debian/patches: Formally update for new release (2.8.1).

* Retire support_boost_1_67 (already applied upstream).
* Update patches that apply with offsets or outright fuzz, or need
  full-fledged porting.

diff --git a/debian/changelog b/debian/changelog
index 9af2b607f930d20472b1c27a8465cf616ef30bb7..976bbd5c54db4f4f801d6a3f0d071bde30e497a1 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
 ncbi-blast+ (2.8.1-1) UNRELEASED; urgency=medium
 
   * New upstream release (NOT RELEASED YET).
+  * debian/patches: Formally update for new release.
+    - Retire support_boost_1_67 (already applied upstream).
+    - Update patches that apply with offsets or outright fuzz, or need
+      full-fledged porting.
 
- -- Aaron M. Ucko <ucko@debian.org>  Sun, 03 Feb 2019 10:38:33 -0500
+ -- Aaron M. Ucko <amu@ucko.debian.net>  Sun, 03 Feb 2019 15:46:14 -0500
 
 ncbi-blast+ (2.7.1-2) unstable; urgency=medium
 

diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile
index e57f4923d84615bc4a4da09863733d6c75248fbb..6222bf3e4ae854675c33e22fff3e1f8725d16c20 100644 (file)
--- a/debian/patches/enable_clean_after_failed_compile
+++ b/debian/patches/enable_clean_after_failed_compile
@@ -5,10 +5,10 @@ Last-Updated: 2013-06-01
 Forwarded: no
 --- a/c++/src/build-system/new_module.sh.in
 +++ b/c++/src/build-system/new_module.sh.in
-@@ -180,7 +180,7 @@ if test -z "$datatool"; then # keep look
-     if test -x "$bindir/datatool"; then
-         datatool=$bindir/datatool
-         COMMON_AddRunpath "$libdir"
+@@ -198,7 +198,7 @@ if test -z "$datatool"; then # keep look
+         if test -n "$DYLD_LIBRARY_PATH"; then
+             wrapper="DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH"
+         fi
 -    else
 +    elif [ "$1" != "purge_sources" ] ; then
          echo "Unable to find datatool." >&2

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 9182e5b8a48c553d267c2262fa63c1a524bf1937..4940c1ba2b0361190570fb795fd78d8076bcf4b1 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/blastinput/Makefile.blastinput.lib
 +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -27,7 +27,9 @@
+@@ -27,7 +27,9 @@ SRC  = $(SRC_CXX)
  
  LIB = blastinput
  
@@ -29,7 +29,7 @@ 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 @@
+@@ -23,6 +23,7 @@ CFLAGS  = $(FAST_CFLAGS)
  LDFLAGS = $(FAST_LDFLAGS)
  WATCHERS = madden camacho fongah2
  
@@ -39,7 +39,7 @@ 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 @@
+@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
  CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
@@ -50,18 +50,18 @@ 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 @@
+@@ -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))
+ LIB = $(LIB_:%=%$(STATIC)) $(LMDB_LIB)
  
  CXXFLAGS = $(FAST_CXXFLAGS)
 --- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
 +++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@
+@@ -8,6 +8,8 @@ LIB = xalgodustmask
  
  SRC = symdust
  
@@ -72,7 +72,7 @@ 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 @@
+@@ -8,6 +8,8 @@ LIB = xalgosegmask
  
  SRC = segmask
  
@@ -83,7 +83,7 @@ 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 @@
+@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
@@ -94,10 +94,10 @@ Last-Update: 2016-12-05
      seqmasks_io
 --- a/c++/src/build-system/library_relations.txt
 +++ b/c++/src/build-system/library_relations.txt
-@@ -1308,7 +1308,7 @@
- xbiosample_util needs $(XFORMAT_LIBS)
- xbiosample_util needs xalnmgr
+@@ -1511,7 +1511,7 @@ xbiosample_util needs mlacli
+ xbiosample_util needs valid
  xbiosample_util needs xmlwrapp
+ xbiosample_util needs xobjutil
 -xblast includes blast
 +xblast needs blast
  xblast needs xalgoblastdbindex
@@ -105,7 +105,7 @@ 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 @@
+@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
        user_agent
  LIB = xcgi
  
@@ -138,7 +138,7 @@ 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 @@
+@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
        commentdiag indentstream html_exception writer_htmlenc
  LIB = xhtml
  
@@ -149,7 +149,7 @@ 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 @@
+@@ -3,6 +3,8 @@ SRC = blast__ blast___ names
  
  DLL_LIB = seqset scoremat
  
@@ -160,7 +160,7 @@ 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 @@
+@@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___
  
  DLL_LIB = xser
  
@@ -182,7 +182,7 @@ 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 @@
+@@ -5,6 +5,8 @@ SRC = id1__ id1___
  
  DLL_LIB = seqset
  
@@ -248,7 +248,7 @@ 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 @@
+@@ -17,7 +17,7 @@ LIB = id2_split
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
  
@@ -259,7 +259,7 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/objmgr/util/Makefile.util.lib
 +++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -14,6 +14,8 @@
+@@ -14,6 +14,8 @@ LIB = xobjutil
  
  DLL_LIB = submit $(SOBJMGR_LIBS)
  
@@ -270,9 +270,9 @@ 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 @@
+@@ -15,6 +15,10 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(O
  
- 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 \
@@ -283,7 +283,7 @@ 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 @@
+@@ -14,6 +14,7 @@ DLL_LIB = xobjutil tables
  
  WATCHERS = grichenk
  
@@ -293,7 +293,7 @@ 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 @@
+@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
  
  CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
@@ -303,18 +303,18 @@ 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 @@
- LIB = seqdb
- DLL_LIB = blastdb $(SOBJMGR_LIBS)
+@@ -29,6 +29,8 @@ LIB = seqdb
+ DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB)
+ LIBS = $(BLAST_THIRD_PARTY_LIBS)
  
 +DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE) 
  CXXFLAGS = $(FAST_CXXFLAGS)
 --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
 +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -11,6 +11,9 @@
+@@ -11,6 +11,9 @@ DLL_LIB = blastdb $(SOBJMGR_LIBS)
  
  LIB = writedb
  
@@ -322,11 +322,11 @@ Last-Update: 2016-12-05
 +          xser sequtil xutil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)  $(BLAST_THIRD_PARTY_INCLUDE)
  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 @@
+@@ -10,6 +10,8 @@ LIB = blast_services
  
  DLL_LIB = xnetblastcli xnetblast
  
@@ -337,18 +337,18 @@ 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 @@
- 
- ASN_DEP = blastdb seqset
+@@ -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
-+
- WATCHERS = camacho
  
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
 --- 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 @@
+@@ -7,6 +7,8 @@ DLL_LIB = blast_services
  
  CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
@@ -359,7 +359,7 @@ 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 @@
+@@ -12,6 +12,9 @@ LIB_OR_DLL = both
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
  
@@ -371,7 +371,7 @@ 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 @@
+@@ -16,6 +16,9 @@ DLL_LIB = $(GENBANK_READER_LDEP)
  
  LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
  
@@ -383,7 +383,7 @@ 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 @@
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
  
@@ -394,7 +394,7 @@ 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 @@
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_READER_LDEP)
  
@@ -405,7 +405,7 @@ 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 @@
+@@ -12,7 +12,10 @@ LIB_OR_DLL = both
  CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
  
  # Dependencies for shared library (disabled due to problems on Darwin)
@@ -419,18 +419,18 @@ 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 @@
+@@ -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
+ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS)
  
 --- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
 +++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@
+@@ -7,6 +7,8 @@ WATCHERS =  jcherry
  
  ASN_DEP = seqset
  
@@ -441,7 +441,7 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/serial/Makefile.serial.lib
 +++ b/c++/src/serial/Makefile.serial.lib
-@@ -20,6 +20,8 @@
+@@ -20,6 +20,8 @@ LIB    = xser
  
  DLL_LIB = xutil
  
@@ -452,7 +452,7 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/util/Makefile.util.lib
 +++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@
+@@ -14,6 +14,7 @@ SRC = random_gen utf8 checksum checksum_
  LIB = xutil
  PROJ_TAG = core
  
@@ -462,7 +462,7 @@ 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 @@
+@@ -7,7 +7,7 @@ LIB = xcompress
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
  
@@ -473,7 +473,7 @@ 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 @@
+@@ -5,7 +5,7 @@ LIB = xregexp
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
  
@@ -484,7 +484,7 @@ 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 @@
+@@ -20,8 +20,7 @@ SRC = read_util format_guess_ex \
        ucscregion_reader struct_cmt_reader \
        message_listener line_error
  
@@ -561,7 +561,7 @@ 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 @@
+@@ -3,6 +3,7 @@ WATCHERS = lavr
  LIB = entrez2
  SRC = entrez2__ entrez2___
  
@@ -581,7 +581,7 @@ 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 @@
+@@ -6,6 +6,7 @@ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG
  LIB = gene_info
  SRC = gene_info gene_info_reader file_utils
  
@@ -611,9 +611,9 @@ 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 @@
+@@ -5,5 +5,7 @@ SRC = mla_client mla_client_
  
- DLL_LIB = xconnect
+ DLL_LIB = mla pubmed medlars xconnect
  
 +DLL_LIB = mla xconnect xser xutil xncbi
 +
@@ -631,7 +631,7 @@ 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 @@
+@@ -7,6 +7,7 @@ DLL_LIB = xconnect
  
  WATCHERS = domrach
  
@@ -641,7 +641,7 @@ 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
-@@ -8,6 +8,7 @@
+@@ -8,6 +8,7 @@ DLL_LIB = xconnect
  
  WATCHERS = bollin holmesbr
  
@@ -651,7 +651,7 @@ 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 @@
+@@ -3,6 +3,7 @@ SRC = valerr__ valerr___
  
  ASN_DEP = seqset
  
@@ -661,7 +661,7 @@ 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 @@
+@@ -6,5 +6,7 @@ DLL_LIB = xregexp
  
  ASN_DEP = general
  
@@ -681,7 +681,7 @@ 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 @@
+@@ -13,6 +13,8 @@ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_
  
  WATCHERS = jianye zaretska madden camacho fongah2
  
@@ -692,17 +692,22 @@ 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 @@
+@@ -10,11 +10,10 @@ SRC = autogenerated_cleanup autogenerate
+       cleanup_utils gene_qual_normalization cleanup_user_object cleanup_author \
+       newcleanupp capitalization_string
  
- LIBS = $(PCRE_LIBS)
+-DLL_LIB = xregexp $(PCRE_LIB)      
++DLL_LIB = xobjutil valid submit taxon3 xregexp $(PCRE_LIB) $(SOBJMGR_LIBS)
+ LIB = xcleanup
  
-+DLL_LIB = xobjutil valid submit taxon3 xregexp $(SOBJMGR_LIBS)
+ LIBS = $(PCRE_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 @@
+@@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect
  
  WATCHERS = ludwigf dicuccio
  
@@ -713,7 +718,7 @@ 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 @@
+@@ -5,5 +5,7 @@ SRC = blastclient blastclient_
  
  DLL_LIB = xconnect
  
@@ -723,7 +728,7 @@ 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 @@
+@@ -6,6 +6,8 @@ LIB = xregexp_template_tester
  DLL_LIB = $(PCRE_LIB)
  LIBS    = $(PCRE_LIBS)
  
@@ -734,7 +739,7 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/algo/blast/api/Makefile.xblast.lib
 +++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -77,11 +77,11 @@
+@@ -77,11 +77,11 @@ deltablast \
  magicblast_options \
  magicblast
  
@@ -750,7 +755,7 @@ Last-Update: 2016-12-05
  CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
 --- a/c++/src/connect/Makefile.xconnect.lib
 +++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
+@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
  LIB      = xconnect
  PROJ_TAG = core
  
@@ -761,7 +766,7 @@ Last-Update: 2016-12-05
  WATCHERS = lavr mcelhany
 --- a/c++/src/objects/seq/Makefile.seq.lib
 +++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,7 +12,7 @@
+@@ -12,7 +12,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
        seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map so_map \
        seq_loc_from_string seq_loc_reverse_complementer
  
@@ -783,7 +788,7 @@ Last-Update: 2016-12-05
      $(SEQ_LIBS) pub
 --- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
 +++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -5,7 +5,7 @@
+@@ -5,7 +5,7 @@ ASN_DEP = entrez2
  LIB = entrez2cli
  SRC = entrez2_client entrez2_client_
  

diff --git a/debian/patches/fix_unit_tests b/debian/patches/fix_unit_tests
index 710165ed5c3e9e2d8834312872eb453096d2193a..e20a43c47fbc86037640061f19b237fb58f9283f 100644 (file)
--- a/debian/patches/fix_unit_tests
+++ b/debian/patches/fix_unit_tests
@@ -5,10 +5,12 @@ Author: Olivier Sallou <osallou@debian.org>
 Last-Updated: 2018-02-11
 --- a/c++/src/algo/blast/Makefile.blast_macros.mk
 +++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -21,5 +21,5 @@
+@@ -21,7 +21,7 @@ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) v
  BLAST_LDEP = xalgoblastdbindex composition_adjustment \
-               xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
-               xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables
+              xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
+              xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables $(LMDB_LIB)
 -BLAST_LIBS = proteinkmer xblast $(BLAST_LDEP)
 +BLAST_LIBS = proteinkmer xblast blast $(BLAST_LDEP)
+ 
  # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+ 

diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index c664ef2a7c47e7f0b9bbc8691ba432ad2891d377..30c971287f2887202e3c8ff5f430d59c66ea0cb3 100644 (file)
--- a/debian/patches/hurd_fixes
+++ b/debian/patches/hurd_fixes
@@ -9,7 +9,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-06-10
 --- a/c++/src/build-system/configure
 +++ b/c++/src/build-system/configure
-@@ -9716,7 +9716,7 @@
+@@ -9891,7 +9891,7 @@ if test -z "$CONF_f_runpath" ; then
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -20,7 +20,7 @@ Last-Update: 2011-06-10
      irix*:* | linux*:KCC | *:Compaq )
 --- a/c++/src/build-system/configure.ac
 +++ b/c++/src/build-system/configure.ac
-@@ -2081,7 +2081,7 @@
+@@ -2131,7 +2131,7 @@ if test -z "$CONF_f_runpath" ; then
      solaris* )
        CONF_f_runpath="-R"
        ;;

diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index a5601282694e626a0e3d7888af6fbde28f001bed..dc82958b75b73de7feb5c1d9067dff31619594ba 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
-@@ -9823,7 +9823,7 @@
+@@ -9999,7 +9999,7 @@ echo "$as_me: error: Unable to find stat
                 break
                 ;;
              /* )
@@ -21,7 +21,7 @@ Last-Update: 2011-08-28
          esac
 --- a/c++/src/build-system/configure.ac
 +++ b/c++/src/build-system/configure.ac
-@@ -2148,7 +2148,7 @@
+@@ -2198,7 +2198,7 @@ case "$compiler:$compiler_version:$with_
                 break
                 ;;
              /* )

diff --git a/debian/patches/series b/debian/patches/series
index a0ae2e07cc083a482b908afc962becbb342b79d9..3791ecc74da105397f07a8651a58682cfea642e6 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -12,4 +12,4 @@ support_x32
 suppress_gnutls_version_check
 optionally_keep_sequence
 fix_unit_tests
-support_boost_1_67
+#support_boost_1_67

diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test
index a4d03234077f36464f532361c86c42041238a337..87cc4460f885b3e2866e646de05786954874cb02 100644 (file)
--- a/debian/patches/skip_services_unit_test
+++ b/debian/patches/skip_services_unit_test
@@ -7,7 +7,7 @@ Last-Updated: 2013-06-01
 +++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
 @@ -11,6 +11,7 @@ LIB = test_boost blast_services xnetblas
  
- LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS)
  
 -CHECK_CMD = blast_services_unit_test
 +# This test requires an internet connection, shouldn't be run on a build server

diff --git a/debian/patches/suppress_gnutls_version_check b/debian/patches/suppress_gnutls_version_check
index 3794f6c1c9ea4b4f314c5ce152d855c663e9eb56..51b9982c2915e93bedd483ad26ca96aec9c5a9f1 100644 (file)
--- a/debian/patches/suppress_gnutls_version_check
+++ b/debian/patches/suppress_gnutls_version_check
@@ -1,6 +1,6 @@
 --- a/c++/src/connect/ncbi_gnutls.c
 +++ b/c++/src/connect/ncbi_gnutls.c
-@@ -661,6 +661,7 @@
+@@ -660,6 +660,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
  
      assert(!s_GnuTlsCredAnon);
  
@@ -8,7 +8,7 @@
      version = gnutls_check_version(0);
      if (strcasecmp(GNUTLS_VERSION, version) != 0) {
          CORE_LOGF(eLOG_Critical,
-@@ -668,6 +669,7 @@
+@@ -667,6 +668,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
                     GNUTLS_VERSION, version));
          assert(0);
      }