fix_lib_deps: Generally fix remaining underlinkage.

Several cases were longstanding.

diff --git a/debian/changelog b/debian/changelog
index 473c347bfff3dab4538efc698bbc8a60943c5a0b..806df3fe1cf1e888835a4a0c2637ac5cd738bdeb 100644 (file)
--- 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 <ucko@debian.org>  Wed, 03 Aug 2016 21:27:29 -0400
+ -- Aaron M. Ucko <ucko@debian.org>  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 a25b2b4e7e256a0856ec1a4e0de4e663710c30e8..f333f81a24fa7806c10f1dc8878f5a3a309782b2 100644 (file)
--- 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
+