +6,8 @@ LIB = xconnext +DLL_LIB = xconnect xncbi + WATCHERS = lavr + + --- a/c++/src/objects/blast/Makefile.blast.lib +++ b/c++/src/objects/blast/Makefile.blast.lib -@@ -1,4 +1,6 @@ +@@ -1,6 +1,8 @@ LIB = xnetblast SRC = blast__ blast___ names +DLL_LIB = scoremat seqset seq xser xncbi + WATCHERS = camacho + + --- a/c++/src/objects/blastxml/Makefile.blastxml.lib +++ b/c++/src/objects/blastxml/Makefile.blastxml.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = blastxml SRC = blastxml__ blastxml___ -+ -+DLL_LIB = xser xncbi ---- a/c++/src/objects/entrez2/Makefile.entrez2.lib -+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib -@@ -2,3 +2,5 @@ - LIB = entrez2 - SRC = entrez2__ entrez2___ -+ +DLL_LIB = xser xncbi ---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib -+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib -@@ -4,3 +4,5 @@ - - LIB = entrez2cli - SRC = entrez2_client entrez2_client_ + -+DLL_LIB = entrez2 xser xconnect xutil xncbi + + USES_LIBRARIES = \ + xser --- a/c++/src/objects/scoremat/Makefile.scoremat.lib +++ b/c++/src/objects/scoremat/Makefile.scoremat.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = scoremat SRC = scoremat__ scoremat___ -+ + +DLL_LIB = seqset seq general xser xncbi ++ + + USES_LIBRARIES = \ + seqset --- a/c++/src/objects/seqedit/Makefile.seqedit.lib +++ b/c++/src/objects/seqedit/Makefile.seqedit.lib -@@ -1,3 +1,4 @@ +@@ -1,6 +1,7 @@ LIB = seqedit SRC = seqedit__ seqedit___ - + +DLL_LIB = seqset seq general xser xncbi + + + USES_LIBRARIES = \ --- a/c++/src/objects/submit/Makefile.submit.lib +++ b/c++/src/objects/submit/Makefile.submit.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = submit SRC = submit__ submit___ -+ + +DLL_LIB = seqset seq biblio general xser xncbi ++ + + USES_LIBRARIES = \ + seqset --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib -@@ -8,5 +8,7 @@ +@@ -8,6 +8,8 @@ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci LIB = xobjutil @@ -295,6 +308,7 @@ Last-Update: 2011-08-28 + WATCHERS = ucko vasilche kornbluh + --- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib +++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib @@ -11,6 +11,7 @@ @@ -318,7 +332,7 @@ Last-Update: 2011-08-28 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,4 +12,7 @@ +@@ -12,6 +12,9 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) @@ -326,9 +340,11 @@ Last-Update: 2011-08-28 + xobjmgr seq xutil xncbi + WATCHERS = vasilche + + --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib -@@ -15,4 +15,7 @@ +@@ -15,6 +15,9 @@ DLL_LIB = DLL_DLIB = $(GENBANK_READER_LDEP) @@ -336,6 +352,8 @@ Last-Update: 2011-08-28 + xser xconnect xcompress xutil xncbi + WATCHERS = vasilche + + --- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib @@ -12,6 +12,8 @@ @@ -360,7 +378,7 @@ Last-Update: 2011-08-28 WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib +++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib -@@ -12,6 +12,9 @@ +@@ -12,7 +12,10 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) # Dependencies for shared library (disabled due to problems on Darwin) @@ -371,6 +389,7 @@ Last-Update: 2011-08-28 + WATCHERS = vasilche + --- a/c++/src/util/compress/api/Makefile.compress.lib +++ b/c++/src/util/compress/api/Makefile.compress.lib @@ -7,7 +7,7 @@ @@ -384,17 +403,19 @@ Last-Update: 2011-08-28 WATCHERS = ivanov --- a/c++/src/util/sequtil/Makefile.sequtil.lib +++ b/c++/src/util/sequtil/Makefile.sequtil.lib -@@ -3,4 +3,6 @@ +@@ -3,6 +3,8 @@ LIB = sequtil SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared +DLL_LIB = xncbi + WATCHERS = shomrat + + --- a/c++/src/corelib/Makefile.test_boost.lib +++ b/c++/src/corelib/Makefile.test_boost.lib @@ -3,6 +3,8 @@ - SRC = test_boost + SRC = test_boost teamcity_messages LIB = test_boost +DLL_LIB = xncbi @@ -415,15 +436,19 @@ Last-Update: 2011-08-28 USE_PCH = no --- a/c++/src/objects/biblio/Makefile.biblio.lib +++ b/c++/src/objects/biblio/Makefile.biblio.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = biblio SRC = biblio__ biblio___ citation_base -+ + +DLL_LIB = general xser xncbi ++ + + USES_LIBRARIES = \ + general --- a/c++/src/objects/blastdb/Makefile.blastdb.lib +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib @@ -1,5 +1,7 @@ - # $Id: Makefile.blastdb.lib 395653 2013-04-12 14:33:22Z vakatov $ + # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $ + +DLL_LIB = seq xser xncbi @@ -432,93 +457,125 @@ Last-Update: 2011-08-28 --- a/c++/src/objects/general/Makefile.general.lib +++ b/c++/src/objects/general/Makefile.general.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = general SRC = general__ general___ uoconv -+ + +DLL_LIB = xser xncbi ++ + + USES_LIBRARIES = \ + xser --- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib +++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib -@@ -3,4 +3,6 @@ +@@ -3,6 +3,8 @@ LIB = genome_collection SRC = genome_collection__ genome_collection___ +DLL_LIB = seq general xser xncbi + WATCHERS = dicuccio + + --- a/c++/src/objects/id1/Makefile.id1.lib +++ b/c++/src/objects/id1/Makefile.id1.lib -@@ -3,4 +3,6 @@ +@@ -3,6 +3,8 @@ LIB = id1 SRC = id1__ id1___ +DLL_LIB = seqset seq xser xncbi + WATCHERS = vasilche + + --- a/c++/src/objects/id2/Makefile.id2.lib +++ b/c++/src/objects/id2/Makefile.id2.lib -@@ -1,4 +1,6 @@ +@@ -1,6 +1,8 @@ LIB = id2 SRC = id2__ id2___ +DLL_LIB = seqsplit seq xser xncbi + WATCHERS = vasilche + + --- a/c++/src/objects/medline/Makefile.medline.lib +++ b/c++/src/objects/medline/Makefile.medline.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = medline SRC = medline__ medline___ -+ + +DLL_LIB = biblio general xser xncbi ++ + + USES_LIBRARIES = \ + biblio --- a/c++/src/objects/pub/Makefile.pub.lib +++ b/c++/src/objects/pub/Makefile.pub.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = pub SRC = pub__ pub___ -+ + +DLL_LIB = medline biblio xser xncbi ++ + + USES_LIBRARIES = \ + medline --- a/c++/src/objects/seq/Makefile.seq.lib +++ b/c++/src/objects/seq/Makefile.seq.lib -@@ -12,4 +12,6 @@ +@@ -12,6 +12,8 @@ seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \ seq_loc_from_string seq_loc_reverse_complementer +DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi + WATCHERS = vasilche grichenk + + --- a/c++/src/objects/seqcode/Makefile.seqcode.lib +++ b/c++/src/objects/seqcode/Makefile.seqcode.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = seqcode SRC = seqcode__ seqcode___ -+ + +DLL_LIB = xser xncbi ++ + + USES_LIBRARIES = \ + xser --- a/c++/src/objects/seqset/Makefile.seqset.lib +++ b/c++/src/objects/seqset/Makefile.seqset.lib -@@ -1,2 +1,4 @@ +@@ -1,6 +1,8 @@ LIB = seqset SRC = seqset__ seqset___ gb_release_file -+ + +DLL_LIB = seq general xser xncbi ++ + + USES_LIBRARIES = \ + $(SEQ_LIBS) pub --- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib +++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib -@@ -1,4 +1,6 @@ +@@ -1,6 +1,8 @@ LIB = seqsplit SRC = seqsplit__ seqsplit___ +DLL_LIB = seqset seq xser xncbi + WATCHERS = vasilche + + --- a/c++/src/serial/Makefile.serial.lib +++ b/c++/src/serial/Makefile.serial.lib -@@ -18,4 +18,6 @@ +@@ -18,6 +18,8 @@ LIB = xser +DLL_LIB = xutil xncbi + WATCHERS = gouriano + + --- a/c++/src/util/Makefile.util.lib +++ b/c++/src/util/Makefile.util.lib @@ -12,6 +12,7 @@ @@ -553,7 +610,7 @@ Last-Update: 2011-08-28 --- a/c++/src/objmgr/split/Makefile.id2_split.lib +++ b/c++/src/objmgr/split/Makefile.id2_split.lib -@@ -17,6 +17,6 @@ +@@ -17,7 +17,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) @@ -561,6 +618,7 @@ Last-Update: 2011-08-28 +DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi WATCHERS = vasilche + --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib @@ -8,6 +8,9 @@ diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index b9e30ad1..73b0d625 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 -@@ -5923,7 +5923,7 @@ +@@ -7479,7 +7479,7 @@ 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 -@@ -1620,7 +1620,7 @@ +@@ -1836,7 +1836,7 @@ break ;; /* ) diff --git a/debian/patches/series b/debian/patches/series index 0bc4d482..b74b155f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -6,4 +6,3 @@ no_multiarch_rpath use_pie_for_apps skip_services_unit_test fix_configure -include_typeinfo diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps index 7e0b2c0d..1900f335 100644 --- a/debian/patches/use_pie_for_apps +++ b/debian/patches/use_pie_for_apps @@ -18,9 +18,9 @@ Last-Update: 2012-05-10 SOURCES = @UNIX_SRC@ $(SRC) ### Standard application build rules -@@ -122,7 +122,7 @@ +@@ -133,7 +133,7 @@ else - $(XAPP): $(XOBJ) $(XLIBDEP) + $(XAPP): $(XOBJ) $(XOBJ2) $(XLIBDEP) @-$(RM) .$(XAPP).stamp - $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER) + $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER) -- 2.30.2