From: Aaron M. Ucko Date: Thu, 4 Aug 2016 01:29:09 +0000 (-0400) Subject: fix_lib_deps: Generally fix remaining underlinkage. X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~213 X-Git-Url: https://dgit.raspbian.org/%22http://www.example.com/cgi/success/%22http:/www.example.com/cgi/success?a=commitdiff_plain;h=bd777cc71f6b82a753ee5e09191ea9bf9523df94;p=ncbi-blast%2B.git fix_lib_deps: Generally fix remaining underlinkage. Several cases were longstanding. --- diff --git a/debian/changelog b/debian/changelog index 473c347b..806df3fe 100644 --- a/debian/changelog +++ b/debian/changelog @@ -5,9 +5,10 @@ ncbi-blast+ (2.4.0-1) UNRELEASED; urgency=medium * Import upstream patch to fix Boost version detection (which missed the 2.4.0 release branch) as debian/patches/fix_version_extraction. * fix_lib_deps: List taxon1 in align_format's overridden DLL_LIB, in - large part to ensure its headers are generated on time. + large part to ensure its headers are generated on time; generally fix + remaining cases of underlinkage (several longstanding). - -- Aaron M. Ucko Wed, 03 Aug 2016 21:27:29 -0400 + -- Aaron M. Ucko Wed, 03 Aug 2016 21:29:09 -0400 ncbi-blast+ (2.3.0-2) unstable; urgency=medium diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index a25b2b4e..f333f81a 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -201,13 +201,14 @@ Last-Update: 2014-12-02 --- a/c++/src/objects/blastdb/Makefile.blastdb.lib +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib -@@ -1,5 +1,7 @@ - # $Id: Makefile.blastdb.lib 468761 2015-05-27 20:14:39Z ucko $ +@@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___ + + DLL_LIB = xser -+ +DLL_LIB = seq xser xncbi - LIB = blastdb - SRC = blastdb__ blastdb___ ++ + WATCHERS = camacho + --- a/c++/src/objects/blastxml/Makefile.blastxml.lib +++ b/c++/src/objects/blastxml/Makefile.blastxml.lib @@ -350,7 +351,7 @@ Last-Update: 2014-12-02 WATCHERS = todorov dicuccio grichenk - -+DLL_LIB = xobjmgr seqset seq xser tables xncbi ++DLL_LIB = xobjutil xobjmgr seqset seq xser tables xncbi USES_LIBRARIES = \ tables xobjutil @@ -612,3 +613,196 @@ Last-Update: 2014-12-02 USES_LIBRARIES = \ medline +--- 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 +--- 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 +--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib ++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib +@@ -5,6 +5,7 @@ ASN_DEP = entrez2 + LIB = entrez2cli + SRC = entrez2_client entrez2_client_ + ++DLL_LIB = entrez2 xconnect xser xutil xncbi + + USES_LIBRARIES = \ + entrez2 xconnect +--- 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 +--- 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 + LIB = gene_info + SRC = gene_info gene_info_reader file_utils + ++DLL_LIB = xncbi + + USES_LIBRARIES = \ + xncbi +--- 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 +--- a/c++/src/objects/mla/Makefile.mla.lib ++++ b/c++/src/objects/mla/Makefile.mla.lib +@@ -1,6 +1,7 @@ + LIB = mla + SRC = mla__ mla___ + ++DLL_LIB = medlars pub pubmed xser xutil xncbi + + USES_LIBRARIES = \ + 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_ + + DLL_LIB = xconnect + ++DLL_LIB = mla xconnect xser xutil xncbi ++ + USES_LIBRARIES = \ + mla xconnect +--- 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 +--- 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 +--- a/c++/src/objects/taxon3/Makefile.taxon3.lib ++++ b/c++/src/objects/taxon3/Makefile.taxon3.lib +@@ -7,6 +7,7 @@ DLL_LIB = xconnect + + WATCHERS = bollin holmesbr + ++DLL_LIB = xconnect seq xser xutil xncbi + + USES_LIBRARIES = \ + $(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___ + + ASN_DEP = seqset + ++DLL_LIB = xser xutil xncbi + + USES_LIBRARIES = \ + xser +--- a/c++/src/objects/valid/Makefile.valid.lib ++++ b/c++/src/objects/valid/Makefile.valid.lib +@@ -4,5 +4,7 @@ SRC = valid__ valid___ + + ASN_DEP = general + ++DLL_LIB = general xser xregexp xutil xncbi ++ + USES_LIBRARIES = \ + general xregexp +--- 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 +--- 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 + + 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 +--- a/c++/src/objtools/cleanup/Makefile.cleanup.lib ++++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib +@@ -15,6 +15,7 @@ LIB = xcleanup + + LIBS = $(PCRE_LIBS) + ++DLL_LIB = xobjutil valid submit taxon3 xregexp $(SOBJMGR_LIBS) + + USES_LIBRARIES = \ + 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 + + WATCHERS = ludwigf dicuccio kornbluh + ++DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \ ++ xobjutil taxon3 $(SOBJMGR_LIBS) + + USES_LIBRARIES = \ + 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_ + + DLL_LIB = xconnect + ++DLL_LIB = xnetblast xconnect xser xutil xncbi ++ + USES_LIBRARIES = \ + 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 + DLL_LIB = $(PCRE_LIB) + LIBS = $(PCRE_LIBS) + ++DLL_LIB = xregexp xncbi ++ + USES_LIBRARIES = \ + xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi +