From: Debian Med Packaging Team Date: Fri, 26 Jul 2024 00:07:36 +0000 (-0400) Subject: ensure that all libraries link against all direct dependencies X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2^2^2^2^2^2~14 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=7b501f6939808ce5519f4d32b45a3adbd1e49443;p=ncbi-blast%2B.git ensure that all libraries link against all direct dependencies * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency loop between libxblast and libxalgoblastdbindex by having the former provide only the C++ BLAST API, leaving the C core only in libblast. * src/build-system/library_relations.txt: Change xblast's relationship to blast from includes to needs, accordingly. * src/algo/blast/Makefile.blast_macros.mk: Add blast to BLAST_LIBS. * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect rather than libconnect for consistency with libblast, which uses the former to keep the aforementioned cycle-breaking from causing inconsistency elsewhere. Debian-Bug: 633567. Author: Aaron M. Ucko Last-Update: 2016-12-05 Gbp-Pq: Name fix_lib_deps --- diff --git a/c++/src/algo/blast/api/Makefile.xblast.lib b/c++/src/algo/blast/api/Makefile.xblast.lib index 522d5fc4..5853e0b4 100644 --- a/c++/src/algo/blast/api/Makefile.xblast.lib +++ b/c++/src/algo/blast/api/Makefile.xblast.lib @@ -79,11 +79,11 @@ magicblast \ blast_node \ blast_usage_report -SRC = $(SRC_C:%=.core_%) $(SRC_CXX) +SRC = $(SRC_CXX) LIB = xblast -DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS) +DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS) blast seqdb seqset seq general xser xconnect sequtil tables xutil xncbi CFLAGS = $(FAST_CFLAGS) CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) diff --git a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib index f6e5d371..e5ba99a7 100644 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -27,7 +27,8 @@ SRC = $(SRC_CXX) LIB = blastinput -DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil sqlitewrapp +DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \ + seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) sqlitewrapp scoremat # should be redundant, given the above :-/ ASN_DEP = seqset xnetblast diff --git a/c++/src/algo/blast/core/Makefile.blast.lib b/c++/src/algo/blast/core/Makefile.blast.lib index bd4f6762..77ff1fab 100644 --- a/c++/src/algo/blast/core/Makefile.blast.lib +++ b/c++/src/algo/blast/core/Makefile.blast.lib @@ -23,6 +23,7 @@ CFLAGS = $(FAST_CFLAGS) LDFLAGS = $(FAST_LDFLAGS) WATCHERS = madden camacho fongah2 +DLL_LIB = composition_adjustment xconnect tables USES_LIBRARIES = \ composition_adjustment connect tables diff --git a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib index 55ea6a52..b7948a69 100644 --- 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 submit WATCHERS = morgulis diff --git a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app index 1214b65c..217ee5bc 100644 --- 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)) $(LMDB_LIB) CXXFLAGS = $(FAST_CXXFLAGS) diff --git a/c++/src/algo/blast/format/Makefile.xblastformat.lib b/c++/src/algo/blast/format/Makefile.xblastformat.lib index 04a9167d..1e197b45 100644 --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib @@ -13,6 +13,8 @@ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) WATCHERS = jianye zaretska madden camacho fongah2 +DLL_LIB = xformat $(BLAST_LIBS) align_format blastxml blastxml2 \ + xhtml xcgi xncbi USES_LIBRARIES = \ $(BLAST_LIBS) align_format blastxml blastxml2 diff --git a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib index c628ae06..c8b9d152 100644 --- 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) diff --git a/c++/src/algo/segmask/Makefile.xalgosegmask.lib b/c++/src/algo/segmask/Makefile.xalgosegmask.lib index e23a4fca..63569588 100644 --- 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) diff --git a/c++/src/algo/winmask/Makefile.xalgowinmask.lib b/c++/src/algo/winmask/Makefile.xalgowinmask.lib index 447449f9..8670dfa9 100644 --- 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 seq_masker_score_mean_glob \ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) - +DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi USES_LIBRARIES = \ seqmasks_io diff --git a/c++/src/build-system/library_relations.txt b/c++/src/build-system/library_relations.txt index 658fc979..f226bfd4 100644 --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt @@ -1369,7 +1369,7 @@ xassembly_svc needs gc_asn_access xbiosample_util needs $(OBJEDIT_LIBS) xbiosample_util needs xmlwrapp xbiosample_util needs xobjutil -xblast includes blast +xblast needs blast xblast needs utrtprof xblast needs xalgoblastdbindex xblast needs xalgodustmask diff --git a/c++/src/cgi/Makefile.cgi.lib b/c++/src/cgi/Makefile.cgi.lib index ebc511f7..d5a05c50 100644 --- a/c++/src/cgi/Makefile.cgi.lib +++ b/c++/src/cgi/Makefile.cgi.lib @@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncbires ref_args cgi_run cgi_util \ user_agent LIB = xcgi +DLL_LIB = xutil xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) WATCHERS = vakatov diff --git a/c++/src/connect/Makefile.xconnect.lib b/c++/src/connect/Makefile.xconnect.lib index 2c943db6..bf97d63e 100644 --- a/c++/src/connect/Makefile.xconnect.lib +++ b/c++/src/connect/Makefile.xconnect.lib @@ -12,6 +12,8 @@ SRC = $(SRC_C) $(SRC_CXX) $(SRC_TLS) LIB = xconnect +DLL_LIB = xncbi + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) PROJ_TAG = core diff --git a/c++/src/corelib/Makefile.test_boost.lib b/c++/src/corelib/Makefile.test_boost.lib index 158f0f91..dea40084 100644 --- 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 diff --git a/c++/src/corelib/Makefile.test_mt.lib b/c++/src/corelib/Makefile.test_mt.lib index 2292c16f..465e86a7 100644 --- 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 diff --git a/c++/src/html/Makefile.html.lib b/c++/src/html/Makefile.html.lib index 5440c0d7..a8ab060b 100644 --- a/c++/src/html/Makefile.html.lib +++ b/c++/src/html/Makefile.html.lib @@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager selection components \ commentdiag indentstream html_exception writer_htmlenc LIB = xhtml +DLL_LIB = xncbi + WATCHERS = ivanov diff --git a/c++/src/objects/blast/Makefile.blast.lib b/c++/src/objects/blast/Makefile.blast.lib index c0d6d597..c410bf6b 100644 --- a/c++/src/objects/blast/Makefile.blast.lib +++ b/c++/src/objects/blast/Makefile.blast.lib @@ -3,6 +3,8 @@ SRC = blast__ blast___ names DLL_LIB = seqset scoremat +DLL_LIB = scoremat seqset seq xser xncbi + WATCHERS = camacho diff --git a/c++/src/objects/blast/Makefile.xnetblastcli.lib b/c++/src/objects/blast/Makefile.xnetblastcli.lib index 05eb98d0..0cbddd87 100644 --- a/c++/src/objects/blast/Makefile.xnetblastcli.lib +++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib @@ -5,5 +5,7 @@ SRC = blastclient blastclient_ DLL_LIB = xconnect +DLL_LIB = xnetblast xconnect xser xutil xncbi + USES_LIBRARIES = \ xconnect xnetblast diff --git a/c++/src/objects/blastdb/Makefile.blastdb.lib b/c++/src/objects/blastdb/Makefile.blastdb.lib index 0e33ddcf..c85fb5f7 100644 --- a/c++/src/objects/blastdb/Makefile.blastdb.lib +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib @@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___ DLL_LIB = xser +DLL_LIB = seq xser xncbi + WATCHERS = camacho diff --git a/c++/src/objects/blastxml/Makefile.blastxml.lib b/c++/src/objects/blastxml/Makefile.blastxml.lib index 9eebea50..2795e05c 100644 --- 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 diff --git a/c++/src/objects/blastxml2/Makefile.blastxml2.lib b/c++/src/objects/blastxml2/Makefile.blastxml2.lib index 9269e019..050965b1 100644 --- a/c++/src/objects/blastxml2/Makefile.blastxml2.lib +++ b/c++/src/objects/blastxml2/Makefile.blastxml2.lib @@ -1,5 +1,7 @@ LIB = blastxml2 SRC = blastxml2__ blastxml2___ +DLL_LIB = xser xutil xncbi + USES_LIBRARIES = \ xser diff --git a/c++/src/objects/entrez2/Makefile.entrez2.lib b/c++/src/objects/entrez2/Makefile.entrez2.lib index 39360dcc..e1c2585e 100644 --- a/c++/src/objects/entrez2/Makefile.entrez2.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2.lib @@ -3,6 +3,7 @@ WATCHERS = lavr LIB = entrez2 SRC = entrez2__ entrez2___ +DLL_LIB = xser xutil xncbi USES_LIBRARIES = \ xser diff --git a/c++/src/objects/entrez2/Makefile.entrez2cli.lib b/c++/src/objects/entrez2/Makefile.entrez2cli.lib index 2bfb592b..28529c21 100644 --- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib @@ -5,7 +5,7 @@ ASN_DEP = entrez2 LIB = entrez2cli SRC = entrez2_client entrez2_client_ -DLL_LIB = entrez2 xconnect +DLL_LIB = entrez2 xconnect xser xutil xncbi USES_LIBRARIES = \ entrez2 xconnect diff --git a/c++/src/objects/gbseq/Makefile.gbseq.lib b/c++/src/objects/gbseq/Makefile.gbseq.lib index c6f78ba4..4374b7ff 100644 --- a/c++/src/objects/gbseq/Makefile.gbseq.lib +++ b/c++/src/objects/gbseq/Makefile.gbseq.lib @@ -1,6 +1,7 @@ LIB = gbseq SRC = gbseq__ gbseq___ +DLL_LIB = xser xutil xncbi USES_LIBRARIES = \ xser diff --git a/c++/src/objects/genomecoll/Makefile.genome_collection.lib b/c++/src/objects/genomecoll/Makefile.genome_collection.lib index 82906c32..8f5881e1 100644 --- 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 smithrg zherikov diff --git a/c++/src/objects/id1/Makefile.id1.lib b/c++/src/objects/id1/Makefile.id1.lib index 3d978e28..348686bc 100644 --- a/c++/src/objects/id1/Makefile.id1.lib +++ b/c++/src/objects/id1/Makefile.id1.lib @@ -5,6 +5,8 @@ SRC = id1__ id1___ DLL_LIB = seqset +DLL_LIB = seqset seq xser xncbi + WATCHERS = vasilche diff --git a/c++/src/objects/id2/Makefile.id2.lib b/c++/src/objects/id2/Makefile.id2.lib index d1659ae0..d1beec78 100644 --- 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 USES_LIBRARIES = \ diff --git a/c++/src/objects/medlars/Makefile.medlars.lib b/c++/src/objects/medlars/Makefile.medlars.lib index 92ffbf80..e9e95abc 100644 --- a/c++/src/objects/medlars/Makefile.medlars.lib +++ b/c++/src/objects/medlars/Makefile.medlars.lib @@ -1,6 +1,7 @@ LIB = medlars SRC = medlars__ medlars___ +DLL_LIB = biblio xser xutil xncbi USES_LIBRARIES = \ biblio diff --git a/c++/src/objects/medline/Makefile.medline.lib b/c++/src/objects/medline/Makefile.medline.lib index cfac0b8b..a01c0fa9 100644 --- a/c++/src/objects/medline/Makefile.medline.lib +++ b/c++/src/objects/medline/Makefile.medline.lib @@ -1,7 +1,7 @@ LIB = medline SRC = medline__ medline___ -DLL_LIB = biblio general +DLL_LIB = biblio general xser xncbi USES_LIBRARIES = \ biblio diff --git a/c++/src/objects/mla/Makefile.mla.lib b/c++/src/objects/mla/Makefile.mla.lib index 4ce0eb46..31bf263e 100644 --- a/c++/src/objects/mla/Makefile.mla.lib +++ b/c++/src/objects/mla/Makefile.mla.lib @@ -1,7 +1,7 @@ LIB = mla SRC = mla__ mla___ -DLL_LIB = medlars +DLL_LIB = medlars pub pubmed xser xutil xncbi USES_LIBRARIES = \ medlars pub pubmed diff --git a/c++/src/objects/mla/Makefile.mlacli.lib b/c++/src/objects/mla/Makefile.mlacli.lib index b1995e8d..55365160 100644 --- 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_ DLL_LIB = mla pubmed medlars xconnect +DLL_LIB = mla xconnect xser xutil xncbi + USES_LIBRARIES = \ mla xconnect diff --git a/c++/src/objects/pub/Makefile.pub.lib b/c++/src/objects/pub/Makefile.pub.lib index e1de6495..4082f0c3 100644 --- a/c++/src/objects/pub/Makefile.pub.lib +++ b/c++/src/objects/pub/Makefile.pub.lib @@ -1,7 +1,7 @@ LIB = pub SRC = pub__ pub___ -DLL_LIB = medline biblio +DLL_LIB = medline biblio xser xncbi USES_LIBRARIES = \ medline diff --git a/c++/src/objects/pubmed/Makefile.pubmed.lib b/c++/src/objects/pubmed/Makefile.pubmed.lib index 19e11d7b..0a45492c 100644 --- a/c++/src/objects/pubmed/Makefile.pubmed.lib +++ b/c++/src/objects/pubmed/Makefile.pubmed.lib @@ -1,6 +1,7 @@ LIB = pubmed SRC = pubmed__ pubmed___ +DLL_LIB = medline biblio xser xutil xncbi USES_LIBRARIES = \ medline diff --git a/c++/src/objects/scoremat/Makefile.scoremat.lib b/c++/src/objects/scoremat/Makefile.scoremat.lib index a83215d8..4651df1e 100644 --- a/c++/src/objects/scoremat/Makefile.scoremat.lib +++ b/c++/src/objects/scoremat/Makefile.scoremat.lib @@ -1,7 +1,7 @@ LIB = scoremat SRC = scoremat__ scoremat___ -DLL_LIB = seqset +DLL_LIB = seqset seq general xser xncbi USES_LIBRARIES = \ seqset diff --git a/c++/src/objects/seq/Makefile.seq.lib b/c++/src/objects/seq/Makefile.seq.lib index d37c4b87..ed1f4545 100644 --- a/c++/src/objects/seq/Makefile.seq.lib +++ b/c++/src/objects/seq/Makefile.seq.lib @@ -12,7 +12,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \ seq_loc_mapper_base seq_align_mapper_base seqlocinfo so_map \ seq_loc_from_string seq_loc_reverse_complementer -DLL_LIB = seqcode pub general xser sequtil +DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi WATCHERS = vasilche grichenk stakhovv gotvyans diff --git a/c++/src/objects/seqcode/Makefile.seqcode.lib b/c++/src/objects/seqcode/Makefile.seqcode.lib index e1a7bf40..869368fe 100644 --- 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 diff --git a/c++/src/objects/seqedit/Makefile.seqedit.lib b/c++/src/objects/seqedit/Makefile.seqedit.lib index 4ee708fc..a23ede98 100644 --- 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 = \ diff --git a/c++/src/objects/seqset/Makefile.seqset.lib b/c++/src/objects/seqset/Makefile.seqset.lib index 7b44c907..595d9a90 100644 --- a/c++/src/objects/seqset/Makefile.seqset.lib +++ b/c++/src/objects/seqset/Makefile.seqset.lib @@ -1,7 +1,7 @@ LIB = seqset SRC = seqset__ seqset___ gb_release_file -DLL_LIB = $(SEQ_LIBS) +DLL_LIB = $(SEQ_LIBS) xser xncbi USES_LIBRARIES = \ $(SEQ_LIBS) pub diff --git a/c++/src/objects/seqsplit/Makefile.seqsplit.lib b/c++/src/objects/seqsplit/Makefile.seqsplit.lib index bf17f46f..bef22f16 100644 --- 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 diff --git a/c++/src/objects/submit/Makefile.submit.lib b/c++/src/objects/submit/Makefile.submit.lib index 2577b2e0..5d401780 100644 --- 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 diff --git a/c++/src/objects/taxon1/Makefile.taxon1.lib b/c++/src/objects/taxon1/Makefile.taxon1.lib index 4d8c561e..c7349389 100644 --- a/c++/src/objects/taxon1/Makefile.taxon1.lib +++ b/c++/src/objects/taxon1/Makefile.taxon1.lib @@ -7,6 +7,7 @@ DLL_LIB = xconnect WATCHERS = domrach +DLL_LIB = xconnect seq xser xutil xncbi USES_LIBRARIES = \ $(SEQ_LIBS) pub xconnect diff --git a/c++/src/objects/taxon3/Makefile.taxon3.lib b/c++/src/objects/taxon3/Makefile.taxon3.lib index dc3307fb..835407c4 100644 --- a/c++/src/objects/taxon3/Makefile.taxon3.lib +++ b/c++/src/objects/taxon3/Makefile.taxon3.lib @@ -8,6 +8,7 @@ DLL_LIB = xconnect WATCHERS = stakhovv holmesbr +DLL_LIB = xconnect seq xser xutil xncbi USES_LIBRARIES = \ $(SEQ_LIBS) pub xconnect diff --git a/c++/src/objects/valerr/Makefile.valerr.lib b/c++/src/objects/valerr/Makefile.valerr.lib index c00a6055..d1cbcccc 100644 --- a/c++/src/objects/valerr/Makefile.valerr.lib +++ b/c++/src/objects/valerr/Makefile.valerr.lib @@ -3,6 +3,7 @@ SRC = valerr__ valerr___ ASN_DEP = seqset +DLL_LIB = xser xutil xncbi USES_LIBRARIES = \ xser diff --git a/c++/src/objects/valid/Makefile.valid.lib b/c++/src/objects/valid/Makefile.valid.lib index aefdc267..23438f8b 100644 --- a/c++/src/objects/valid/Makefile.valid.lib +++ b/c++/src/objects/valid/Makefile.valid.lib @@ -6,5 +6,7 @@ DLL_LIB = xregexp ASN_DEP = general +DLL_LIB = general xser xregexp xutil xncbi + USES_LIBRARIES = \ general xregexp diff --git a/c++/src/objects/variation/Makefile.variation.lib b/c++/src/objects/variation/Makefile.variation.lib index ea013fbc..a6dcb834 100644 --- a/c++/src/objects/variation/Makefile.variation.lib +++ b/c++/src/objects/variation/Makefile.variation.lib @@ -1,6 +1,7 @@ LIB = variation SRC = variation__ variation___ +DLL_LIB = seq xser xutil xncbi USES_LIBRARIES = \ $(SEQ_LIBS) pub diff --git a/c++/src/objmgr/split/Makefile.id2_split.lib b/c++/src/objmgr/split/Makefile.id2_split.lib index b12ccfd3..e2177489 100644 --- 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 diff --git a/c++/src/objmgr/util/Makefile.util.lib b/c++/src/objmgr/util/Makefile.util.lib index 3387d795..1fb5a885 100644 --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib @@ -14,6 +14,8 @@ LIB = xobjutil DLL_LIB = submit $(SOBJMGR_LIBS) +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi + WATCHERS = ucko vasilche diff --git a/c++/src/objtools/align_format/Makefile.align_format.lib b/c++/src/objtools/align_format/Makefile.align_format.lib index 87bccf0f..ea2e843e 100644 --- a/c++/src/objtools/align_format/Makefile.align_format.lib +++ b/c++/src/objtools/align_format/Makefile.align_format.lib @@ -15,6 +15,10 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) +DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \ + xobjmgr xnetblast blastdb gene_info taxon1 seqset seq general xser \ + xcgi xhtml tables xncbi + ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST # CFLAGS = $(FAST_CFLAGS) # CXXFLAGS = $(FAST_CXXFLAGS) diff --git a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib index f762fb13..3ce898ce 100644 --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib @@ -14,6 +14,7 @@ DLL_LIB = xobjutil tables WATCHERS = grichenk +DLL_LIB = xobjutil xobjmgr seqset seq xser tables xncbi USES_LIBRARIES = \ tables xobjutil diff --git a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib index f9096871..233ade36 100644 --- 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 blastdb_formatter seq_formatter 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) diff --git a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib index 26b29228..0777632a 100644 --- 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_CPPFLAGS) LIB = gene_info SRC = gene_info gene_info_reader file_utils +DLL_LIB = xncbi USES_LIBRARIES = \ xncbi diff --git a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib index f010abcf..7962bbea 100644 --- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib @@ -27,9 +27,10 @@ seqidlist_reader \ tax4blastsqlite LIB = seqdb -DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp LIBS = $(BLAST_THIRD_PARTY_LIBS) +DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp + CFLAGS = $(FAST_CFLAGS) CPPFLAGS = -DNCBI_MODULE=BLASTDB $(SQLITE3_INCLUDE) $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE) CXXFLAGS = $(FAST_CXXFLAGS) diff --git a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib index c9a026fb..49a36686 100644 --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib @@ -11,6 +11,9 @@ DLL_LIB = blastdb $(SOBJMGR_LIBS) LIB = writedb +DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \ + xser sequtil xutil xncbi + CFLAGS = $(FAST_CFLAGS) CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE) CXXFLAGS = $(FAST_CXXFLAGS) diff --git a/c++/src/objtools/blast/services/Makefile.blast_services.lib b/c++/src/objtools/blast/services/Makefile.blast_services.lib index 8d2fee28..c794e023 100644 --- 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 DLL_LIB = xnetblastcli xnetblast +DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi + CFLAGS = $(FAST_CFLAGS) # -DNCBI_MODULE=NETBLAST moved to blast_services.*pp to avoid misnamed modules in DLL configurations CPPFLAGS = $(ORIG_CPPFLAGS) diff --git a/c++/src/objtools/cleanup/Makefile.cleanup.lib b/c++/src/objtools/cleanup/Makefile.cleanup.lib index 74a1c345..0276016a 100644 --- a/c++/src/objtools/cleanup/Makefile.cleanup.lib +++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib @@ -11,7 +11,7 @@ SRC = autogenerated_cleanup autogenerated_extended_cleanup cleanup \ cleanup_pub newcleanupp capitalization_string fix_feature_id \ cleanup_message influenza_set -DLL_LIB = $(OBJEDIT_LIBS) xregexp $(PCRE_LIB) +DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS) LIB = xcleanup LIBS = $(PCRE_LIBS) diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib index e2f9bcf5..df53141d 100644 --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib @@ -3,7 +3,7 @@ LIB = ncbi_xloader_blastdb SRC = bdbloader cached_sequence local_blastdb_adapter -DLL_LIB = seqdb +DLL_LIB = seqdb xobjmgr seqset seq xncbi CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) diff --git 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 index 7228f3e5..4a0b2417 100644 --- 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 CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) +DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi + ASN_DEP = blastdb xnetblast WATCHERS = camacho diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib index 1c6004f8..b39e89e3 100644 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib @@ -12,6 +12,10 @@ LIB_OR_DLL = both # Dependencies for shared library DLL_LIB = general ncbi_xreader$(DLL) $(GENBANK_PSG_CLIENT_LDEP) +DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \ + id2 id1 ncbi_xreader $(GENBANK_PSG_CLIENT_LDEP) xobjmgr \ + seq xutil xncbi + LIBS = $(GENBANK_THIRD_PARTY_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib index f0fb8e0f..4dc09356 100644 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib @@ -16,6 +16,9 @@ DLL_LIB = $(GENBANK_READER_LDEP) LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) +DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ + xser xconnect xcompress xutil xncbi + WATCHERS = vasilche diff --git a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib index e88475d6..67e99b26 100644 --- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib @@ -12,6 +12,8 @@ LIB_OR_DLL = both # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) +DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) WATCHERS = vasilche diff --git a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib index abce7716..b0ee90f9 100644 --- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib +++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib @@ -12,6 +12,8 @@ LIB_OR_DLL = both # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_READER_LDEP) +DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) WATCHERS = vasilche diff --git 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 index b8dfdb95..f8ca7bf8 100644 --- 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 diff --git a/c++/src/objtools/format/Makefile.xformat.lib b/c++/src/objtools/format/Makefile.xformat.lib index 1abc4d42..98c6b227 100644 --- a/c++/src/objtools/format/Makefile.xformat.lib +++ b/c++/src/objtools/format/Makefile.xformat.lib @@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect WATCHERS = dicuccio gotvyans +DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \ + xobjutil taxon3 $(SOBJMGR_LIBS) USES_LIBRARIES = \ gbseq xalnmgr xcleanup diff --git a/c++/src/objtools/readers/Makefile.xobjread.lib b/c++/src/objtools/readers/Makefile.xobjread.lib index a5192c8b..c5bd99a4 100644 --- a/c++/src/objtools/readers/Makefile.xobjread.lib +++ b/c++/src/objtools/readers/Makefile.xobjread.lib @@ -29,6 +29,6 @@ SRC = reader_message reader_listener reader_message_handler \ message_listener line_error -DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging +DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging pub xser xncbi USES_LIBRARIES = submit xlogging diff --git a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib index ad8c50d5..6b21fb8d 100644 --- 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 LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) diff --git a/c++/src/objtools/simple/Makefile.xobjsimple.lib b/c++/src/objtools/simple/Makefile.xobjsimple.lib index 474723cc..e7751476 100644 --- 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 diff --git a/c++/src/serial/Makefile.serial.lib b/c++/src/serial/Makefile.serial.lib index 082d1101..e7696b59 100644 --- a/c++/src/serial/Makefile.serial.lib +++ b/c++/src/serial/Makefile.serial.lib @@ -20,6 +20,8 @@ LIB = xser DLL_LIB = xutil +DLL_LIB = xutil xncbi + WATCHERS = gouriano diff --git a/c++/src/util/Makefile.util.lib b/c++/src/util/Makefile.util.lib index a62a4d27..9ddef4fb 100644 --- a/c++/src/util/Makefile.util.lib +++ b/c++/src/util/Makefile.util.lib @@ -15,6 +15,7 @@ SRC = random_gen utf8 checksum checksum_cityhash checksum_farmhash \ LIB = xutil PROJ_TAG = core +DLL_LIB = xncbi LIBS = $(ORIG_LIBS) WATCHERS = vakatov diff --git a/c++/src/util/compress/api/Makefile.compress.lib b/c++/src/util/compress/api/Makefile.compress.lib index 952fba47..d930d08d 100644 --- 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) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) +DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) xutil xncbi LIBS = $(BZ2_LIBS) $(LZO_LIBS) $(Z_LIBS) $(ZSTD_LIBS) $(ORIG_LIBS) WATCHERS = ivanov diff --git a/c++/src/util/sequtil/Makefile.sequtil.lib b/c++/src/util/sequtil/Makefile.sequtil.lib index 2190e289..0673acc4 100644 --- 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 = grichenk ucko diff --git a/c++/src/util/xregexp/Makefile.xregexp.lib b/c++/src/util/xregexp/Makefile.xregexp.lib index 81e0f3c2..8cdc395b 100644 --- a/c++/src/util/xregexp/Makefile.xregexp.lib +++ b/c++/src/util/xregexp/Makefile.xregexp.lib @@ -5,7 +5,7 @@ LIB = xregexp CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) $(PCRE2_INCLUDE) -DLL_LIB = $(PCRE_LIB) xutil +DLL_LIB = $(PCRE_LIB) xutil xncbi LIBS = $(PCRE_LIBS) $(PCRE2_LIBS) USES_LIBRARIES = \ diff --git a/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib index ad577966..99b883bb 100644 --- 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 DLL_LIB = $(PCRE_LIB) LIBS = $(PCRE_LIBS) +DLL_LIB = xregexp xncbi + USES_LIBRARIES = \ xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi