prepare new upstream 2.6.0, update patches

diff --git a/debian/changelog b/debian/changelog
index 076803d65e84a57c4f6b9380730fb7f26c6fea1d..d2557df633c5131da1112dd27f6f44df810a562a 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+ncbi-blast+ (2.6.0-1) UNRELEASED; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou@debian.org>  Sun, 15 Jan 2017 17:12:27 +0000
+
 ncbi-blast+ (2.5.0-4) unstable; urgency=medium
 
   * New optionally_keep_sequence patch to hang on to sequence data even if

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 6901fcd54697cc00544cc0ea94bca2f4eb165059..0692cafef4e1d79b6ce38117ce3de554a50fa410 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -16,7 +16,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2016-12-05
 --- a/c++/src/algo/blast/api/Makefile.xblast.lib
 +++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -76,14 +76,15 @@ deltablast \
+@@ -76,14 +76,15 @@
  magicblast_options \
  magicblast
  
@@ -36,7 +36,7 @@ Last-Update: 2016-12-05
  CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
 +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -26,7 +26,9 @@ SRC  = $(SRC_CXX)
+@@ -27,7 +27,9 @@
  
  LIB = blastinput
  
@@ -49,7 +49,7 @@ Last-Update: 2016-12-05
  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 @@ CFLAGS  = $(FAST_CFLAGS)
+@@ -23,6 +23,7 @@
  LDFLAGS = $(FAST_LDFLAGS)
  WATCHERS = madden camacho fongah2
  
@@ -59,7 +59,7 @@ Last-Update: 2016-12-05
      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)
  
@@ -70,7 +70,7 @@ Last-Update: 2016-12-05
  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 \
@@ -81,7 +81,7 @@ Last-Update: 2016-12-05
  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
  
@@ -92,7 +92,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -103,7 +103,7 @@ Last-Update: 2016-12-05
  
 --- 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)
  
@@ -114,7 +114,7 @@ Last-Update: 2016-12-05
      seqmasks_io
 --- a/c++/src/build-system/library_relations.txt
 +++ b/c++/src/build-system/library_relations.txt
-@@ -1287,7 +1287,7 @@ xbiosample_util needs $(OBJEDIT_LIBS)
+@@ -1287,7 +1287,7 @@
  xbiosample_util needs $(XFORMAT_LIBS)
  xbiosample_util needs xalnmgr
  xbiosample_util needs xmlwrapp
@@ -125,7 +125,7 @@ Last-Update: 2016-12-05
  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
  
@@ -136,7 +136,7 @@ Last-Update: 2016-12-05
  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
  
@@ -169,7 +169,7 @@ Last-Update: 2016-12-05
  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
  
@@ -180,7 +180,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -191,7 +191,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -213,7 +213,7 @@ Last-Update: 2016-12-05
      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
  
@@ -235,7 +235,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -301,7 +301,7 @@ Last-Update: 2016-12-05
      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)
  
@@ -312,7 +312,7 @@ Last-Update: 2016-12-05
  
 --- 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)
  
@@ -323,7 +323,7 @@ Last-Update: 2016-12-05
  
 --- 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)
  
@@ -336,7 +336,7 @@ Last-Update: 2016-12-05
  # CXXFLAGS = $(FAST_CXXFLAGS)
 --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
 +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -14,6 +14,7 @@ DLL_LIB = tables
+@@ -14,6 +14,7 @@
  
  WATCHERS = grichenk
  
@@ -346,7 +346,7 @@ Last-Update: 2016-12-05
      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)
  
@@ -356,7 +356,7 @@ Last-Update: 2016-12-05
  # 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)
  
@@ -367,7 +367,7 @@ Last-Update: 2016-12-05
  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
  
@@ -379,7 +379,7 @@ Last-Update: 2016-12-05
  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
  
@@ -390,7 +390,7 @@ Last-Update: 2016-12-05
  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
  
@@ -401,7 +401,7 @@ Last-Update: 2016-12-05
  
 --- 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)
  
@@ -412,7 +412,7 @@ Last-Update: 2016-12-05
  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)
  
@@ -424,7 +424,7 @@ Last-Update: 2016-12-05
  
 --- 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)
+@@ -16,6 +16,9 @@
  
  LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
  
@@ -436,7 +436,7 @@ Last-Update: 2016-12-05
  
 --- 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)
  
@@ -447,7 +447,7 @@ Last-Update: 2016-12-05
  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)
  
@@ -458,7 +458,7 @@ Last-Update: 2016-12-05
  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)
@@ -472,7 +472,7 @@ Last-Update: 2016-12-05
  
 --- 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
@@ -483,7 +483,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -494,7 +494,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -505,7 +505,7 @@ Last-Update: 2016-12-05
  
 --- 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
  
@@ -515,7 +515,7 @@ Last-Update: 2016-12-05
  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)
  
@@ -526,7 +526,7 @@ Last-Update: 2016-12-05
  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)
  
@@ -537,16 +537,16 @@ Last-Update: 2016-12-05
  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 \
-       ucscregion_reader \
+@@ -20,8 +20,7 @@
+       ucscregion_reader struct_cmt_reader \
        message_listener line_error
  
 -
 -DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil
 +DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil pub xser xncbi
  
- 
- 
+ USES_LIBRARIES =  \
+     creaders submit
 --- a/c++/src/util/sequtil/Makefile.sequtil.lib
 +++ b/c++/src/util/sequtil/Makefile.sequtil.lib
 @@ -3,6 +3,8 @@
@@ -614,7 +614,7 @@ Last-Update: 2016-12-05
      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___
  
@@ -624,7 +624,7 @@ Last-Update: 2016-12-05
      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_
  
@@ -644,7 +644,7 @@ Last-Update: 2016-12-05
      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
  
@@ -674,7 +674,7 @@ Last-Update: 2016-12-05
      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
  
@@ -694,7 +694,7 @@ Last-Update: 2016-12-05
      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
  
@@ -704,7 +704,7 @@ Last-Update: 2016-12-05
      $(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
  
@@ -714,7 +714,7 @@ Last-Update: 2016-12-05
      $(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
  
@@ -724,7 +724,7 @@ Last-Update: 2016-12-05
      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
  
@@ -744,7 +744,7 @@ Last-Update: 2016-12-05
      $(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
  
@@ -755,7 +755,7 @@ Last-Update: 2016-12-05
      $(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)
  
@@ -765,7 +765,7 @@ Last-Update: 2016-12-05
      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
  
@@ -776,7 +776,7 @@ Last-Update: 2016-12-05
      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
  
@@ -786,7 +786,7 @@ Last-Update: 2016-12-05
      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)
  
@@ -797,7 +797,7 @@ Last-Update: 2016-12-05
  
 --- 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 \
+@@ -18,7 +18,7 @@
  BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
  
  # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS

diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 870d1879dfcc1db955bd37bdbd74c867407002a0..15cd5e30425c40576716efea60bd37a32242ad79 100644 (file)
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-08-28
 --- a/c++/src/build-system/configure
 +++ b/c++/src/build-system/configure
-@@ -9264,7 +9264,7 @@
+@@ -9285,7 +9285,7 @@
                 break
                 ;;
              /* )