Update patches again for 2.16.0(+ds).

diff --git a/debian/patches/allow_pcre2 b/debian/patches/allow_pcre2
index bfef446e474ad19c263967be6fbe02471831c3eb..0472bde075976ca4f426ce70c6271e8d842f009e 100644 (file)
--- a/debian/patches/allow_pcre2
+++ b/debian/patches/allow_pcre2
@@ -191,7 +191,7 @@ c++/src/build-system/project_tree_builder.ini elided.
  else
     PCREPOSIX_LIBS=`echo "$PCRE_LIBS" | sed -e 's/-lpcre/-lpcreposix -lpcre/'`
  fi
-@@ -9765,6 +9788,7 @@ AC_SUBST(BZ2_LIB)
+@@ -9871,6 +9894,7 @@ AC_SUBST(BZ2_LIB)
  AC_SUBST(ZSTD_STATIC_LIBS)
  AC_SUBST(PCREPOSIX_LIBS)
  AC_SUBST(PCRE_LIB)

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 7780f29bff9b35d508a6dfd7f1831dea6b17c23b..bcdf0fa2928f4b2319d6c358ba873e0da0161482 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -696,7 +696,7 @@ Last-Update: 2016-12-05
 +++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib
 @@ -11,7 +11,7 @@ SRC = autogenerated_cleanup autogenerate
        cleanup_pub newcleanupp capitalization_string fix_feature_id \
-       cleanup_message huge_file_cleanup influenza_set
+       cleanup_message influenza_set
  
 -DLL_LIB = $(OBJEDIT_LIBS) xregexp $(PCRE_LIB)
 +DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS)

diff --git a/debian/patches/run_perl_directly b/debian/patches/run_perl_directly
index 7adece183b7c693ea7291e85fb4906839a4efca6..af73bca118041cb2e876a90ad7ab0cb75bbc62b4 100644 (file)
--- a/debian/patches/run_perl_directly
+++ b/debian/patches/run_perl_directly
@@ -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 672917 2023-09-18 17:55:38Z ivanov $
+ # $Id: update_blastdb.pl 681901 2024-04-17 13:16:37Z ivanov $
  # ===========================================================================
  #

diff --git a/debian/patches/spelling b/debian/patches/spelling
index 1f4b2f4fbe7b23a191cd0c9258893d664eb40464..c53355278a56c04ea039d8edd71f082429eb013c 100644 (file)
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -77,7 +77,7 @@ Subject: Spelling fixes
          if (widths_determined[seg]) {
 --- a/c++/src/objects/seqfeat/institution_codes.inc
 +++ b/c++/src/objects/seqfeat/institution_codes.inc
-@@ -788,7 +788,7 @@ static const char* const kInstitutionCol
+@@ -791,7 +791,7 @@ static const char* const kInstitutionCol
  "BPPT-ESC\tc\tBPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit\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",
@@ -88,7 +88,7 @@ Subject: Spelling fixes
  "BRB\ts\tBrassica Resource Bank\t\t\t",
 --- a/c++/src/objects/seqfeat/institution_codes.txt
 +++ b/c++/src/objects/seqfeat/institution_codes.txt
-@@ -752,7 +752,7 @@ BPM        s       Beipiao Paleontological Museum
+@@ -755,7 +755,7 @@ BPM        s       Beipiao Paleontological Museum
  BPPT-ESC      c       BPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit                  
  BPU   s       Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology                    
  BR<BEL>       s       Botanic Garden Meise                    
@@ -121,7 +121,7 @@ Subject: Spelling fixes
              
 --- a/c++/src/objtools/format/flat_file_config.cpp
 +++ b/c++/src/objtools/format/flat_file_config.cpp
-@@ -654,7 +654,7 @@ void CFlatFileConfig::AddArgumentDescrip
+@@ -655,7 +655,7 @@ void CFlatFileConfig::AddArgumentDescrip
  
           // from
           arg_desc->AddOptionalKey("from", "From",