debian/patches: Update for new upstream release (2.12.0[+ds]).

* fix_lib_deps, fix_unit_tests, spelling: Formally refresh to eliminate
  fuzz.
* fix_x86isms: Retire (fully incorporated upstream.)
* run_perl_directly: Formally update to reflect current $Id$ comment.
* support_x32: Forward-port.
* tune_lmdb_defaults: Keep just the MIPS tuneup; upstream's settings
  should now be fine elsewhere.

diff --git a/debian/changelog b/debian/changelog
index f79691df1390859ff2f9ec16cb9ee609d4ee0aaa..808d7e58ea3c6c92d1b2abdfbb3bf5d9e1788a31 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,16 @@
 ncbi-blast+ (2.12.0+ds-1) UNRELEASED; urgency=medium
 
   * New upstream release.  (NOT RELEASED YET.)
+  * debian/patches: Update accordingly.
+    - fix_lib_deps, fix_unit_tests, spelling: Formally refresh to eliminate
+      fuzz.
+    - fix_x86isms: Retire (fully incorporated upstream.)
+    - run_perl_directly: Formally update to reflect current $Id$ comment.
+    - support_x32: Forward-port.
+    - tune_lmdb_defaults: Keep just the MIPS tuneup; upstream's settings
+      should now be fine elsewhere.
 
- -- Aaron M. Ucko <ucko@debian.org>  Wed, 01 Dec 2021 21:32:28 -0500
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 01 Dec 2021 21:49:05 -0500
 
 ncbi-blast+ (2.11.0+ds-1) unstable; urgency=medium
 

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 90a475e027d4de8f3557b53f22539a14d95e2e7e..7a26bdd6dcbd6fbc258e54016a449b5cb03e7ba3 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -94,7 +94,7 @@ Last-Update: 2016-12-05
      seqmasks_io
 --- a/c++/src/build-system/library_relations.txt
 +++ b/c++/src/build-system/library_relations.txt
-@@ -1553,7 +1553,7 @@ xbiosample_util needs mlacli
+@@ -1603,7 +1603,7 @@ xbiosample_util needs mlacli
  xbiosample_util needs valid
  xbiosample_util needs xmlwrapp
  xbiosample_util needs xobjutil
@@ -201,7 +201,7 @@ Last-Update: 2016-12-05
 +
  WATCHERS = vasilche
  
- 
+ USES_LIBRARIES =  \
 --- a/c++/src/objects/seqcode/Makefile.seqcode.lib
 +++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
 @@ -1,6 +1,8 @@
@@ -361,7 +361,7 @@ Last-Update: 2016-12-05
 +++ 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 = ncbi_xreader$(DLL) $(GENBANK_PSG_CLIENT_LDEP)
+ DLL_LIB = general ncbi_xreader$(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 \
@@ -485,7 +485,7 @@ Last-Update: 2016-12-05
  USES_LIBRARIES =  \
 --- a/c++/src/objtools/readers/Makefile.xobjread.lib
 +++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -27,6 +27,6 @@ SRC = reader_message reader_listener rea
+@@ -29,6 +29,6 @@ SRC = reader_message reader_listener rea
        message_listener line_error
  
  
@@ -750,19 +750,19 @@ 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 @@ UNIX_SRC = $(LOCAL_LBSM)
+@@ -13,6 +13,8 @@ UNIX_SRC = $(LOCAL_LBSM)
+ 
  LIB      = xconnect
- PROJ_TAG = core
  
 +DLL_LIB = xncbi
 +
  LIBS     = $(NETWORK_LIBS) $(ORIG_LIBS)
  
- WATCHERS = lavr mcelhany
+ PROJ_TAG = core
 --- a/c++/src/objects/seq/Makefile.seq.lib
 +++ b/c++/src/objects/seq/Makefile.seq.lib
 @@ -12,7 +12,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
-       seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map so_map \
+       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

diff --git a/debian/patches/fix_unit_tests b/debian/patches/fix_unit_tests
index d75b78b1783861e44fd5204b7d2178d26d70f035..ef4a22621ef458a198479999da1ec11cd45f5de6 100644 (file)
--- a/debian/patches/fix_unit_tests
+++ b/debian/patches/fix_unit_tests
@@ -5,8 +5,8 @@ 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
-@@ -21,7 +21,7 @@
- BLAST_LDEP = xalgoblastdbindex composition_adjustment \
+@@ -21,7 +21,7 @@ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) v
+ BLAST_LDEP = utrtprof xalgoblastdbindex composition_adjustment \
               xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
               xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables $(LMDB_LIB)
 -BLAST_LIBS = proteinkmer xblast $(BLAST_LDEP)

diff --git a/debian/patches/fix_x86isms b/debian/patches/fix_x86isms
deleted file mode 100644 (file)
index 1683357..0000000
--- a/debian/patches/fix_x86isms
+++ /dev/null
@@ -1,18 +0,0 @@
---- a/c++/src/corelib/ncbi_system.cpp
-+++ b/c++/src/corelib/ncbi_system.cpp
-@@ -1422,6 +1422,7 @@ CCpuFeatures::InstructionSet::Instructio
-       f81_ECX_  { 0 },
-       f81_EDX_  { 0 }
- {
-+#if defined(__i386__)  ||  defined(__x86_64__)
-     int nIds   = 0;
-     int nExIds = 0;
- 
-@@ -1506,6 +1507,7 @@ CCpuFeatures::InstructionSet::Instructio
-         memcpy(brand + 32, m_ExtData[4].data(), sizeof(registers));
-         m_BrandStr = brand;
-     }
-+#endif
- };
- 
- 

diff --git a/debian/patches/run_perl_directly b/debian/patches/run_perl_directly
index ed84d7be8b4279cca62b97a6abf915c7c87bb84e..aa72d5ef4b091420eeec0f38dd1b8c6fa76bd3d6 100644 (file)
--- a/debian/patches/run_perl_directly
+++ b/debian/patches/run_perl_directly
@@ -1,5 +1,5 @@
 Author: Aaron M. Ucko <ucko@debian.org>
-Date:   Sun Apr 26 11:28:03 2020 -0400
+Date:   Wed, 01 Dec 2021 21:38:20 -0500
 Description: Bypass env in Perl script shebangs.
 
 --- a/c++/src/app/blast/update_blastdb.pl
@@ -7,6 +7,6 @@ Description: Bypass env in Perl script shebangs.
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env perl
 +#!/usr/bin/perl
- # $Id: update_blastdb.pl 608596 2020-05-19 10:56:17Z ivanov $
+ # $Id: update_blastdb.pl 632592 2021-06-03 13:20:59Z ivanov $
  # ===========================================================================
  #

diff --git a/debian/patches/series b/debian/patches/series
index 69b0517d39761e68ec84118f23af6e743cbf62e7..a30023b7b545bd7dfbffe7abd86a40bdb29b2b24 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -16,4 +16,3 @@ spelling
 support_gcc10
 run_perl_directly
 tune_lmdb_defaults
-fix_x86isms

diff --git a/debian/patches/spelling b/debian/patches/spelling
index b6da0056b27ef6dc85f7ff72edd8236303624ce7..608a4cd41ebf15e0932b302864e4fe0d0880fe53 100644 (file)
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -2,7 +2,7 @@ From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Spelling fixes
 --- a/c++/include/objtools/alnmgr/seqids_extractor.hpp
 +++ b/c++/include/objtools/alnmgr/seqids_extractor.hpp
-@@ -232,7 +232,7 @@
+@@ -232,7 +232,7 @@ public:
                          else if (*id_vec[i] != *id) {
                              string err("Inconsistent Seq-ids found in seg ");
                              err += NStr::NumericToString(i) +
@@ -13,7 +13,7 @@ Subject: Spelling fixes
                          }
 --- a/c++/src/algo/blast/api/blast_setup_cxx.cpp
 +++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp
-@@ -784,7 +784,7 @@
+@@ -784,7 +784,7 @@ SetupSubjects_OMF(IBlastQuerySource& sub
                        if(warning != kEmptyStr){
                                warning += ": ";
                        }
@@ -24,7 +24,7 @@ Subject: Spelling fixes
                }
 --- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
 +++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
-@@ -75,7 +75,7 @@
+@@ -75,7 +75,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory
          }
          else NCBI_THROW( CSeqMaskerOstatFactoryException,
                           eBadName,
@@ -33,7 +33,7 @@ Subject: Spelling fixes
      }
      catch( CException & e ) {
          NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
-@@ -113,7 +113,7 @@
+@@ -113,7 +113,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory
          }
          else NCBI_THROW( CSeqMaskerOstatFactoryException,
                           eBadName,
@@ -44,7 +44,7 @@ Subject: Spelling fixes
          NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
 --- a/c++/src/app/blastdb/blastdbcheck.cpp
 +++ b/c++/src/app/blastdb/blastdbcheck.cpp
-@@ -232,7 +232,7 @@
+@@ -245,7 +245,7 @@ void CBlastDbCheckApplication::Init(void
           "Require that all sequences in the database have taxid set.");
  
      arg_desc->AddFlag
@@ -55,7 +55,7 @@ Subject: Spelling fixes
      SetupArgDescriptions(arg_desc.release());
 --- a/c++/src/app/blastdb/makeprofiledb.cpp
 +++ b/c++/src/app/blastdb/makeprofiledb.cpp
-@@ -546,13 +546,13 @@
+@@ -609,13 +609,13 @@ CMakeProfileDBApp::x_CheckInputScoremat(
  
                if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength()))
                {
@@ -71,7 +71,7 @@ Subject: Spelling fixes
                        NCBI_THROW(CInputException, eInvalidInput,  err);
                }
  
-@@ -605,13 +605,13 @@
+@@ -668,13 +668,13 @@ CMakeProfileDBApp::x_CheckInputScoremat(
  
                if(sm_invalid == sm)
                {
@@ -87,7 +87,7 @@ Subject: Spelling fixes
                NCBI_THROW(CInputException, eInvalidInput,  err);
        }
  
-@@ -1563,7 +1563,7 @@
+@@ -1816,7 +1816,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co
      if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
      {
        *m_LogFile << filename +
@@ -95,10 +95,10 @@ Subject: Spelling fixes
 +                      " was excluded: it contains an invalid CD \n";
        return false;
      }
- 
+     return true;
 --- a/c++/src/connect/ncbi_lbos.c
 +++ b/c++/src/connect/ncbi_lbos.c
-@@ -951,7 +951,7 @@
+@@ -951,7 +951,7 @@ static char * s_LBOS_UrlReadAll(SConnNet
                                             sizeof(char) * (strlen(buf) + 1))) ) 
      {
          CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using "
@@ -109,7 +109,7 @@ Subject: Spelling fixes
      }
 --- a/c++/src/objects/seqalign/Dense_seg.cpp
 +++ b/c++/src/objects/seqalign/Dense_seg.cpp
-@@ -988,7 +988,7 @@
+@@ -988,7 +988,7 @@ void CDense_seg::RemapToLoc(TDim row, co
              if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
                  NCBI_THROW(CSeqalignException, eInvalidInputData,
                             "CDense_seg::RemapToLoc():"
@@ -120,7 +120,7 @@ Subject: Spelling fixes
          }
 --- a/c++/src/objects/seqalign/Seq_align.cpp
 +++ b/c++/src/objects/seqalign/Seq_align.cpp
-@@ -872,7 +872,7 @@
+@@ -872,7 +872,7 @@ CSeq_align::CreateDensegFromStdseg(SSeqI
          if (dim != ss.GetDim()  ||  row != dim) {
              NCBI_THROW(CSeqalignException, eInvalidInputAlignment,
                         "CreateDensegFromStdseg(): "
@@ -131,7 +131,7 @@ Subject: Spelling fixes
          if (widths_determined[seg]) {
 --- a/c++/src/objects/seqfeat/institution_codes.inc
 +++ b/c++/src/objects/seqfeat/institution_codes.inc
-@@ -687,7 +687,7 @@
+@@ -728,7 +728,7 @@ static const char* const kInstitutionCol
  "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t",
  "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t",
  "BR<BEL>\ts\tBotanic Garden Meise\t\t\t",
@@ -139,10 +139,10 @@ Subject: Spelling fixes
 +"BR<BRA>\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t",
  "BRA\ts\tSlovak National Museum, Botany Department\t\t\t",
  "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t",
- "BRBA\ts\tUniversidade Federal do Oeste da Bahia\t\t\t",
+ "BRB\ts\tBrassica Resource Bank\t\t\t",
 --- a/c++/src/objects/seqfeat/institution_codes.txt
 +++ b/c++/src/objects/seqfeat/institution_codes.txt
-@@ -654,7 +654,7 @@
+@@ -695,7 +695,7 @@ BPPT-ESC   c       BPPT Ethanol-Single Cell Prot
  BPS   s       California Department of Food and Agriculture                   
  BPU   s       Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology                    
  BR<BEL>       s       Botanic Garden Meise                    
@@ -150,10 +150,10 @@ Subject: Spelling fixes
 +BR<BRA>       c       Johanna Dobereiner Biological Resource Center (CRB-JD)                  
  BRA   s       Slovak National Museum, Botany Department                       
  BRAD  s       University of Bradford, Biology Department                      
- BRBA  s       Universidade Federal do Oeste da Bahia                  
+ BRB   s       Brassica Resource Bank                  
 --- a/c++/src/objmgr/util/sequence.cpp
 +++ b/c++/src/objmgr/util/sequence.cpp
-@@ -274,7 +274,7 @@
+@@ -274,7 +274,7 @@ string GetProteinName(const CBioseq_Hand
      if ( best_feats.empty() ) {
          NCBI_THROW_FMT(CObjMgrException, eFindFailed,
                         "GetProteinName("<<GetId(seq, eGetId_Best)<<"): "
@@ -164,7 +164,7 @@ Subject: Spelling fixes
          NCBI_THROW_FMT(CObjMgrException, eFindConflict,
 --- a/c++/src/objtools/align_format/taxFormat.cpp
 +++ b/c++/src/objtools/align_format/taxFormat.cpp
-@@ -588,7 +588,7 @@
+@@ -588,7 +588,7 @@ void CTaxFormat::x_LoadTaxTree(void)
              }            
          }
          if (!tax_load_ok) {
@@ -175,7 +175,7 @@ Subject: Spelling fixes
              
 --- a/c++/src/objtools/format/flat_file_config.cpp
 +++ b/c++/src/objtools/format/flat_file_config.cpp
-@@ -623,7 +623,7 @@
+@@ -639,7 +639,7 @@ void CFlatFileConfig::AddArgumentDescrip
  
           // from
           arg_desc->AddOptionalKey("from", "From",
@@ -186,7 +186,7 @@ Subject: Spelling fixes
           arg_desc->AddOptionalKey("to", "To",
 --- a/c++/src/objtools/readers/agp_converter.cpp
 +++ b/c++/src/objtools/readers/agp_converter.cpp
-@@ -728,7 +728,7 @@
+@@ -728,7 +728,7 @@ void CAgpConverter::x_SetUpObjectOpening
          submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());
          submit_block_writer.Flush();
          seq_sub_header_strm << "," << endl;
@@ -197,7 +197,7 @@ Subject: Spelling fixes
          out_sObjectClosingString = "} }" + out_sObjectClosingString;
 --- a/c++/src/objtools/readers/agp_util.cpp
 +++ b/c++/src/objtools/readers/agp_util.cpp
-@@ -67,7 +67,7 @@
+@@ -173,7 +173,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
  
      "object_beg != previous object_end + 1",
      "no valid AGP lines",
@@ -206,7 +206,7 @@ Subject: Spelling fixes
      "in \"Scaffold from component\" file, invalid scaffold-breaking gap",
      "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
  
-@@ -87,7 +87,7 @@
+@@ -193,7 +193,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
      // Content Warnings
      "gap at the end of object (OK if X is the circular chromosome/plasmid)",
      "gap at the beginning of object ",
@@ -217,7 +217,7 @@ Subject: Spelling fixes
      "the span overlaps a previous span for this component",
 --- a/c++/src/objtools/readers/agp_validate_reader.cpp
 +++ b/c++/src/objtools/readers/agp_validate_reader.cpp
-@@ -300,7 +300,7 @@
+@@ -300,7 +300,7 @@ void CAgpValidateReader::OnGapOrComponen
        int prev_comp_file=spans.rbegin()->file_num;
        int prev_comp_line=spans.rbegin()->line_num;
        if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) {
@@ -228,7 +228,7 @@ Subject: Spelling fixes
            sameComId_otherScaf += ":";
 --- a/c++/src/util/compress/api/compress.cpp
 +++ b/c++/src/util/compress/api/compress.cpp
-@@ -160,7 +160,7 @@
+@@ -160,7 +160,7 @@ bool CCompression::x_DecompressFile(CCom
      while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {
          os.write(buf.get(), nread);
          if ( !os.good() ) {

diff --git a/debian/patches/support_x32 b/debian/patches/support_x32
index e5da646adabf298c4bd19b41149b505dcf807d25..7e166d8cd9e5bd8bf669081751a997768ae7aed4 100644 (file)
--- a/debian/patches/support_x32
+++ b/debian/patches/support_x32
@@ -1,16 +1,16 @@
 Author: Aaron M. Ucko <ucko@debian.org>
-Date:   Fri Aug 5 19:42:47 2016 -0400
+Date:   Wed, 01 Dec 2021 21:37:42 -0500
 Description: Support x32
 
 Avoid picking up wrong inline assembly.
 --- a/c++/include/corelib/impl/ncbi_atomic_defs.h
 +++ b/c++/include/corelib/impl/ncbi_atomic_defs.h
-@@ -119,7 +119,7 @@ extern "C" {
-   ((defined(__sparc) && !defined(__sparcv9))  ||  \
-    defined(__i386)  ||  defined(__sparc)  ||  defined(__x86_64)  &&  \
-    (!defined(__GLIBCXX__)  ||  !defined(NCBI_TCHECK)))
--#  if defined(__x86_64)
-+#  if defined(__x86_64)  &&  !defined(_ILP32)
+@@ -120,7 +120,7 @@ extern "C" {
+   (defined(__i386)  ||  defined(__sparc)  ||  defined(__x86_64)  || \
+    defined(__aarch64__))  && \
+   (!defined(__GLIBCXX__)  ||  !defined(NCBI_TCHECK))
+-#  if defined(__x86_64)  ||  defined(__aarch64__)
++#  if (defined(__x86_64)  &&  !defined(_ILP32))  ||  defined(__aarch64__)
  #    define NCBI_COUNTER_64_BIT
  #  endif
  #  ifdef NCBI_COUNTER_64_BIT

diff --git a/debian/patches/tune_lmdb_defaults b/debian/patches/tune_lmdb_defaults
index 32645bbb03fe410af3bd344a7fa8227dcfbf6c8e..080d9b565c37af922273e19f4c7eeaa9b080abe3 100644 (file)
--- a/debian/patches/tune_lmdb_defaults
+++ b/debian/patches/tune_lmdb_defaults
@@ -1,20 +1,14 @@
 --- a/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp
 +++ b/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp
-@@ -51,9 +51,15 @@ BEGIN_NCBI_SCOPE
- #ifdef NCBI_OS_MSWIN
+@@ -52,7 +52,11 @@ BEGIN_NCBI_SCOPE
  #define DEFAULT_LMDB_MAP_SIZE 500000
  #define DEFAULT_TAXID_MAP_SIZE 500000
-+#elif defined(__mips__)
-+#define DEFAULT_LMDB_MAP_SIZE (640 * 1024 * 1024)
-+#define DEFAULT_TAXID_MAP_SIZE (640 * 1024 * 1024)
-+#elif NCBI_PLATFORM_BITS < 64
-+#define DEFAULT_LMDB_MAP_SIZE (750 * 1000 * 1000)
-+#define DEFAULT_TAXID_MAP_SIZE (750 * 1000 * 1000)
  #else
--#define DEFAULT_LMDB_MAP_SIZE 300000000000
--#define DEFAULT_TAXID_MAP_SIZE 100000000000
-+#define DEFAULT_LMDB_MAP_SIZE (20UL * 1000 * 1000 * 1000)
-+#define DEFAULT_TAXID_MAP_SIZE (20UL * 1000 * 1000 * 1000)
++#ifdef __mips__
++#define DEFAULT_LMDB_MAP_SIZE (640 * 1024 * 1024)
++#else
+ #define DEFAULT_LMDB_MAP_SIZE 700000000
++#endif
+ #define DEFAULT_TAXID_MAP_SIZE 300000000
  #endif
  
- /// This class supports creation of a string accession to integer OID