debian/control

@@ -15,7 +15,11 @@ Build-Depends-Arch: 2to3,
                libmbedtls-dev,
                libpcre3-dev,
                time,
-               zlib1g-dev
+               zlib1g-dev,
+               procps,
+               libbackward-cpp-dev,
+               libdw-dev,
+               libmsgsl-dev
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
 Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git

debian/patches/series

@@ -11,3 +11,5 @@ suppress_gnutls_version_check
 optionally_keep_sequence
 fix_unit_tests
 system_mbedtls_only
+reprobuild
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Spelling fixes
+--- ncbi-blastplus.orig/c++/include/objtools/alnmgr/seqids_extractor.hpp
++++ ncbi-blastplus/c++/include/objtools/alnmgr/seqids_extractor.hpp
+@@ -232,7 +232,7 @@
+                         else if (*id_vec[i] != *id) {
+                             string err("Inconsistent Seq-ids found in seg ");
+                             err += NStr::NumericToString(i) +
+-                                ".  Excpected " + id_vec[i]->AsString() +
++                                ".  Expected " + id_vec[i]->AsString() +
+                                 ", encountered " + id->AsString() + ".";
+                             NCBI_THROW(CAlnException, eInvalidSeqId, err);
+                         }
+--- ncbi-blastplus.orig/c++/src/algo/blast/api/blast_setup_cxx.cpp
++++ ncbi-blastplus/c++/src/algo/blast/api/blast_setup_cxx.cpp
+@@ -784,7 +784,7 @@
+         		if(warning != kEmptyStr){
+         			warning += ": ";
+         		}
+-        		warning += "Subject sequence contians no data";
++        		warning += "Subject sequence contains no data";
+         		ERR_POST(Warning << warning);
+         		continue;
+         	}
+--- ncbi-blastplus.orig/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
++++ ncbi-blastplus/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
+@@ -75,7 +75,7 @@
+         }
+         else NCBI_THROW( CSeqMaskerOstatFactoryException,
+                          eBadName,
+-                         "unkown unit counts format" );
++                         "unknown unit counts format" );
+     }
+     catch( CException & e ) {
+         NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
+@@ -113,7 +113,7 @@
+         }
+         else NCBI_THROW( CSeqMaskerOstatFactoryException,
+                          eBadName,
+-                         "unkown unit counts format" );
++                         "unknown unit counts format" );
+     }
+     catch( CException & e ) {
+         NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
+--- ncbi-blastplus.orig/c++/src/app/blastdb/blastdbcheck.cpp
++++ ncbi-blastplus/c++/src/app/blastdb/blastdbcheck.cpp
+@@ -232,7 +232,7 @@
+          "Require that all sequences in the database have taxid set.");
+ 
+     arg_desc->AddFlag
+-        ("cdd_delta", "Do aditional tests for a CDD database for DELTA-BLAST");
++        ("cdd_delta", "Do additional tests for a CDD database for DELTA-BLAST");
+ 
+     // Setup arg.descriptions for this application
+     SetupArgDescriptions(arg_desc.release());
+--- ncbi-blastplus.orig/c++/src/app/blastdb/makeprofiledb.cpp
++++ ncbi-blastplus/c++/src/app/blastdb/makeprofiledb.cpp
+@@ -546,13 +546,13 @@
+ 
+ 		if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength()))
+ 		{
+-			string err = filename + " contians no bioseq data";
++			string err = filename + " contains no bioseq data";
+ 			NCBI_THROW(CInputException, eInvalidInput,  err);
+ 		}
+ 
+ 		if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns())
+ 		{
+-			string err = filename + " contians no info on num of columns or num of rows";
++			string err = filename + " contains no info on num of columns or num of rows";
+ 			NCBI_THROW(CInputException, eInvalidInput,  err);
+ 		}
+ 
+@@ -605,13 +605,13 @@
+ 
+ 		if(sm_invalid == sm)
+ 		{
+-			string err = filename + " contians no pssm or residue frequencies";
++			string err = filename + " contains no pssm or residue frequencies";
+ 			NCBI_THROW(CInputException, eInvalidInput,  err);
+ 		}
+ 	}
+ 	else
+ 	{
+-		string err = filename + " contians no scoremat";
++		string err = filename + " contains no scoremat";
+ 		NCBI_THROW(CInputException, eInvalidInput,  err);
+ 	}
+ 
+@@ -1563,7 +1563,7 @@
+     if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
+     {
+     	*m_LogFile << filename +
+-    			" was excluded: it conatins an invalid CD \n";
++    			" was excluded: it contains an invalid CD \n";
+     	return false;
+     }
+ 
+--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos.c
++++ ncbi-blastplus/c++/src/connect/ncbi_lbos.c
+@@ -951,7 +951,7 @@
+                                            sizeof(char) * (strlen(buf) + 1))) ) 
+     {
+         CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using "
+-                               "original stirng");
++                               "original string");
+     }  else  {
+         buf = realloc_result;
+     }
+--- ncbi-blastplus.orig/c++/src/objects/seqalign/Dense_seg.cpp
++++ ncbi-blastplus/c++/src/objects/seqalign/Dense_seg.cpp
+@@ -988,7 +988,7 @@
+             if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
+                 NCBI_THROW(CSeqalignException, eInvalidInputData,
+                            "CDense_seg::RemapToLoc():"
+-                           " The strand should be the same accross"
++                           " The strand should be the same across"
+                            " the input seq-loc");
+             }
+         }
+--- ncbi-blastplus.orig/c++/src/objects/seqalign/Seq_align.cpp
++++ ncbi-blastplus/c++/src/objects/seqalign/Seq_align.cpp
+@@ -872,7 +872,7 @@
+         if (dim != ss.GetDim()  ||  row != dim) {
+             NCBI_THROW(CSeqalignException, eInvalidInputAlignment,
+                        "CreateDensegFromStdseg(): "
+-                       "Inconsistent dimentions!");
++                       "Inconsistent dimensions!");
+         }
+ 
+         if (widths_determined[seg]) {
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.inc
++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.inc
+@@ -661,7 +661,7 @@
+ "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",
+-"BR<BRA>\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t",
++"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",
+ "BRC\ts\tBotanical Record Club\t\t\t",
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.txt
++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.txt
+@@ -628,7 +628,7 @@
+ 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			
+-BR<BRA>	c	Johanna Dobereiner Biological Resouce Center (CRB-JD)			
++BR<BRA>	c	Johanna Dobereiner Biological Resource Center (CRB-JD)			
+ BRA	s	Slovak National Museum, Botany Department			
+ BRAD	s	University of Bradford, Biology Department			
+ BRC	s	Botanical Record Club			
+--- ncbi-blastplus.orig/c++/src/objmgr/util/sequence.cpp
++++ ncbi-blastplus/c++/src/objmgr/util/sequence.cpp
+@@ -274,7 +274,7 @@
+     if ( best_feats.empty() ) {
+         NCBI_THROW_FMT(CObjMgrException, eFindFailed,
+                        "GetProteinName("<<GetId(seq, eGetId_Best)<<"): "
+-                       "the sequence does't have prot feature");
++                       "the sequence doesn't have prot feature");
+     }
+     if ( best_feats.size() > 1 ) {
+         NCBI_THROW_FMT(CObjMgrException, eFindConflict,
+--- ncbi-blastplus.orig/c++/src/objtools/align_format/taxFormat.cpp
++++ ncbi-blastplus/c++/src/objtools/align_format/taxFormat.cpp
+@@ -587,7 +587,7 @@
+             }            
+         }
+         if (!tax_load_ok) {
+-            NCBI_THROW(CException, eUnknown,"Taxonomic load was not successfull.");
++            NCBI_THROW(CException, eUnknown,"Taxonomic load was not successful.");
+         }
+         m_TaxTreeLoaded = true;
+             
+--- ncbi-blastplus.orig/c++/src/objtools/format/flat_file_config.cpp
++++ ncbi-blastplus/c++/src/objtools/format/flat_file_config.cpp
+@@ -614,7 +614,7 @@
+ 
+          // from
+          arg_desc->AddOptionalKey("from", "From",
+-                                  "Begining of shown range", CArgDescriptions::eInteger);
++                                  "Beginning of shown range", CArgDescriptions::eInteger);
+ 
+          // to
+          arg_desc->AddOptionalKey("to", "To",
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_converter.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_converter.cpp
+@@ -728,7 +728,7 @@
+         submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());
+         submit_block_writer.Flush();
+         seq_sub_header_strm << "," << endl;
+-        seq_sub_header_strm << "data entrys {" << endl;
++        seq_sub_header_strm << "data entries {" << endl;
+ 
+         out_sObjectOpeningString = seq_sub_header_strm.str();
+         out_sObjectClosingString = "} }" + out_sObjectClosingString;
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_util.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_util.cpp
+@@ -67,7 +67,7 @@
+ 
+     "object_beg != previous object_end + 1",
+     "no valid AGP lines",
+-    "consequtive gaps lines with the same type and linkage",
++    "consecutive gaps lines with the same type and linkage",
+     "in \"Scaffold from component\" file, invalid scaffold-breaking gap",
+     "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
+ 
+@@ -88,7 +88,7 @@
+     // Content Warnings
+     "gap at the end of object (OK if X is the circular chromosome/plasmid)",
+     "gap at the beginning of object ",
+-    "two consequtive gap lines (e.g. a gap at the end of "
++    "two consecutive gap lines (e.g. a gap at the end of "
+         "a scaffold, two non scaffold-breaking gaps, ...)",
+     "no components in object",
+     "the span overlaps a previous span for this component",
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_validate_reader.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_validate_reader.cpp
+@@ -295,7 +295,7 @@
+       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) {
+-        sameComId_otherScaf="; previous occurance at ";
++        sameComId_otherScaf="; previous occurrence at ";
+         if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) {
+           sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file);
+           sameComId_otherScaf += ":";
+--- ncbi-blastplus.orig/c++/src/util/compress/api/compress.cpp
++++ ncbi-blastplus/c++/src/util/compress/api/compress.cpp
+@@ -160,7 +160,7 @@
+     while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {
+         os.write(buf.get(), nread);
+         if ( !os.good() ) {
+-            SetError(-1, "Error writing to ouput file");
++            SetError(-1, "Error writing to output file");
+             return false;
+         }
+     }

debian/rules

@@ -4,6 +4,8 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+export HOME=$(CURDIR)/fakehome
+
 NUMJOBS=1
 ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
     NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
@@ -62,6 +64,7 @@ endif
 
 override_dh_auto_configure-indep:;
 override_dh_auto_configure-arch: $(PREBUILT_DATATOOL_EXE)
+	mkdir -p $(HOME)
 	cd c++  &&  CONFIG_SHELL=/bin/bash \
             ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
 	    ||  (tail -v -n +0 config.log BUILD/status/config.log; exit 1)
@@ -102,7 +105,7 @@ override_dh_install-arch:
 	   > $(instroot)/bin/windowmasker_2.2.22_adapter
 	2to3 -w $(instroot)/bin/windowmasker_2.2.22_adapter
 	chmod +x $(instroot)/bin/windowmasker_2.2.22_adapter
-	rm $(instroot)/bin/windowmasker_2.2.22_adapter.py
+	rm $(instroot)/bin/windowmasker_2.2.22_adapter.py*
 # Clean up tests, demos, and internal build tools
 	rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
 	    $(instroot)/bin/datatool $(instroot)/bin/run_with_lock \

debian/watch

 version=3
-opts=pasv,filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \
-     ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate
+opts=filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \
+     https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate