From ce70ead6c6d1781e84d681d7d998bdedea7e6f9b Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Wed, 1 Dec 2021 21:49:06 -0500 Subject: [PATCH] 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. --- debian/changelog | 10 ++++++- debian/patches/fix_lib_deps | 16 +++++------ debian/patches/fix_unit_tests | 4 +-- debian/patches/fix_x86isms | 18 ------------ debian/patches/run_perl_directly | 4 +-- debian/patches/series | 1 - debian/patches/spelling | 48 +++++++++++++++---------------- debian/patches/support_x32 | 14 ++++----- debian/patches/tune_lmdb_defaults | 20 +++++-------- 9 files changed, 59 insertions(+), 76 deletions(-) delete mode 100644 debian/patches/fix_x86isms diff --git a/debian/changelog b/debian/changelog index f79691df..808d7e58 100644 --- 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 Wed, 01 Dec 2021 21:32:28 -0500 + -- Aaron M. Ucko 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 90a475e0..7a26bdd6 100644 --- 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 d75b78b1..ef4a2262 100644 --- a/debian/patches/fix_unit_tests +++ b/debian/patches/fix_unit_tests @@ -5,8 +5,8 @@ Author: Olivier Sallou 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 index 1683357a..00000000 --- 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 ed84d7be..aa72d5ef 100644 --- a/debian/patches/run_perl_directly +++ b/debian/patches/run_perl_directly @@ -1,5 +1,5 @@ Author: Aaron M. Ucko -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 69b0517d..a30023b7 100644 --- 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 b6da0056..608a4cd4 100644 --- a/debian/patches/spelling +++ b/debian/patches/spelling @@ -2,7 +2,7 @@ From: Michael R. Crusoe 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\ts\tBotanic Garden Meise\t\t\t", @@ -139,10 +139,10 @@ Subject: Spelling fixes +"BR\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 s Botanic Garden Meise @@ -150,10 +150,10 @@ Subject: Spelling fixes +BR 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("<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 e5da646a..7e166d8c 100644 --- a/debian/patches/support_x32 +++ b/debian/patches/support_x32 @@ -1,16 +1,16 @@ Author: Aaron M. Ucko -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 32645bbb..080d9b56 100644 --- 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 -- 2.30.2