From 2dd0c04784f63e023e48a02fba588bae43d78cee Mon Sep 17 00:00:00 2001 From: Olivier Sallou Date: Thu, 10 Dec 2015 13:00:26 +0000 Subject: [PATCH] prepare new upstream release 2.2.31 --- debian/changelog | 8 + debian/patches/allow_gcc5 | 4 +- debian/patches/fix_lib_deps | 1295 ++++++++++++++--------------- debian/patches/no_multiarch_rpath | 4 +- debian/patches/series | 2 +- debian/rules | 7 +- 6 files changed, 661 insertions(+), 659 deletions(-) diff --git a/debian/changelog b/debian/changelog index 78e5afa8..8fc12c15 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,11 @@ +ncbi-blast+ (2.2.31-1) UNRELEASED; urgency=medium + + * New upstream release + * Allow parallel build (Closes: #798277). Thanks to Aron Xu + * GCC break fix (recompile with gcc5, Closes: #793263). + + -- Olivier Sallou Thu, 10 Dec 2015 13:37:03 +0100 + ncbi-blast+ (2.2.30-4) unstable; urgency=medium * d/patches/fix_compilation: Add an upstream patch to diff --git a/debian/patches/allow_gcc5 b/debian/patches/allow_gcc5 index ea7a602c..3814965e 100644 --- a/debian/patches/allow_gcc5 +++ b/debian/patches/allow_gcc5 @@ -5,7 +5,7 @@ Forwarded: yes Last-Updated: 2015-02-16 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -5819,14 +5819,10 @@ ncbi_compiler_ver="0" +@@ -5819,14 +5819,10 @@ if test "$GCC" = "yes" ; then compiler_ver="`$real_CXX -dumpversion 2>&1`" @@ -26,7 +26,7 @@ Last-Updated: 2015-02-16 compiler="KCC" --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -800,14 +800,10 @@ ncbi_compiler_ver="0" +@@ -800,14 +800,10 @@ if test "$GCC" = "yes" ; then compiler_ver="`$real_CXX -dumpversion 2>&1`" diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 13dffeee..086900a8 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -13,656 +13,645 @@ 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/core/Makefile.blast.lib -+++ b/c++/src/algo/blast/core/Makefile.blast.lib -@@ -21,6 +21,7 @@ LIB = blast - CFLAGS = $(FAST_CFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = composition_adjustment xconnect tables - - 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 @@ SRC = sequence_istream_fasta \ - CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi -+ - ASN_DEP = seqset - - WATCHERS = morgulis ---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib -+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib -@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml blastxml2 xhtml xcgi -+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ -+ 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 -@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s - 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 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb - user_agent - LIB = xcgi - -+DLL_LIB = xutil xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) - - WATCHERS = vakatov ---- 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 - 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 -@@ -3,6 +3,7 @@ ASN_DEP = xnetblast - 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 @@ SRC = format_flags align_format_util sho - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - -+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \ -+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \ -+ xcgi xhtml tables xncbi -+ - ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST - # CFLAGS = $(FAST_CFLAGS) - # CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge - - 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 -@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \ - 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 -@@ -12,7 +12,7 @@ mask_writer_seqloc \ - mask_writer_blastdb_maskinfo - - ASN_DEP = seqset --DLL_LIB = seqdb blastdb -+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 @@ WATCHERS = jcherry - - ASN_DEP = seqset - -+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi -+ - LIB = xobjsimple - SRC = simple_om - ---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -24,6 +24,8 @@ seqdbobj - - LIB = seqdb - -+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - 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 -@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_ - - 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 @@ SRC = bdbloader_rmt remote_blastdb_adapt - - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - -+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi -+ - ASN_DEP = blastdb xnetblast - - WATCHERS = camacho ---- 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 - --SRC = $(SRC_C:%=.core_%) $(SRC_CXX) -+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%) - - LIB = xblast - - 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) - 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) - - LIB = blastinput - --DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil -+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \ -+ $(OBJREAD_LIBS) $(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 ---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib -+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib -@@ -8,6 +8,8 @@ LIB = xalgodustmask - - SRC = symdust - -+DLL_LIB = xobjmgr seq xncbi -+ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - ---- a/c++/src/connect/Makefile.xconnect.lib -+++ b/c++/src/connect/Makefile.xconnect.lib -@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM) - LIB = xconnect - PROJ_TAG = core - -+DLL_LIB = xncbi -+ - LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) - - WATCHERS = lavr ---- a/c++/src/connect/ext/Makefile.xconnext.lib -+++ b/c++/src/connect/ext/Makefile.xconnext.lib -@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper - - LIB = xconnext - -+DLL_LIB = xconnect xncbi -+ - WATCHERS = lavr - - ---- a/c++/src/objects/blast/Makefile.blast.lib -+++ b/c++/src/objects/blast/Makefile.blast.lib -@@ -1,6 +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 -@@ -1,6 +1,8 @@ - LIB = blastxml - SRC = blastxml__ blastxml___ - -+DLL_LIB = xser xncbi -+ - - USES_LIBRARIES = \ - xser ---- a/c++/src/objects/scoremat/Makefile.scoremat.lib -+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib -@@ -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 -@@ -1,6 +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 -@@ -1,6 +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 -@@ -8,6 +8,8 @@ ASN_DEP = submit - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci - LIB = xobjutil - -+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi -+ - 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 @@ SRC = seq_writer blastdb_dataextract bla - - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - -+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi - - ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST - # 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 @@ SRC = blast_services - - LIB = blast_services - -+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS) - CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,6 +12,9 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \ -+ id2 id1 ncbi_xreader 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 -@@ -15,6 +15,9 @@ LIB_OR_DLL = both - DLL_LIB = - DLL_DLIB = $(GENBANK_READER_LDEP) - -+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ -+ xser xconnect xcompress xutil xncbi -+ - WATCHERS = vasilche - - ---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - - WATCHERS = vasilche ---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib -+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = xconnect ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - - 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 - CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) - - # Dependencies for shared library (disabled due to problems on Darwin) --# DLL_LIB = xconnect ncbi_xreader$(DLL) -+DLL_LIB = xconnect ncbi_xreader$(DLL) -+ -+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi -+ - - WATCHERS = vasilche - ---- a/c++/src/util/compress/api/Makefile.compress.lib -+++ b/c++/src/util/compress/api/Makefile.compress.lib -@@ -7,7 +7,7 @@ LIB = xcompress - - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - --DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) -+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi - LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS) - - WATCHERS = ivanov ---- a/c++/src/util/sequtil/Makefile.sequtil.lib -+++ b/c++/src/util/sequtil/Makefile.sequtil.lib -@@ -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 teamcity_messages - LIB = test_boost - -+DLL_LIB = xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - - REQUIRES = Boost.Test.Included ---- a/c++/src/corelib/Makefile.test_mt.lib -+++ b/c++/src/corelib/Makefile.test_mt.lib -@@ -3,6 +3,8 @@ - SRC = test_mt - LIB = test_mt - -+DLL_LIB = xncbi -+ - # REQUIRES = MT - - USE_PCH = no ---- a/c++/src/objects/biblio/Makefile.biblio.lib -+++ b/c++/src/objects/biblio/Makefile.biblio.lib -@@ -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 427424 2014-02-20 13:38:50Z gouriano $ - -+ -+DLL_LIB = seq xser xncbi - LIB = blastdb - SRC = blastdb__ blastdb___ - ---- a/c++/src/objects/general/Makefile.general.lib -+++ b/c++/src/objects/general/Makefile.general.lib -@@ -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 -@@ -3,6 +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 -@@ -3,6 +3,8 @@ ASN_DEP = seq - 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 -@@ -1,6 +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 -@@ -1,6 +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 -@@ -1,6 +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 -@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport - 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 -@@ -1,6 +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 -@@ -1,6 +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 -@@ -1,6 +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 -@@ -18,6 +18,8 @@ SRC = \ - - 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 @@ SRC = random_gen utf8 checksum bytesrc s - LIB = xutil - PROJ_TAG = core - -+DLL_LIB = xncbi - LIBS = $(ORIG_LIBS) - - WATCHERS = vakatov kornbluh ---- a/c++/src/util/xregexp/Makefile.xregexp.lib -+++ b/c++/src/util/xregexp/Makefile.xregexp.lib -@@ -6,7 +6,7 @@ LIB = xregexp - - CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) - --DLL_LIB = $(PCRE_LIB) -+DLL_LIB = $(PCRE_LIB) xncbi - LIBS = $(PCRE_LIBS) - - WATCHERS = ivanov ---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib -+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib -@@ -8,6 +8,8 @@ LIB = xalgosegmask - - SRC = segmask - -+DLL_LIB = blast xobjmgr xncbi -+ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - ---- 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 - - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - --DLL_LIB = $(SOBJMGR_LIBS) -+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 @@ SRC = writedb writedb_impl writedb_volum - - LIB = writedb - -+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \ -+ xser sequtil xutil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - CXXFLAGS = $(FAST_CXXFLAGS) ---- 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/dbindex/makeindex/Makefile.makeindex.app -+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app -@@ -2,7 +2,7 @@ APP = makembindex - SRC = main mkindex_app - - LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \ -- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS) -+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - - CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/build-system/library_relations.txt -+++ b/c++/src/build-system/library_relations.txt -@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS) - xasmcompare needs pub - xasn needs xhtml - xasn needs3party $(NCBI_C_ncbi) --xblast includes blast -+xblast needs blast - xblast needs xalgoblastdbindex - xblast needs xalgodustmask - xblast needs xalgowinmask +--- a/c++/src/algo/blast/Makefile.blast_macros.mk ++++ b/c++/src/algo/blast/Makefile.blast_macros.mk +@@ -18,7 +18,7 @@ + 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 @@ + deltablast_options \ + deltablast + +-SRC = $(SRC_C:%=.core_%) $(SRC_CXX) ++SRC = $(SRC_CXX) # $(SRC_C:%=.core_%) + + LIB = xblast + + 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) + 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 @@ + + LIB = blastinput + +-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ++ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \ ++ $(OBJREAD_LIBS) $(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 +--- a/c++/src/algo/blast/core/Makefile.blast.lib ++++ b/c++/src/algo/blast/core/Makefile.blast.lib +@@ -21,6 +21,7 @@ + CFLAGS = $(FAST_CFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = composition_adjustment xconnect tables + + WATCHERS = madden camacho fongah2 + +--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib ++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +@@ -11,6 +11,8 @@ + CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi ++ + ASN_DEP = seqset + + 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 @@ + SRC = main mkindex_app + + LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \ +- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS) ++ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS) + LIB = $(LIB_:%=%$(STATIC)) + + CXXFLAGS = $(FAST_CXXFLAGS) +--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib ++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib +@@ -7,7 +7,8 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) + +-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi ++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ ++ seq general xser tables xncbi blastxml2 + + WATCHERS = jianye zaretska madden camacho fongah2 + +--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib ++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib +@@ -8,6 +8,8 @@ + + SRC = symdust + ++DLL_LIB = xobjmgr seq xncbi ++ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + +--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib ++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib +@@ -8,6 +8,8 @@ + + SRC = segmask + ++DLL_LIB = blast xobjmgr xncbi ++ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + +--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib ++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -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/build-system/library_relations.txt ++++ b/c++/src/build-system/library_relations.txt +@@ -1163,7 +1163,7 @@ + xasmcompare needs pub + xasn needs xhtml + xasn needs3party $(NCBI_C_ncbi) +-xblast includes blast ++xblast needs blast + xblast needs xalgoblastdbindex + xblast needs xalgodustmask + xblast needs xalgowinmask +--- a/c++/src/cgi/Makefile.cgi.lib ++++ b/c++/src/cgi/Makefile.cgi.lib +@@ -9,6 +9,8 @@ + user_agent + LIB = xcgi + ++DLL_LIB = xutil xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov +--- a/c++/src/connect/Makefile.xconnect.lib ++++ b/c++/src/connect/Makefile.xconnect.lib +@@ -14,6 +14,8 @@ + LIB = xconnect + PROJ_TAG = core + ++DLL_LIB = xncbi ++ + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr +--- a/c++/src/corelib/Makefile.test_boost.lib ++++ b/c++/src/corelib/Makefile.test_boost.lib +@@ -3,6 +3,8 @@ + SRC = test_boost teamcity_messages + LIB = test_boost + ++DLL_LIB = xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) + + REQUIRES = Boost.Test.Included +--- a/c++/src/corelib/Makefile.test_mt.lib ++++ b/c++/src/corelib/Makefile.test_mt.lib +@@ -3,6 +3,8 @@ + SRC = test_mt + LIB = test_mt + ++DLL_LIB = xncbi ++ + # REQUIRES = MT + + USE_PCH = no +--- a/c++/src/html/Makefile.html.lib ++++ b/c++/src/html/Makefile.html.lib +@@ -7,6 +7,8 @@ + commentdiag indentstream html_exception writer_htmlenc + LIB = xhtml + ++DLL_LIB = xncbi ++ + WATCHERS = ivanov + + +--- a/c++/src/objects/biblio/Makefile.biblio.lib ++++ b/c++/src/objects/biblio/Makefile.biblio.lib +@@ -1,6 +1,8 @@ + LIB = biblio + SRC = biblio__ biblio___ citation_base + ++DLL_LIB = general xser xncbi ++ + + USES_LIBRARIES = \ + general +--- a/c++/src/objects/blast/Makefile.blast.lib ++++ b/c++/src/objects/blast/Makefile.blast.lib +@@ -1,6 +1,8 @@ + LIB = xnetblast + SRC = blast__ blast___ names + ++DLL_LIB = scoremat seqset seq xser xncbi ++ + WATCHERS = camacho + + +--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib ++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib +@@ -3,6 +3,7 @@ + LIB = xnetblastcli + SRC = blastclient blastclient_ + ++DLL_LIB = xnetblast xser xconnect xutil xncbi + + USES_LIBRARIES = \ + xconnect xnetblast +--- a/c++/src/objects/blastdb/Makefile.blastdb.lib ++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib +@@ -1,5 +1,7 @@ + # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $ + ++ ++DLL_LIB = seq xser xncbi + LIB = blastdb + SRC = blastdb__ blastdb___ + +--- a/c++/src/objects/blastxml/Makefile.blastxml.lib ++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib +@@ -1,6 +1,8 @@ + LIB = blastxml + SRC = blastxml__ blastxml___ + ++DLL_LIB = xser xncbi ++ + + USES_LIBRARIES = \ + xser +--- a/c++/src/objects/general/Makefile.general.lib ++++ b/c++/src/objects/general/Makefile.general.lib +@@ -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 +@@ -3,6 +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 +@@ -3,6 +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 +@@ -1,6 +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 +@@ -1,6 +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 +@@ -1,6 +1,8 @@ + LIB = pub + SRC = pub__ pub___ + ++DLL_LIB = medline biblio xser xncbi ++ + + USES_LIBRARIES = \ + medline +--- a/c++/src/objects/scoremat/Makefile.scoremat.lib ++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib +@@ -1,6 +1,8 @@ + LIB = scoremat + SRC = scoremat__ scoremat___ + ++DLL_LIB = seqset seq general xser xncbi ++ + + USES_LIBRARIES = \ + seqset +--- a/c++/src/objects/seq/Makefile.seq.lib ++++ b/c++/src/objects/seq/Makefile.seq.lib +@@ -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 +@@ -1,6 +1,8 @@ + LIB = seqcode + SRC = seqcode__ seqcode___ + ++DLL_LIB = xser xncbi ++ + + USES_LIBRARIES = \ + xser +--- a/c++/src/objects/seqedit/Makefile.seqedit.lib ++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib +@@ -1,6 +1,7 @@ + LIB = seqedit + SRC = seqedit__ seqedit___ +- ++ ++DLL_LIB = seqset seq general xser xncbi + + + USES_LIBRARIES = \ +--- a/c++/src/objects/seqset/Makefile.seqset.lib ++++ b/c++/src/objects/seqset/Makefile.seqset.lib +@@ -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 +@@ -1,6 +1,8 @@ + LIB = seqsplit + SRC = seqsplit__ seqsplit___ + ++DLL_LIB = seqset seq xser xncbi ++ + WATCHERS = vasilche + + +--- a/c++/src/objects/submit/Makefile.submit.lib ++++ b/c++/src/objects/submit/Makefile.submit.lib +@@ -1,6 +1,8 @@ + LIB = submit + SRC = submit__ submit___ + ++DLL_LIB = seqset seq biblio general xser xncbi ++ + + USES_LIBRARIES = \ + seqset +--- a/c++/src/objmgr/split/Makefile.id2_split.lib ++++ b/c++/src/objmgr/split/Makefile.id2_split.lib +@@ -17,7 +17,7 @@ + + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + +-DLL_LIB = $(SOBJMGR_LIBS) ++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi + + WATCHERS = vasilche + +--- a/c++/src/objmgr/util/Makefile.util.lib ++++ b/c++/src/objmgr/util/Makefile.util.lib +@@ -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 + ++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi ++ + WATCHERS = ucko vasilche kornbluh + + +--- a/c++/src/objtools/align_format/Makefile.align_format.lib ++++ b/c++/src/objtools/align_format/Makefile.align_format.lib +@@ -13,6 +13,10 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) + ++DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \ ++ xobjmgr xnetblast blastdb gene_info seqset seq general xser \ ++ xcgi xhtml tables xncbi ++ + ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST + # CFLAGS = $(FAST_CFLAGS) + # CXXFLAGS = $(FAST_CXXFLAGS) +--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib ++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +@@ -12,7 +12,7 @@ + + WATCHERS = todorov dicuccio grichenk + +- ++DLL_LIB = 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 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) + ++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi + + ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST + # CFLAGS = $(FAST_CFLAGS) +--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib ++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +@@ -24,6 +24,8 @@ + + LIB = seqdb + ++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi ++ + CFLAGS = $(FAST_CFLAGS) + CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) + 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 @@ + + LIB = writedb + ++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \ ++ xser sequtil xutil xncbi ++ + CFLAGS = $(FAST_CFLAGS) + CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) +--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib ++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib +@@ -8,6 +8,8 @@ + + LIB = blast_services + ++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi ++ + CFLAGS = $(FAST_CFLAGS) + CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS) + 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 +@@ -7,6 +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 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) + ++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi ++ + ASN_DEP = blastdb xnetblast + + WATCHERS = camacho +--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib ++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +@@ -12,6 +12,9 @@ + # Dependencies for shared library + DLL_LIB = ncbi_xreader$(DLL) + ++DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \ ++ id2 id1 ncbi_xreader 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 +@@ -15,6 +15,9 @@ + DLL_LIB = + DLL_DLIB = $(GENBANK_READER_LDEP) + ++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ ++ xser xconnect xcompress xutil xncbi ++ + WATCHERS = vasilche + + +--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib ++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +@@ -12,6 +12,8 @@ + # Dependencies for shared library + DLL_LIB = ncbi_xreader$(DLL) + ++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + + WATCHERS = vasilche +--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib ++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib +@@ -12,6 +12,8 @@ + # Dependencies for shared library + DLL_LIB = xconnect ncbi_xreader$(DLL) + ++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + + 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 @@ + CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) + + # Dependencies for shared library (disabled due to problems on Darwin) +-# DLL_LIB = xconnect ncbi_xreader$(DLL) ++DLL_LIB = xconnect ncbi_xreader$(DLL) ++ ++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi ++ + + WATCHERS = vasilche + +--- a/c++/src/objtools/readers/Makefile.xobjread.lib ++++ b/c++/src/objtools/readers/Makefile.xobjread.lib +@@ -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 +@@ -12,7 +12,7 @@ + mask_writer_blastdb_maskinfo + + ASN_DEP = seqset +-DLL_LIB = seqdb blastdb ++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 @@ + + ASN_DEP = seqset + ++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi ++ + LIB = xobjsimple + SRC = simple_om + +--- a/c++/src/serial/Makefile.serial.lib ++++ b/c++/src/serial/Makefile.serial.lib +@@ -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 @@ + LIB = xutil + PROJ_TAG = core + ++DLL_LIB = xncbi + LIBS = $(ORIG_LIBS) + + WATCHERS = vakatov kornbluh +--- a/c++/src/util/compress/api/Makefile.compress.lib ++++ b/c++/src/util/compress/api/Makefile.compress.lib +@@ -7,7 +7,7 @@ + + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + +-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) ++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi + LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS) + + WATCHERS = ivanov +--- a/c++/src/util/sequtil/Makefile.sequtil.lib ++++ b/c++/src/util/sequtil/Makefile.sequtil.lib +@@ -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/util/xregexp/Makefile.xregexp.lib ++++ b/c++/src/util/xregexp/Makefile.xregexp.lib +@@ -6,7 +6,7 @@ + + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) + +-DLL_LIB = $(PCRE_LIB) ++DLL_LIB = $(PCRE_LIB) xncbi + LIBS = $(PCRE_LIBS) + + WATCHERS = ivanov diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index 73b0d625..169cc2fe 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -7479,7 +7479,7 @@ +@@ -7480,7 +7480,7 @@ break ;; /* ) @@ -21,7 +21,7 @@ Last-Update: 2011-08-28 esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -1836,7 +1836,7 @@ +@@ -1837,7 +1837,7 @@ break ;; /* ) diff --git a/debian/patches/series b/debian/patches/series index 74dbdd0e..0c3e318a 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,5 @@ enable_clean_after_failed_compile -hurd_fixes +#hurd_fixes legacy_rename_rpsblast fix_lib_deps no_multiarch_rpath diff --git a/debian/rules b/debian/rules index 84034370..fa3df8ae 100755 --- a/debian/rules +++ b/debian/rules @@ -4,6 +4,11 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +NUMJOBS=1 +ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) +endif + DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \ --without-makefile-auto-update --with-flat-makefile --without-caution \ @@ -42,7 +47,7 @@ override_dh_auto_configure: override_dh_auto_build: cd c++/BUILD/build && \ - make -f Makefile.flat all_projects="$(proj)" + make -j$(NUMJOBS) -f Makefile.flat all_projects="$(proj)" # make all_r -- 2.30.2