From 19a32770759c2fd739108707f81e2881d0f76390 Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Thu, 25 Jul 2024 20:06:32 -0400 Subject: [PATCH] Update patches again for 2.16.0(+ds). --- debian/patches/allow_pcre2 | 2 +- debian/patches/fix_lib_deps | 2 +- debian/patches/run_perl_directly | 2 +- debian/patches/spelling | 6 +++--- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/debian/patches/allow_pcre2 b/debian/patches/allow_pcre2 index bfef446e..0472bde0 100644 --- 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 7780f29b..bcdf0fa2 100644 --- 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 7adece18..af73bca1 100644 --- 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 1f4b2f4f..c5335527 100644 --- 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\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 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", -- 2.30.2