From: Olivier Sallou Date: Thu, 1 Dec 2016 14:42:13 +0000 (+0100) Subject: new upstream release 2.5.0, update patches to match release X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~198 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=87072b8536628e3b55bed49026ae73ce749cfeb4;p=ncbi-blast%2B.git new upstream release 2.5.0, update patches to match release --- diff --git a/debian/changelog b/debian/changelog index da01b5c3..d4b1cf98 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ncbi-blast+ (2.5.0-1) unstable; urgency=medium + + * New upstream release + + -- Olivier Sallou Thu, 01 Dec 2016 14:40:17 +0100 + ncbi-blast+ (2.4.0-3) unstable; urgency=medium * debian/rules: diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index f333f81a..57cbc8c8 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -13,22 +13,11 @@ Subject: ensure that all libraries link against all direct dependencies Debian-Bug: 633567. Author: Aaron M. Ucko Last-Update: 2014-12-02 ---- a/c++/src/algo/blast/Makefile.blast_macros.mk -+++ b/c++/src/algo/blast/Makefile.blast_macros.mk -@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \ - BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS) - - # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS --BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \ -+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \ - xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \ - $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr - # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS) --- a/c++/src/algo/blast/api/Makefile.xblast.lib +++ b/c++/src/algo/blast/api/Makefile.xblast.lib -@@ -74,14 +74,15 @@ cdd_pssm_input \ - deltablast_options \ - deltablast +@@ -76,14 +76,15 @@ + magicblast_options \ + magicblast -SRC = $(SRC_C:%=.core_%) $(SRC_CXX) +SRC = $(SRC_CXX) # $(SRC_C:%=.core_%) @@ -46,7 +35,7 @@ Last-Update: 2014-12-02 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib -@@ -24,7 +24,9 @@ SRC = $(SRC_CXX) +@@ -26,7 +26,9 @@ LIB = blastinput @@ -59,8 +48,8 @@ Last-Update: 2014-12-02 ASN_DEP = seqset xnetblast --- a/c++/src/algo/blast/core/Makefile.blast.lib +++ b/c++/src/algo/blast/core/Makefile.blast.lib -@@ -23,6 +23,7 @@ LDFLAGS = $(FAST_LDFLAGS) - +@@ -23,6 +23,7 @@ + LDFLAGS = $(FAST_LDFLAGS) WATCHERS = madden camacho fongah2 +DLL_LIB = composition_adjustment xconnect tables @@ -69,7 +58,7 @@ Last-Update: 2014-12-02 composition_adjustment connect tables --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib -@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \ +@@ -11,6 +11,8 @@ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) @@ -80,7 +69,7 @@ Last-Update: 2014-12-02 WATCHERS = morgulis --- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app +++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app -@@ -2,7 +2,7 @@ APP = makembindex +@@ -2,7 +2,7 @@ SRC = main mkindex_app LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \ @@ -91,7 +80,7 @@ Last-Update: 2014-12-02 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib +++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib -@@ -8,6 +8,8 @@ LIB = xalgodustmask +@@ -8,6 +8,8 @@ SRC = symdust @@ -102,7 +91,7 @@ Last-Update: 2014-12-02 --- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib +++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib -@@ -8,6 +8,8 @@ LIB = xalgosegmask +@@ -8,6 +8,8 @@ SRC = segmask @@ -113,7 +102,7 @@ Last-Update: 2014-12-02 --- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib +++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib -@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s +@@ -21,7 +21,7 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) @@ -124,7 +113,7 @@ Last-Update: 2014-12-02 seqmasks_io --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt -@@ -1331,7 +1331,7 @@ xbiosample_util needs $(OBJEDIT_LIBS) +@@ -1287,7 +1287,7 @@ xbiosample_util needs $(XFORMAT_LIBS) xbiosample_util needs xalnmgr xbiosample_util needs xmlwrapp @@ -135,7 +124,7 @@ Last-Update: 2014-12-02 xblast needs xalgowinmask --- a/c++/src/cgi/Makefile.cgi.lib +++ b/c++/src/cgi/Makefile.cgi.lib -@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb +@@ -9,6 +9,8 @@ user_agent LIB = xcgi @@ -146,7 +135,7 @@ Last-Update: 2014-12-02 WATCHERS = vakatov --- a/c++/src/connect/Makefile.xconnect.lib +++ b/c++/src/connect/Makefile.xconnect.lib -@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM) +@@ -14,6 +14,8 @@ LIB = xconnect PROJ_TAG = core @@ -179,7 +168,7 @@ Last-Update: 2014-12-02 USE_PCH = no --- a/c++/src/html/Makefile.html.lib +++ b/c++/src/html/Makefile.html.lib -@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se +@@ -7,6 +7,8 @@ commentdiag indentstream html_exception writer_htmlenc LIB = xhtml @@ -190,7 +179,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objects/blast/Makefile.blast.lib +++ b/c++/src/objects/blast/Makefile.blast.lib -@@ -3,6 +3,8 @@ SRC = blast__ blast___ names +@@ -3,6 +3,8 @@ DLL_LIB = seqset scoremat @@ -201,7 +190,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objects/blastdb/Makefile.blastdb.lib +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib -@@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___ +@@ -5,6 +5,8 @@ DLL_LIB = xser @@ -223,7 +212,7 @@ Last-Update: 2014-12-02 xser --- a/c++/src/objects/id1/Makefile.id1.lib +++ b/c++/src/objects/id1/Makefile.id1.lib -@@ -5,6 +5,8 @@ SRC = id1__ id1___ +@@ -5,6 +5,8 @@ DLL_LIB = seqset @@ -245,7 +234,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objects/seq/Makefile.seq.lib +++ b/c++/src/objects/seq/Makefile.seq.lib -@@ -14,6 +14,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport +@@ -14,6 +14,8 @@ DLL_LIB = seqcode pub general xser sequtil @@ -311,7 +300,7 @@ Last-Update: 2014-12-02 seqset --- a/c++/src/objmgr/split/Makefile.id2_split.lib +++ b/c++/src/objmgr/split/Makefile.id2_split.lib -@@ -17,7 +17,7 @@ LIB = id2_split +@@ -17,7 +17,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) @@ -322,18 +311,18 @@ Last-Update: 2014-12-02 --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib -@@ -11,6 +11,8 @@ LIB = xobjutil +@@ -11,6 +11,8 @@ DLL_LIB = $(SOBJMGR_LIBS) +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi + - WATCHERS = ucko vasilche kornbluh + WATCHERS = ucko vasilche --- a/c++/src/objtools/align_format/Makefile.align_format.lib +++ b/c++/src/objtools/align_format/Makefile.align_format.lib -@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho +@@ -13,6 +13,10 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) @@ -346,18 +335,17 @@ Last-Update: 2014-12-02 # CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -@@ -14,7 +14,7 @@ DLL_LIB = tables +@@ -14,6 +14,7 @@ - WATCHERS = todorov dicuccio grichenk + WATCHERS = grichenk -- +DLL_LIB = xobjutil xobjmgr seqset seq xser tables xncbi USES_LIBRARIES = \ tables xobjutil --- 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 @@ SRC = seq_writer blastdb_dataextract bla +@@ -11,6 +11,7 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) @@ -367,7 +355,7 @@ Last-Update: 2014-12-02 # CFLAGS = $(FAST_CFLAGS) --- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -25,6 +25,8 @@ seqdbobj +@@ -25,6 +25,8 @@ LIB = seqdb DLL_LIB = blastdb $(SOBJMGR_LIBS) @@ -378,7 +366,7 @@ Last-Update: 2014-12-02 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib -@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum +@@ -8,6 +8,9 @@ LIB = writedb @@ -390,18 +378,18 @@ Last-Update: 2014-12-02 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/blast/services/Makefile.blast_services.lib +++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib -@@ -10,6 +10,8 @@ LIB = blast_services +@@ -10,6 +10,8 @@ DLL_LIB = xnetblastcli xnetblast +DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi + CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS) - CXXFLAGS = $(FAST_CXXFLAGS) + # -DNCBI_MODULE=NETBLAST moved to blast_services.*pp to avoid misnamed modules in DLL configurations + CPPFLAGS = $(ORIG_CPPFLAGS) --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -@@ -9,6 +9,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_ +@@ -9,6 +9,8 @@ ASN_DEP = blastdb seqset @@ -412,7 +400,7 @@ Last-Update: 2014-12-02 --- 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 -@@ -7,6 +7,8 @@ DLL_LIB = blast_services +@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) @@ -423,7 +411,7 @@ Last-Update: 2014-12-02 WATCHERS = camacho --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,6 +12,9 @@ LIB_OR_DLL = both +@@ -12,6 +12,9 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) @@ -435,9 +423,9 @@ Last-Update: 2014-12-02 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib -@@ -14,6 +14,9 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = $(GENBANK_READER_LDEP) +@@ -16,6 +16,9 @@ + + LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) +DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ + xser xconnect xcompress xutil xncbi @@ -447,7 +435,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both +@@ -12,6 +12,8 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) @@ -458,7 +446,7 @@ Last-Update: 2014-12-02 WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib +++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both +@@ -12,6 +12,8 @@ # Dependencies for shared library DLL_LIB = xconnect ncbi_xreader$(DLL) @@ -469,7 +457,7 @@ Last-Update: 2014-12-02 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 -@@ -12,7 +12,10 @@ LIB_OR_DLL = both +@@ -12,7 +12,10 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) # Dependencies for shared library (disabled due to problems on Darwin) @@ -483,7 +471,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib -@@ -12,7 +12,7 @@ mask_writer_seqloc \ +@@ -12,7 +12,7 @@ mask_writer_blastdb_maskinfo ASN_DEP = seqset @@ -494,7 +482,7 @@ Last-Update: 2014-12-02 --- a/c++/src/objtools/simple/Makefile.xobjsimple.lib +++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib -@@ -7,6 +7,8 @@ WATCHERS = jcherry +@@ -7,6 +7,8 @@ ASN_DEP = seqset @@ -505,7 +493,7 @@ Last-Update: 2014-12-02 --- a/c++/src/serial/Makefile.serial.lib +++ b/c++/src/serial/Makefile.serial.lib -@@ -20,6 +20,8 @@ LIB = xser +@@ -20,6 +20,8 @@ DLL_LIB = xutil @@ -516,17 +504,17 @@ Last-Update: 2014-12-02 --- a/c++/src/util/Makefile.util.lib +++ b/c++/src/util/Makefile.util.lib -@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s +@@ -12,6 +12,7 @@ LIB = xutil PROJ_TAG = core +DLL_LIB = xncbi LIBS = $(ORIG_LIBS) - WATCHERS = vakatov kornbluh + WATCHERS = vakatov --- a/c++/src/util/compress/api/Makefile.compress.lib +++ b/c++/src/util/compress/api/Makefile.compress.lib -@@ -7,7 +7,7 @@ LIB = xcompress +@@ -7,7 +7,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) @@ -537,7 +525,7 @@ Last-Update: 2014-12-02 WATCHERS = ivanov --- a/c++/src/util/xregexp/Makefile.xregexp.lib +++ b/c++/src/util/xregexp/Makefile.xregexp.lib -@@ -5,7 +5,7 @@ LIB = xregexp +@@ -5,7 +5,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) @@ -548,7 +536,7 @@ Last-Update: 2014-12-02 USES_LIBRARIES = \ --- a/c++/src/objtools/readers/Makefile.xobjread.lib +++ b/c++/src/objtools/readers/Makefile.xobjread.lib -@@ -20,8 +20,7 @@ SRC = read_util format_guess_ex \ +@@ -20,8 +20,7 @@ ucscregion_reader \ message_listener line_error @@ -625,7 +613,7 @@ Last-Update: 2014-12-02 xser --- a/c++/src/objects/entrez2/Makefile.entrez2.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2.lib -@@ -3,6 +3,7 @@ WATCHERS = lavr +@@ -3,6 +3,7 @@ LIB = entrez2 SRC = entrez2__ entrez2___ @@ -635,7 +623,7 @@ Last-Update: 2014-12-02 xser --- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib -@@ -5,6 +5,7 @@ ASN_DEP = entrez2 +@@ -5,6 +5,7 @@ LIB = entrez2cli SRC = entrez2_client entrez2_client_ @@ -655,7 +643,7 @@ Last-Update: 2014-12-02 xser --- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib +++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib -@@ -6,6 +6,7 @@ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG +@@ -6,6 +6,7 @@ LIB = gene_info SRC = gene_info gene_info_reader file_utils @@ -685,7 +673,7 @@ Last-Update: 2014-12-02 medlars pub pubmed --- a/c++/src/objects/mla/Makefile.mlacli.lib +++ b/c++/src/objects/mla/Makefile.mlacli.lib -@@ -5,5 +5,7 @@ SRC = mla_client mla_client_ +@@ -5,5 +5,7 @@ DLL_LIB = xconnect @@ -705,7 +693,7 @@ Last-Update: 2014-12-02 medline --- a/c++/src/objects/taxon1/Makefile.taxon1.lib +++ b/c++/src/objects/taxon1/Makefile.taxon1.lib -@@ -7,6 +7,7 @@ DLL_LIB = xconnect +@@ -7,6 +7,7 @@ WATCHERS = domrach @@ -715,7 +703,7 @@ Last-Update: 2014-12-02 $(SEQ_LIBS) pub xconnect --- a/c++/src/objects/taxon3/Makefile.taxon3.lib +++ b/c++/src/objects/taxon3/Makefile.taxon3.lib -@@ -7,6 +7,7 @@ DLL_LIB = xconnect +@@ -7,6 +7,7 @@ WATCHERS = bollin holmesbr @@ -725,7 +713,7 @@ Last-Update: 2014-12-02 $(SEQ_LIBS) pub xconnect --- a/c++/src/objects/valerr/Makefile.valerr.lib +++ b/c++/src/objects/valerr/Makefile.valerr.lib -@@ -3,6 +3,7 @@ SRC = valerr__ valerr___ +@@ -3,6 +3,7 @@ ASN_DEP = seqset @@ -735,7 +723,7 @@ Last-Update: 2014-12-02 xser --- a/c++/src/objects/valid/Makefile.valid.lib +++ b/c++/src/objects/valid/Makefile.valid.lib -@@ -4,5 +4,7 @@ SRC = valid__ valid___ +@@ -4,5 +4,7 @@ ASN_DEP = general @@ -755,7 +743,7 @@ Last-Update: 2014-12-02 $(SEQ_LIBS) pub --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib -@@ -11,6 +11,8 @@ DLL_LIB = $(BLAST_LIBS) align_format bla +@@ -11,6 +11,8 @@ WATCHERS = jianye zaretska madden camacho fongah2 @@ -766,7 +754,7 @@ Last-Update: 2014-12-02 $(BLAST_LIBS) align_format blastxml blastxml2 --- a/c++/src/objtools/cleanup/Makefile.cleanup.lib +++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib -@@ -15,6 +15,7 @@ LIB = xcleanup +@@ -15,6 +15,7 @@ LIBS = $(PCRE_LIBS) @@ -776,9 +764,9 @@ Last-Update: 2014-12-02 submit valid xobjutil --- a/c++/src/objtools/format/Makefile.xformat.lib +++ b/c++/src/objtools/format/Makefile.xformat.lib -@@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect +@@ -22,6 +22,8 @@ - WATCHERS = ludwigf dicuccio kornbluh + WATCHERS = ludwigf dicuccio +DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \ + xobjutil taxon3 $(SOBJMGR_LIBS) @@ -787,7 +775,7 @@ Last-Update: 2014-12-02 gbseq mlacli xalnmgr xcleanup --- a/c++/src/objects/blast/Makefile.xnetblastcli.lib +++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib -@@ -5,5 +5,7 @@ SRC = blastclient blastclient_ +@@ -5,5 +5,7 @@ DLL_LIB = xconnect @@ -797,7 +785,7 @@ Last-Update: 2014-12-02 xconnect xnetblast --- a/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib +++ b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib -@@ -6,6 +6,8 @@ LIB = xregexp_template_tester +@@ -6,6 +6,8 @@ DLL_LIB = $(PCRE_LIB) LIBS = $(PCRE_LIBS) diff --git a/debian/patches/fix_version_extraction b/debian/patches/fix_version_extraction index 14951cc0..650370ef 100644 --- a/debian/patches/fix_version_extraction +++ b/debian/patches/fix_version_extraction @@ -1,94 +1,5 @@ ---- a/c++/src/build-system/configure -+++ b/c++/src/build-system/configure -@@ -31352,15 +31352,21 @@ cat confdefs.h >>conftest.$ac_ext - cat >>conftest.$ac_ext <<_ACEOF - /* end confdefs.h. */ - -+cat >/dev/null <<_NCBI_EOF - #include --ncbi_cv_lib_berkeley_db_version=DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH -+_NCBI_EOF -+get_DB_VERSION() { -+ grep '^[^#]' <<_NCBI_EOF -+DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH -+_NCBI_EOF -+} -+ncbi_cv_lib_berkeley_db_version=\`get_DB_VERSION | tr -cd 0123456789.\` - - _ACEOF -- eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" \ -- 2>&5 | grep '^ncbi_cv_' \ -- | tr -d "$wschars" > conftest.sh -+ eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" > conftest.sh \ -+ 2>&5 - . ./conftest.sh -- rm -f contest* -+ rm -f conftest* - - fi - { echo "$as_me:$LINENO: result: $ncbi_cv_lib_berkeley_db_version" >&5 -@@ -33569,16 +33575,27 @@ cat confdefs.h >>conftest.$ac_ext - cat >>conftest.$ac_ext <<_ACEOF - /* end confdefs.h. */ - -+cat >/dev/null <<_NCBI_EOF - #include --ncbi_cv_lib_boost_version_num=BOOST_VERSION --ncbi_cv_lib_boost_version=BOOST_LIB_VERSION -+_NCBI_EOF -+get_BOOST_VERSION() { -+ grep '^[^#]' <<_NCBI_EOF -+BOOST_VERSION -+_NCBI_EOF -+} -+get_BOOST_LIB_VERSION() { -+ grep '^[^#]' <<_NCBI_EOF -+BOOST_LIB_VERSION -+_NCBI_EOF -+} -+ncbi_cv_lib_boost_version_num=\`get_BOOST_VERSION\` -+ncbi_cv_lib_boost_version=\`get_BOOST_LIB_VERSION | tr -d '"'\` - - _ACEOF -- eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" \ -- 2>&5 | grep '^ncbi_cv_' \ -- | tr -d "$wschars" > conftest.sh -+ eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" > conftest.sh \ -+ 2>&5 - . ./conftest.sh -- rm -f contest* -+ rm -f conftest* - - fi - { echo "$as_me:$LINENO: result: $ncbi_cv_lib_boost_version" >&5 --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -4905,14 +4905,20 @@ if test "$with_bdb" != "no" ; then - AC_CACHE_CHECK([Berkeley DB version (4.3 or newer required)], - ncbi_cv_lib_berkeley_db_version, - [AC_LANG_CONFTEST([AC_LANG_SOURCE([[ -+cat >/dev/null <<_NCBI_EOF - #include --ncbi_cv_lib_berkeley_db_version=DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH -+_NCBI_EOF -+get_DB_VERSION() { -+ grep '^[^#]' <<_NCBI_EOF -+DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH -+_NCBI_EOF -+} -+ncbi_cv_lib_berkeley_db_version=\`get_DB_VERSION | tr -cd 0123456789.\` - ]])]) -- eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" \ -- 2>&AS_MESSAGE_LOG_FD | grep '^ncbi_cv_' \ -- | tr -d "$wschars" > conftest.sh -+ eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" > conftest.sh \ -+ 2>&AS_MESSAGE_LOG_FD - . ./conftest.sh -- rm -f contest* -+ rm -f conftest* - ]) - case "$ncbi_cv_lib_berkeley_db_version" in - 1.* | 2.* | 3.* | 4.[[0-2]].* ) @@ -5181,15 +5187,26 @@ if test "$with_boost" != "no"; then AC_CACHE_CHECK([Boost version], ncbi_cv_lib_boost_version, diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index 6d2c913a..13d20726 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 -@@ -9000,7 +9000,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -9157,7 +9157,7 @@ solaris* ) CONF_f_runpath="-R" ;; @@ -20,7 +20,7 @@ Last-Update: 2011-06-10 irix*:* | linux*:KCC | *:Compaq ) --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -1894,7 +1894,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -1939,7 +1939,7 @@ solaris* ) CONF_f_runpath="-R" ;; diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index 70543bb9..870d1879 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 -@@ -9107,7 +9107,7 @@ echo "$as_me: WARNING: Unable to find st +@@ -9264,7 +9264,7 @@ break ;; /* ) @@ -21,7 +21,7 @@ Last-Update: 2011-08-28 esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -1961,7 +1961,7 @@ case "$compiler:$compiler_version:$with_ +@@ -2006,7 +2006,7 @@ break ;; /* ) diff --git a/debian/patches/series b/debian/patches/series index 2fd0e8c0..37dc5489 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -6,6 +6,6 @@ no_multiarch_rpath use_pie_for_apps skip_services_unit_test fix_configure -fix_version_extraction -support_recent_boost +#fix_version_extraction +#support_recent_boost support_x32 diff --git a/debian/patches/support_recent_boost b/debian/patches/support_recent_boost index 8e7bc855..d223c850 100644 --- a/debian/patches/support_recent_boost +++ b/debian/patches/support_recent_boost @@ -1,252 +1,3 @@ ---- a/c++/src/corelib/teamcity_boost.cpp -+++ b/c++/src/corelib/teamcity_boost.cpp -@@ -1,83 +1,106 @@ - /* Copyright 2011 JetBrains s.r.o. -- * -+ * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at -- * -+ * - * http://www.apache.org/licenses/LICENSE-2.0 -- * -+ * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. -- * -+ * - * $Id: teamcity_boost.cpp 488254 2015-12-29 13:56:26Z ivanov $ - */ - - #include - --#include - #include - #include - #include --#include -+#include -+#include -+#include -+ -+// In 1.59.0, they changed the name of this enum value, so we have to this hacky thing... -+#include -+#if BOOST_VERSION >= 105900 -+ #define TUT_CASE_IDENTIFIER boost::unit_test::TUT_CASE -+ #define CURRENT_TEST_NAME boost::unit_test_framework::framework::current_test_case().full_name() -+#else -+ #define TUT_CASE_IDENTIFIER boost::unit_test::tut_case -+ #define CURRENT_TEST_NAME boost::unit_test_framework::framework::current_test_case().p_name -+#endif - - #include "teamcity_messages.h" - --/// --// NOTE: Using namespace boost::unit_test breaks GPIPE Static build!! --/// --//using namespace boost::unit_test; --using namespace std; -- --namespace JetBrains { -+namespace jetbrains { namespace teamcity { -+const std::string ASSERT_CTX = "Assertion occurred in a following context:"; -+const std::string FAILURE_CTX = "Failure occurred in a following context:"; - - // Custom formatter for TeamCity messages - class TeamcityBoostLogFormatter: public boost::unit_test::unit_test_log_formatter { - TeamcityMessages messages; - std::string currentDetails; -+ std::string currentContextDetails; - std::string flowId; - - public: - TeamcityBoostLogFormatter(const std::string &_flowId); - TeamcityBoostLogFormatter(); - -- void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount); -- void log_finish(std::ostream&); -- void log_build_info(std::ostream&); -+ virtual ~TeamcityBoostLogFormatter() {} -+ -+ virtual void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount); -+ virtual void log_finish(std::ostream&); -+ virtual void log_build_info(std::ostream&); - -- void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu); -- void test_unit_finish(std::ostream&, -+ virtual void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu); -+ virtual void test_unit_finish(std::ostream&, - boost::unit_test::test_unit const& tu, - unsigned long elapsed); -- void test_unit_skipped(std::ostream&, boost::unit_test::test_unit const& tu); -+ virtual void test_unit_skipped(std::ostream&, boost::unit_test::test_unit const& tu); -+ virtual void test_unit_skipped(std::ostream&, -+ boost::unit_test::test_unit const& tu, -+ boost::unit_test::const_string reason); - -- void log_exception(std::ostream&, -+ virtual void log_exception(std::ostream&, - boost::unit_test::log_checkpoint_data const&, - boost::unit_test::const_string explanation); -+ virtual void log_exception_start(std::ostream&, -+ boost::unit_test::log_checkpoint_data const&, -+ const boost::execution_exception&); -+ virtual void log_exception_finish(std::ostream&); - -- void log_entry_start(std::ostream&, -- boost::unit_test::log_entry_data const&, -+ virtual void log_entry_start(std::ostream & out, -+ boost::unit_test::log_entry_data const & entry_data, - log_entry_types let); -- void log_entry_value(std::ostream&, boost::unit_test::const_string value); -- void log_entry_finish(std::ostream&); -+ virtual void log_entry_value(std::ostream&, boost::unit_test::const_string value); -+ virtual void log_entry_finish(std::ostream&); -+ -+ virtual void entry_context_start(std::ostream&, boost::unit_test::log_level); -+ virtual void log_entry_context(std::ostream&, boost::unit_test::const_string); -+ virtual void entry_context_finish(std::ostream&); - }; - - // Fake fixture to register formatter - struct TeamcityFormatterRegistrar { - TeamcityFormatterRegistrar() { -- if (JetBrains::underTeamcity()) { -- boost::unit_test::unit_test_log.set_formatter(new JetBrains::TeamcityBoostLogFormatter()); -- boost::unit_test::unit_test_log.set_threshold_level(boost::unit_test::runtime_config::log_level()); -+ if (underTeamcity()) { -+ boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter()); -+ boost::unit_test::unit_test_log.set_threshold_level -+ (RTCFG(but::log_level, LOG_LEVEL, log_level)); - } - } - }; -+ - BOOST_GLOBAL_FIXTURE(TeamcityFormatterRegistrar); - - // Formatter implementation --string toString(boost::unit_test::const_string bstr) { -- stringstream ss; -+static std::string toString(boost::unit_test::const_string bstr) { -+ std::stringstream ss; - - ss << bstr; - -@@ -92,19 +115,19 @@ TeamcityBoostLogFormatter::TeamcityBoost - : flowId(getFlowIdFromEnvironment()) - {} - --void TeamcityBoostLogFormatter::log_start(ostream &out, boost::unit_test::counter_t test_cases_amount) -+void TeamcityBoostLogFormatter::log_start(std::ostream &/*out*/, boost::unit_test::counter_t /*test_cases_amount*/) - {} - --void TeamcityBoostLogFormatter::log_finish(ostream &out) -+void TeamcityBoostLogFormatter::log_finish(std::ostream &/*out*/) - {} - --void TeamcityBoostLogFormatter::log_build_info(ostream &out) -+void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/) - {} - --void TeamcityBoostLogFormatter::test_unit_start(ostream &out, boost::unit_test::test_unit const& tu) { -+void TeamcityBoostLogFormatter::test_unit_start(std::ostream &out, boost::unit_test::test_unit const& tu) { - messages.setOutput(out); - -- if (tu.p_type == boost::unit_test::tut_case) { -+ if (tu.p_type == TUT_CASE_IDENTIFIER) { - messages.testStarted(tu.p_name, flowId); - } else { - messages.suiteStarted(tu.p_name, flowId); -@@ -113,11 +136,11 @@ void TeamcityBoostLogFormatter::test_uni - currentDetails.clear(); - } - --void TeamcityBoostLogFormatter::test_unit_finish(ostream &out, boost::unit_test::test_unit const& tu, unsigned long elapsed) { -+void TeamcityBoostLogFormatter::test_unit_finish(std::ostream &out, boost::unit_test::test_unit const& tu, unsigned long elapsed) { - messages.setOutput(out); - - boost::unit_test::test_results const& tr = boost::unit_test::results_collector.results(tu.p_id); -- if (tu.p_type == boost::unit_test::tut_case) { -+ if (tu.p_type == TUT_CASE_IDENTIFIER) { - if(!tr.passed()) { - if(tr.p_skipped) { - messages.testIgnored(tu.p_name, "ignored", flowId); -@@ -134,27 +157,62 @@ void TeamcityBoostLogFormatter::test_uni - } - } - --void TeamcityBoostLogFormatter::test_unit_skipped(ostream &out, boost::unit_test::test_unit const& tu) -+void TeamcityBoostLogFormatter::test_unit_skipped(std::ostream &/*out*/, boost::unit_test::test_unit const& /*tu*/) - {} - --void TeamcityBoostLogFormatter::log_exception(ostream &out, boost::unit_test::log_checkpoint_data const&, boost::unit_test::const_string explanation) { -- string what = toString(explanation); -+void TeamcityBoostLogFormatter::test_unit_skipped(std::ostream &out, boost::unit_test::test_unit const& tu, boost::unit_test::const_string reason) -+{ -+ messages.testIgnored(tu.p_name, toString(reason), flowId); -+} -+ -+void TeamcityBoostLogFormatter::log_exception(std::ostream &out, boost::unit_test::log_checkpoint_data const &, boost::unit_test::const_string explanation) { -+ std::string what = toString(explanation); - -- out << what << endl; -+ out << what << std::endl; - currentDetails += what + "\n"; - } - --void TeamcityBoostLogFormatter::log_entry_start(ostream&, boost::unit_test::log_entry_data const&, log_entry_types let) --{} -+void TeamcityBoostLogFormatter::log_exception_start(std::ostream &out, boost::unit_test::log_checkpoint_data const &data, const boost::execution_exception& excpt) { -+ log_exception(out, data, excpt.what()); -+} -+ -+void TeamcityBoostLogFormatter::log_exception_finish(std::ostream &/*out*/) {} - --void TeamcityBoostLogFormatter::log_entry_value(ostream &out, boost::unit_test::const_string value) { -+ -+void TeamcityBoostLogFormatter::log_entry_start(std::ostream & out, boost::unit_test::log_entry_data const & entry_data, log_entry_types /*let*/) -+{ -+ std::stringstream ss(std::ios_base::out); -+ -+ out << entry_data.m_file_name << "(" << entry_data.m_line_num << "): "; -+ ss << entry_data.m_file_name << "(" << entry_data.m_line_num << "): "; -+ -+ currentDetails += ss.str(); -+} -+ -+void TeamcityBoostLogFormatter::log_entry_value(std::ostream &out, boost::unit_test::const_string value) { - out << value; - currentDetails += toString(value); - } - --void TeamcityBoostLogFormatter::log_entry_finish(ostream &out) { -- out << endl; -+void TeamcityBoostLogFormatter::log_entry_finish(std::ostream &out) { -+ out << std::endl; - currentDetails += "\n"; - } - -+void TeamcityBoostLogFormatter::entry_context_start(std::ostream &out, boost::unit_test::log_level l) { -+ const std::string& initial_msg = (l == boost::unit_test::log_successful_tests ? ASSERT_CTX : FAILURE_CTX); -+ out << initial_msg; -+ currentContextDetails = initial_msg; - } -+ -+void TeamcityBoostLogFormatter::log_entry_context(std::ostream &out, boost::unit_test::const_string ctx) { -+ out << "\n " << ctx; -+ currentContextDetails += "\n " + toString(ctx); -+} -+ -+void TeamcityBoostLogFormatter::entry_context_finish(std::ostream &out) { -+ out.flush(); -+ messages.testOutput(CURRENT_TEST_NAME, currentContextDetails, flowId, TeamcityMessages::StdErr); -+} -+ -+}} // namespace teamcity, jetbrains --- a/c++/src/corelib/teamcity_messages.cpp +++ b/c++/src/corelib/teamcity_messages.cpp @@ -15,40 +15,61 @@ diff --git a/debian/patches/support_x32 b/debian/patches/support_x32 index 8c8874fc..df9fb959 100644 --- a/debian/patches/support_x32 +++ b/debian/patches/support_x32 @@ -1,6 +1,6 @@ --- a/c++/include/corelib/impl/ncbi_atomic_defs.h +++ b/c++/include/corelib/impl/ncbi_atomic_defs.h -@@ -117,7 +117,7 @@ extern "C" { +@@ -117,7 +117,7 @@ ((defined(__i386) || defined(__sparc) || defined(__x86_64)) && \ !defined(__GLIBCPP__) /* < 3.0 or >= 3.4 */) && \ (!defined(__GLIBCXX__) || !defined(NCBI_TCHECK)))