From abe67c72cfb015f1947a0ed33fd100635d9a5ab4 Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Wed, 17 Jul 2024 21:39:29 -0400 Subject: [PATCH] d/patches: Update for new release (2.15.0[+ds]), mostly formally. --- debian/changelog | 3 +- .../patches/enable_clean_after_failed_compile | 2 +- debian/patches/fix_lib_deps | 53 ++--- debian/patches/fix_unit_tests | 6 +- debian/patches/hurd_fixes | 4 +- debian/patches/no_multiarch_rpath | 4 +- debian/patches/optin_usage_report | 8 +- debian/patches/optionally_keep_sequence | 4 +- debian/patches/reprobuild | 193 ++++-------------- debian/patches/run_perl_directly | 2 +- debian/patches/skip_services_unit_test | 6 +- debian/patches/spelling | 76 +------ debian/patches/support_gcc10 | 4 +- debian/patches/suppress_tls_version_checks | 24 +-- debian/patches/system_mbedtls_only | 12 +- debian/patches/use_pie_for_apps | 4 +- 16 files changed, 122 insertions(+), 283 deletions(-) diff --git a/debian/changelog b/debian/changelog index 159c867d..bb87383d 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,8 +2,9 @@ ncbi-blast+ (2.15.0+ds-1) UNRELEASED; urgency=medium * New upstream release, which should be (more than) new enough for recent q2-feature-classifier. (Closes: #1074316.) (NOT RELEASED YET.) + * debian/patches: Update for new release, mostly formally. - -- Aaron M. Ucko Wed, 17 Jul 2024 21:23:09 -0400 + -- Aaron M. Ucko Wed, 17 Jul 2024 21:39:28 -0400 ncbi-blast+ (2.12.0+ds-4) unstable; urgency=medium diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile index 179768ed..96b9b268 100644 --- a/debian/patches/enable_clean_after_failed_compile +++ b/debian/patches/enable_clean_after_failed_compile @@ -5,7 +5,7 @@ Last-Updated: 2013-06-01 Forwarded: no --- a/c++/src/build-system/new_module.sh.in +++ b/c++/src/build-system/new_module.sh.in -@@ -198,7 +198,7 @@ +@@ -203,7 +203,7 @@ if test -z "$datatool"; then # keep look if test -n "$DYLD_LIBRARY_PATH"; then wrapper="DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH" fi diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 7a26bdd6..b90c0a39 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -16,14 +16,13 @@ Author: Aaron M. Ucko Last-Update: 2016-12-05 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib -@@ -27,7 +27,9 @@ SRC = $(SRC_CXX) +@@ -27,7 +27,8 @@ SRC = $(SRC_CXX) LIB = blastinput --DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil -+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \ -+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \ -+ scoremat seqset seq xser xutil xncbi +-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil sqlitewrapp ++DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \ ++ seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) sqlitewrapp scoremat # should be redundant, given the above :-/ ASN_DEP = seqset xnetblast @@ -94,15 +93,15 @@ Last-Update: 2016-12-05 seqmasks_io --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt -@@ -1603,7 +1603,7 @@ xbiosample_util needs mlacli - xbiosample_util needs valid +@@ -1369,7 +1369,7 @@ xassembly_svc needs gc_asn_access + xbiosample_util needs $(OBJEDIT_LIBS) xbiosample_util needs xmlwrapp xbiosample_util needs xobjutil -xblast includes blast +xblast needs blast + xblast needs utrtprof xblast needs xalgoblastdbindex xblast needs xalgodustmask - xblast needs xalgowinmask --- a/c++/src/cgi/Makefile.cgi.lib +++ b/c++/src/cgi/Makefile.cgi.lib @@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb @@ -303,14 +302,17 @@ Last-Update: 2016-12-05 # CFLAGS = $(FAST_CFLAGS) --- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -29,6 +29,8 @@ LIB = seqdb - DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) +@@ -27,9 +27,10 @@ seqidlist_reader \ + tax4blastsqlite + + LIB = seqdb +-DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp LIBS = $(BLAST_THIRD_PARTY_LIBS) -+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi ++DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp + CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE) + CPPFLAGS = -DNCBI_MODULE=BLASTDB $(SQLITE3_INCLUDE) $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE) CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib @@ -467,9 +469,9 @@ Last-Update: 2016-12-05 CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) --DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) -+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi - LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS) +-DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) ++DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) xutil xncbi + LIBS = $(BZ2_LIBS) $(LZO_LIBS) $(Z_LIBS) $(ZSTD_LIBS) $(ORIG_LIBS) WATCHERS = ivanov --- a/c++/src/util/xregexp/Makefile.xregexp.lib @@ -478,15 +480,15 @@ Last-Update: 2016-12-05 CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) --DLL_LIB = $(PCRE_LIB) -+DLL_LIB = $(PCRE_LIB) xncbi +-DLL_LIB = $(PCRE_LIB) xutil ++DLL_LIB = $(PCRE_LIB) xutil xncbi LIBS = $(PCRE_LIBS) USES_LIBRARIES = \ --- a/c++/src/objtools/readers/Makefile.xobjread.lib +++ b/c++/src/objtools/readers/Makefile.xobjread.lib @@ -29,6 +29,6 @@ SRC = reader_message reader_listener rea - message_listener line_error + message_listener line_error -DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging @@ -600,10 +602,11 @@ Last-Update: 2016-12-05 biblio --- a/c++/src/objects/mla/Makefile.mla.lib +++ b/c++/src/objects/mla/Makefile.mla.lib -@@ -1,6 +1,7 @@ +@@ -1,7 +1,7 @@ LIB = mla SRC = mla__ mla___ +-DLL_LIB = medlars +DLL_LIB = medlars pub pubmed xser xutil xncbi USES_LIBRARIES = \ @@ -642,7 +645,7 @@ Last-Update: 2016-12-05 +++ b/c++/src/objects/taxon3/Makefile.taxon3.lib @@ -8,6 +8,7 @@ DLL_LIB = xconnect - WATCHERS = bollin holmesbr + WATCHERS = stakhovv holmesbr +DLL_LIB = xconnect seq xser xutil xncbi @@ -693,7 +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 + cleanup_message huge_file_cleanup influenza_set -DLL_LIB = $(OBJEDIT_LIBS) xregexp $(PCRE_LIB) +DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS) @@ -704,13 +707,13 @@ Last-Update: 2016-12-05 +++ b/c++/src/objtools/format/Makefile.xformat.lib @@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect - WATCHERS = ludwigf dicuccio + WATCHERS = dicuccio gotvyans +DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \ + xobjutil taxon3 $(SOBJMGR_LIBS) USES_LIBRARIES = \ - gbseq mlacli xalnmgr xcleanup + gbseq xalnmgr xcleanup --- a/c++/src/objects/blast/Makefile.xnetblastcli.lib +++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib @@ -5,5 +5,7 @@ SRC = blastclient blastclient_ @@ -750,7 +753,7 @@ 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 -@@ -13,6 +13,8 @@ UNIX_SRC = $(LOCAL_LBSM) +@@ -12,6 +12,8 @@ SRC = $(SRC_C) $(SRC_CXX) $(SRC_TLS LIB = xconnect @@ -768,7 +771,7 @@ Last-Update: 2016-12-05 -DLL_LIB = seqcode pub general xser sequtil +DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi - WATCHERS = vasilche grichenk bollin ludwigf + WATCHERS = vasilche grichenk stakhovv gotvyans --- a/c++/src/objects/seqset/Makefile.seqset.lib +++ b/c++/src/objects/seqset/Makefile.seqset.lib diff --git a/debian/patches/fix_unit_tests b/debian/patches/fix_unit_tests index ef4a2262..4687884f 100644 --- a/debian/patches/fix_unit_tests +++ b/debian/patches/fix_unit_tests @@ -5,10 +5,10 @@ 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_SRA_LIBS=blast_sra $(SRAXF_LIBS) v - BLAST_LDEP = utrtprof xalgoblastdbindex composition_adjustment \ +@@ -22,7 +22,7 @@ BLAST_LDEP = utrtprof xalgoblastdbindex xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \ - xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables $(LMDB_LIB) + xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb \ + sqlitewrapp scoremat tables $(LMDB_LIB) -BLAST_LIBS = proteinkmer xblast $(BLAST_LDEP) +BLAST_LIBS = proteinkmer xblast blast $(BLAST_LDEP) diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index d28a3f79..7c7ac40f 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -9,7 +9,7 @@ Author: Aaron M. Ucko Last-Update: 2020-09-19 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -10354,7 +10354,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -10806,7 +10806,7 @@ if test -z "$CONF_f_runpath" ; then CONF_f_runpath="-R" ;; linux*:[GI]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \ @@ -20,7 +20,7 @@ Last-Update: 2020-09-19 irix*:* | linux*:KCC | *:Compaq ) --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -2213,7 +2213,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -2419,7 +2419,7 @@ if test -z "$CONF_f_runpath" ; then CONF_f_runpath="-R" ;; linux*:[[GI]]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \ diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index de626df0..842d3978 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -10126,7 +10126,7 @@ +@@ -10912,7 +10912,7 @@ case "$compiler:$compiler_version:$with_ break ;; /* ) @@ -21,7 +21,7 @@ Last-Update: 2011-08-28 esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -2243,7 +2243,7 @@ +@@ -2486,7 +2486,7 @@ case "$compiler:$compiler_version:$with_ break ;; /* ) diff --git a/debian/patches/optin_usage_report b/debian/patches/optin_usage_report index 47c641c5..8a73c3f8 100644 --- a/debian/patches/optin_usage_report +++ b/debian/patches/optin_usage_report @@ -7,7 +7,7 @@ Last-Updated: 202-02-10 Forwarded: no --- a/c++/src/algo/blast/api/blast_usage_report.cpp +++ b/c++/src/algo/blast/api/blast_usage_report.cpp -@@ -184,6 +184,7 @@ +@@ -190,6 +190,7 @@ void CBlastUsageReport::AddParam(EUsageP void CBlastUsageReport::x_CheckBlastUsageEnv() { char * blast_usage_env = getenv("BLAST_USAGE_REPORT"); @@ -15,7 +15,7 @@ Forwarded: no if(blast_usage_env != NULL){ bool enable = NStr::StringToBool(blast_usage_env); if (!enable) { -@@ -192,6 +193,10 @@ +@@ -198,6 +199,10 @@ void CBlastUsageReport::x_CheckBlastUsag LOG_POST(Info <<"Phone home disabled"); return ; } @@ -25,8 +25,8 @@ Forwarded: no + return; } - CNcbiIstrstream empty_stream(kEmptyCStr); -@@ -204,10 +209,15 @@ + CNcbiIstrstream empty_stream(kEmptyStr); +@@ -210,10 +215,15 @@ void CBlastUsageReport::x_CheckBlastUsag LOG_POST(Info <<"Phone home disabled by config setting"); return ; } diff --git a/debian/patches/optionally_keep_sequence b/debian/patches/optionally_keep_sequence index 311b06de..0b48dc46 100644 --- a/debian/patches/optionally_keep_sequence +++ b/debian/patches/optionally_keep_sequence @@ -6,7 +6,7 @@ Description: Hang on to sequence data even if -parse_deflines recognized a non-l "true" value (English-only, case-insensitive true, t, yes, y, or 1). --- a/c++/src/algo/blast/api/search_strategy.cpp +++ b/c++/src/algo/blast/api/search_strategy.cpp -@@ -544,6 +544,11 @@ +@@ -560,6 +560,11 @@ void CExportStrategy::x_Process_Pssm(CRe m_QueueSearchRequest->SetService(new_service); } @@ -18,7 +18,7 @@ Description: Hang on to sequence data even if -parse_deflines recognized a non-l void CExportStrategy::x_Process_Query(CRef & query) { if (query.Empty()) -@@ -565,7 +570,7 @@ +@@ -581,7 +586,7 @@ void CExportStrategy::x_Process_Query(CR // Check if there are any range restrictions applied and if local IDs are // being used to determine how to specify the query sequence(s) diff --git a/debian/patches/reprobuild b/debian/patches/reprobuild index 6767d9ca..2206de50 100644 --- a/debian/patches/reprobuild +++ b/debian/patches/reprobuild @@ -2,7 +2,7 @@ Author: Michael R. Crusoe Description: make the build more reproducible --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -2914,13 +2914,13 @@ case "$host_os" in +@@ -3138,13 +3138,13 @@ case "$host_os" in linux*) kver=`uname -r | sed -e 's/-.*//'` libcver=`ldd --version | awk 'NR == 1 { print $NF }'` @@ -73,7 +73,7 @@ Description: make the build more reproducible NCBI_MAKE_MODULE(NCBI_MODULE)) --- a/c++/include/corelib/test_boost.hpp +++ b/c++/include/corelib/test_boost.hpp -@@ -273,7 +273,7 @@ static ::NCBI_NS_NCBI::SNcbiTestRegistra +@@ -343,7 +343,7 @@ static ::NCBI_NS_NCBI::SNcbiTestRegistra BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \ boost::unit_test::make_test_case( \ &BOOST_AUTO_TC_INVOKER( test_name ), #test_name, \ @@ -84,7 +84,7 @@ Description: make the build more reproducible decorators ); \ --- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp +++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp -@@ -1124,7 +1124,7 @@ void SeqDB_FileIntegrityAssert(const str +@@ -1123,7 +1123,7 @@ void SeqDB_FileIntegrityAssert(const str #define SEQDB_FILE_ASSERT(YESNO) \ do { \ if (! (YESNO)) { \ @@ -130,160 +130,47 @@ Description: make the build more reproducible --- a/c++/src/connect/mbedtls/mbedtls/debug.h +++ b/c++/src/connect/mbedtls/mbedtls/debug.h -@@ -41,28 +41,28 @@ - #define MBEDTLS_DEBUG_STRIP_PARENS( ... ) __VA_ARGS__ +@@ -39,33 +39,33 @@ + #define MBEDTLS_DEBUG_STRIP_PARENS(...) __VA_ARGS__ - #define MBEDTLS_SSL_DEBUG_MSG( level, args ) \ -- mbedtls_debug_print_msg( ssl, level, __FILE__, __LINE__, \ -+ mbedtls_debug_print_msg( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, \ - MBEDTLS_DEBUG_STRIP_PARENS args ) + #define MBEDTLS_SSL_DEBUG_MSG(level, args) \ +- mbedtls_debug_print_msg(ssl, level, __FILE__, __LINE__, \ ++ mbedtls_debug_print_msg(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, \ + MBEDTLS_DEBUG_STRIP_PARENS args) - #define MBEDTLS_SSL_DEBUG_RET( level, text, ret ) \ -- mbedtls_debug_print_ret( ssl, level, __FILE__, __LINE__, text, ret ) -+ mbedtls_debug_print_ret( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, ret ) + #define MBEDTLS_SSL_DEBUG_RET(level, text, ret) \ +- mbedtls_debug_print_ret(ssl, level, __FILE__, __LINE__, text, ret) ++ mbedtls_debug_print_ret(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, ret) - #define MBEDTLS_SSL_DEBUG_BUF( level, text, buf, len ) \ -- mbedtls_debug_print_buf( ssl, level, __FILE__, __LINE__, text, buf, len ) -+ mbedtls_debug_print_buf( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, buf, len ) + #define MBEDTLS_SSL_DEBUG_BUF(level, text, buf, len) \ +- mbedtls_debug_print_buf(ssl, level, __FILE__, __LINE__, text, buf, len) ++ mbedtls_debug_print_buf(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, buf, len) #if defined(MBEDTLS_BIGNUM_C) - #define MBEDTLS_SSL_DEBUG_MPI( level, text, X ) \ -- mbedtls_debug_print_mpi( ssl, level, __FILE__, __LINE__, text, X ) -+ mbedtls_debug_print_mpi( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X ) + #define MBEDTLS_SSL_DEBUG_MPI(level, text, X) \ +- mbedtls_debug_print_mpi(ssl, level, __FILE__, __LINE__, text, X) ++ mbedtls_debug_print_mpi(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X) #endif #if defined(MBEDTLS_ECP_C) - #define MBEDTLS_SSL_DEBUG_ECP( level, text, X ) \ -- mbedtls_debug_print_ecp( ssl, level, __FILE__, __LINE__, text, X ) -+ mbedtls_debug_print_ecp( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X ) + #define MBEDTLS_SSL_DEBUG_ECP(level, text, X) \ +- mbedtls_debug_print_ecp(ssl, level, __FILE__, __LINE__, text, X) ++ mbedtls_debug_print_ecp(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X) #endif #if defined(MBEDTLS_X509_CRT_PARSE_C) - #define MBEDTLS_SSL_DEBUG_CRT( level, text, crt ) \ -- mbedtls_debug_print_crt( ssl, level, __FILE__, __LINE__, text, crt ) -+ mbedtls_debug_print_crt( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, crt ) + #define MBEDTLS_SSL_DEBUG_CRT(level, text, crt) \ +- mbedtls_debug_print_crt(ssl, level, __FILE__, __LINE__, text, crt) ++ mbedtls_debug_print_crt(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, crt) + #endif + + #if defined(MBEDTLS_ECDH_C) + #define MBEDTLS_SSL_DEBUG_ECDH(level, ecdh, attr) \ +- mbedtls_debug_printf_ecdh(ssl, level, __FILE__, __LINE__, ecdh, attr) ++ mbedtls_debug_printf_ecdh(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, ecdh, attr) #endif #else /* MBEDTLS_DEBUG_C */ ---- a/c++/src/connect/ncbi_lbos_cxx.cpp -+++ b/c++/src/connect/ncbi_lbos_cxx.cpp -@@ -146,7 +146,7 @@ std::string CLBOSIpCache::HostnameResolv - { - /* Hostname should not be empty in any case */ - if (hostname.empty()) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eUnknown, - "Internal error in LBOS Client IP Cache. Please contact developer", - eLBOS_BadRequest); -@@ -218,7 +218,7 @@ static void s_ProcessResult(unsigned sho - if (lbos_answer != NULL) { - message << " " << lbos_answer; - } -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::s_HTTPCodeToEnum(result), - message.str(), result); - } -@@ -249,7 +249,7 @@ void LBOS::Announce(const string& servi - /* If we could not parse healthcheck URL, throw "Invalid Arguments" */ - if (cur_host.empty()) { - ConnNetInfo_Destroy(healthcheck_info); -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - NStr::IntToString(eLBOS_InvalidArgs), - eLBOS_InvalidArgs); -@@ -308,7 +308,7 @@ void LBOS::AnnounceFromRegistry(const st - port_int = NStr::StringToInt(port_str); - } - catch (...) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "Could not parse port \"" + port_str + - "\" in section \"" + reg_section + "\"", -@@ -316,7 +316,7 @@ void LBOS::AnnounceFromRegistry(const st - } - if (port_int < 1 || port_int > 65535) - { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "Invalid server port \"" + port_str + - "\" in section \"" + reg_section + "\"", -@@ -624,7 +624,7 @@ void LBOS::CMetaData::Set(const CTempStr - /* Forbidden names for meta parameters */ - if (name == "version" || name == "ip" || name == "port" || name == "check" - || name == "format" || name == "name") { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "This name cannot be used for metadata", - eLBOS_InvalidArgs); -@@ -680,7 +680,7 @@ void LBOS::CMetaData::SetRate(const stri - SetRate(NStr::StringToInt(rate)); - } - catch (const CStringException&) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "Could not parse string value for SetRate", - eLBOS_InvalidArgs); -@@ -707,7 +707,7 @@ double LBOS::CMetaData::GetRate() const - return NStr::StringToDouble(rate); - } - catch (const CStringException&) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "Value in \"rate\" meta parameter cannot " - "be represented as an integer", -@@ -719,7 +719,7 @@ double LBOS::CMetaData::GetRate() const - void LBOS::CMetaData::SetType(const string& host_type) - { - if (host_type.find_first_of(" \t\n\v\f\r") != string::npos) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "This convenience function throws on whitespace characters " - "in \"type\" meta parameter. If you know what you are doing, " -@@ -760,7 +760,7 @@ void LBOS::CMetaData::SetType(EHostType - SetType(""); - break; - default: -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, "Unknown EHostType " - "value. If you are sure that a correct value is " - "used, please tell the developer about this issue", -@@ -794,7 +794,7 @@ void LBOS::CMetaData::SetType(ESERV_Type - SetType("FIREWALL"); - break; - default: -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, "Unknown ESERV_Type " - "value. If you are sure that a correct value is " - "used, please tell the developer about this issue", -@@ -825,7 +825,7 @@ void LBOS::CMetaData::SetType(int host_t - SetType(""); - break; - default: -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, "Unknown EHostType " - "value. If you are sure that a correct value is " - "used, please tell the developer about this issue", -@@ -871,7 +871,7 @@ LBOS::CMetaData::EHostType LBOS::CMetaDa - void LBOS::CMetaData::SetExtra(const string& extra) - { - if (extra.find_first_of(" \t\n\v\f\r") != string::npos) { -- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL, -+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL, - CLBOSException::eInvalidArgs, - "This convenience function throws on whitespace characters " - "in \"extra\" meta parameter. If you know what you are doing, " --- a/c++/src/connect/ncbi_monkey.cpp +++ b/c++/src/connect/ncbi_monkey.cpp @@ -83,7 +83,7 @@ const string kEnablField @@ -542,7 +429,7 @@ Description: make the build more reproducible bool s_IsTaxNameElement(const string& value) { -@@ -1367,7 +1367,7 @@ static const char* const s_StopWords[] = +@@ -1376,7 +1376,7 @@ static const char* const s_StopWords[] = }; typedef CStaticArraySet TCStopWordStrSet; @@ -553,24 +440,26 @@ Description: make the build more reproducible bool CBioSource::IsStopWord(const string& value) --- a/c++/src/objects/seqfeat/SubSource.cpp +++ b/c++/src/objects/seqfeat/SubSource.cpp -@@ -3120,7 +3120,7 @@ static const char* const s_Countries[] = +@@ -3225,7 +3225,9 @@ static const char* const s_Countries[] = + "Zambia", "Zimbabwe" }; - typedef CStaticArraySet TCStrSet; -static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), __FILE__, __LINE__); -+static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__); ++static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), ++ "c+++/src/objects/seqfeat/SubSource.cpp", ++ __LINE__); // former legal country names, must be in alphabetical order (case sensitive) static const char* const s_Former_Countries[] = { -@@ -3140,7 +3140,7 @@ static const char* const s_Former_Countr +@@ -3246,7 +3248,7 @@ static const char* const s_Former_Countr "Yugoslavia", "Zaire" }; -static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), __FILE__, __LINE__); +static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__); - bool CCountries::IsValid(const string& country) - { + // null term exemption values, must be in alphabetical order (case sensitive) + static const char* const s_Null_Countries[] = { --- a/c++/src/serial/datatool/classstr.cpp +++ b/c++/src/serial/datatool/classstr.cpp @@ -850,7 +850,7 @@ mem_simple = false; @@ -584,7 +473,7 @@ Description: make the build more reproducible " }\n"; --- a/c++/src/serial/serialobject.cpp +++ b/c++/src/serial/serialobject.cpp -@@ -295,7 +295,7 @@ void CSerialObject::ThrowUnassigned(TMem +@@ -299,7 +299,7 @@ void CSerialObject::ThrowUnassigned(TMem // set temporary diag compile info to use argument file name and line #undef DIAG_COMPILE_INFO #define DIAG_COMPILE_INFO \ @@ -593,7 +482,7 @@ Description: make the build more reproducible file_line? file_line: __LINE__, \ NCBI_CURRENT_FUNCTION, \ NCBI_MAKE_MODULE(NCBI_MODULE)) -@@ -303,7 +303,7 @@ void CSerialObject::ThrowUnassigned(TMem +@@ -307,7 +307,7 @@ void CSerialObject::ThrowUnassigned(TMem // restore original diag compile info definition #undef DIAG_COMPILE_INFO #define DIAG_COMPILE_INFO \ diff --git a/debian/patches/run_perl_directly b/debian/patches/run_perl_directly index aa72d5ef..7adece18 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 632592 2021-06-03 13:20:59Z ivanov $ + # $Id: update_blastdb.pl 672917 2023-09-18 17:55:38Z ivanov $ # =========================================================================== # diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test index a97840fe..309f9443 100644 --- a/debian/patches/skip_services_unit_test +++ b/debian/patches/skip_services_unit_test @@ -5,9 +5,9 @@ Description: test require internet connection Last-Updated: 2013-06-01 --- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app +++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app -@@ -11,6 +11,7 @@ - - LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) +@@ -12,6 +12,7 @@ LIB = test_boost blast_services xnetblas + LIBS = $(BLAST_THIRD_PARTY_LIBS) $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) \ + $(ORIG_LIBS) -CHECK_CMD = blast_services_unit_test +# This test requires an internet connection, shouldn't be run on a build server diff --git a/debian/patches/spelling b/debian/patches/spelling index 608a4cd4..1f4b2f4f 100644 --- a/debian/patches/spelling +++ b/debian/patches/spelling @@ -11,17 +11,6 @@ Subject: Spelling fixes ", encountered " + id->AsString() + "."; NCBI_THROW(CAlnException, eInvalidSeqId, err); } ---- a/c++/src/algo/blast/api/blast_setup_cxx.cpp -+++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp -@@ -784,7 +784,7 @@ SetupSubjects_OMF(IBlastQuerySource& sub - if(warning != kEmptyStr){ - warning += ": "; - } -- warning += "Subject sequence contians no data"; -+ warning += "Subject sequence contains no data"; - ERR_POST(Warning << warning); - continue; - } --- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp +++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp @@ -75,7 +75,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory @@ -55,39 +44,7 @@ Subject: Spelling fixes SetupArgDescriptions(arg_desc.release()); --- a/c++/src/app/blastdb/makeprofiledb.cpp +++ b/c++/src/app/blastdb/makeprofiledb.cpp -@@ -609,13 +609,13 @@ CMakeProfileDBApp::x_CheckInputScoremat( - - 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); - } - -@@ -668,13 +668,13 @@ CMakeProfileDBApp::x_CheckInputScoremat( - - 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); - } - -@@ -1816,7 +1816,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co +@@ -1838,7 +1838,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid) { *m_LogFile << filename + @@ -96,20 +53,9 @@ Subject: Spelling fixes return false; } return true; ---- a/c++/src/connect/ncbi_lbos.c -+++ b/c++/src/connect/ncbi_lbos.c -@@ -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 " -- "original stirng"); -+ "original string"); - } else { - buf = realloc_result; - } --- a/c++/src/objects/seqalign/Dense_seg.cpp +++ b/c++/src/objects/seqalign/Dense_seg.cpp -@@ -988,7 +988,7 @@ void CDense_seg::RemapToLoc(TDim row, co +@@ -980,7 +980,7 @@ void CDense_seg::RemapToLoc(TDim row, co if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) { NCBI_THROW(CSeqalignException, eInvalidInputData, "CDense_seg::RemapToLoc():" @@ -131,8 +77,8 @@ Subject: Spelling fixes if (widths_determined[seg]) { --- a/c++/src/objects/seqfeat/institution_codes.inc +++ b/c++/src/objects/seqfeat/institution_codes.inc -@@ -728,7 +728,7 @@ static const char* const kInstitutionCol - "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t", +@@ -788,7 +788,7 @@ 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", -"BR\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t", @@ -142,8 +88,8 @@ 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 -@@ -695,7 +695,7 @@ BPPT-ESC c BPPT Ethanol-Single Cell Prot - BPS s California Department of Food and Agriculture +@@ -752,7 +752,7 @@ 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 -BR c Johanna Dobereiner Biological Resouce Center (CRB-JD) @@ -153,7 +99,7 @@ Subject: Spelling fixes BRB s Brassica Resource Bank --- a/c++/src/objmgr/util/sequence.cpp +++ b/c++/src/objmgr/util/sequence.cpp -@@ -274,7 +274,7 @@ string GetProteinName(const CBioseq_Hand +@@ -385,7 +385,7 @@ string GetProteinName(const CBioseq_Hand if ( best_feats.empty() ) { NCBI_THROW_FMT(CObjMgrException, eFindFailed, "GetProteinName("<AddOptionalKey("from", "From", @@ -228,8 +174,8 @@ 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 @@ bool CCompression::x_DecompressFile(CCom - while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) { +@@ -165,7 +165,7 @@ bool CCompression::x_DecompressFile(CCom + while ( (nread = src_file.Read(buf.get(), file_io_bufsize)) > 0 ) { os.write(buf.get(), nread); if ( !os.good() ) { - SetError(-1, "Error writing to ouput file"); diff --git a/debian/patches/support_gcc10 b/debian/patches/support_gcc10 index 5e002472..9af97f4b 100644 --- a/debian/patches/support_gcc10 +++ b/debian/patches/support_gcc10 @@ -7,11 +7,9 @@ Debian-Bug: 957581. narrowing errors for cases with the high bit set when that field is a 32-bit signed integer (as on i386). -Index: b/c++/src/corelib/ncbifile.cpp -=================================================================== --- a/c++/src/corelib/ncbifile.cpp +++ b/c++/src/corelib/ncbifile.cpp -@@ -5129,7 +5129,7 @@ void s_GetFileSystemInfo(const string& +@@ -5178,7 +5178,7 @@ void s_GetFileSystemInfo(const string& GET_STATFS_INFO; if (flags & (fFSI_Type | fFSI_DiskSpace)) { diff --git a/debian/patches/suppress_tls_version_checks b/debian/patches/suppress_tls_version_checks index a49e0c61..39dc4b5a 100644 --- a/debian/patches/suppress_tls_version_checks +++ b/debian/patches/suppress_tls_version_checks @@ -8,36 +8,36 @@ Description: suppress gnu TLS and mbed TLS version checks --- a/c++/src/connect/ncbi_gnutls.c +++ b/c++/src/connect/ncbi_gnutls.c -@@ -692,6 +692,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull +@@ -748,6 +748,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull assert(!s_GnuTlsCredAnon); +#if 0 version = gnutls_check_version(0); if (strcasecmp(GNUTLS_VERSION, version) != 0) { - CORE_LOGF(eLOG_Critical, -@@ -699,6 +700,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull - GNUTLS_VERSION, version)); + CORE_LOGF_X(26, eLOG_Critical, +@@ -755,6 +756,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull + GNUTLS_VERSION, version)); assert(0); } +#endif - if (!pull || !push) - return eIO_InvalidArg; + CORE_TRACE("GnuTlsInit(): Enter"); + --- a/c++/src/connect/ncbi_mbedtls.c +++ b/c++/src/connect/ncbi_mbedtls.c -@@ -665,12 +665,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull +@@ -728,12 +728,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull char buf[32]; mbedtls_version_get_string(version); +#if 0 if (strcasecmp(MBEDTLS_VERSION_STRING, version) != 0) { - CORE_LOGF(eLOG_Critical, - ("%s version mismatch: %s headers vs. %s runtime", - kMbedTls, MBEDTLS_VERSION_STRING, version)); + CORE_LOGF_X(5, eLOG_Critical, + ("%s version mismatch: %s headers vs. %s runtime", + kMbedTls, MBEDTLS_VERSION_STRING, version)); assert(0); } +#endif - if (!pull || !push) - return eIO_InvalidArg; + CORE_TRACE("MbedTlsInit(): Enter"); + diff --git a/debian/patches/system_mbedtls_only b/debian/patches/system_mbedtls_only index 394f3eaf..b4617dc2 100644 --- a/debian/patches/system_mbedtls_only +++ b/debian/patches/system_mbedtls_only @@ -3,17 +3,19 @@ Date: Wed, 01 Dec 2021 23:33:11 -0500 Subject: Omit convenience mbed TLS copy --- a/c++/src/connect/Makefile.connssl.lib +++ b/c++/src/connect/Makefile.connssl.lib -@@ -2,7 +2,9 @@ +@@ -1,8 +1,10 @@ + # $Id: Makefile.connssl.lib 642488 2021-12-20 21:00:34Z ucko $ - CPPFLAGS = $(TLS_INCLUDE) $(ORIG_CPPFLAGS) +-CPPFLAGS = $(TLS_INCLUDE) -I$(srcdir)/mbedtls $(ORIG_CPPFLAGS) ++CPPFLAGS = $(TLS_INCLUDE) $(ORIG_CPPFLAGS) -SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls \ +SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls + +SRC_MBEDTLS_UNUSED = \ - mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/asn1parse \ - mbedtls/asn1write mbedtls/base64 mbedtls/bignum mbedtls/blowfish \ - mbedtls/camellia mbedtls/ccm mbedtls/cipher mbedtls/cipher_wrap \ + mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/aria \ + mbedtls/asn1parse mbedtls/asn1write mbedtls/base64 mbedtls/bignum \ + mbedtls/blowfish mbedtls/camellia mbedtls/ccm mbedtls/chacha20 \ --- a/c++/src/connect/connect_misc_impl.hpp +++ b/c++/src/connect/connect_misc_impl.hpp @@ -30,11 +30,10 @@ diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps index ab72b526..139a8580 100644 --- a/debian/patches/use_pie_for_apps +++ b/debian/patches/use_pie_for_apps @@ -7,7 +7,7 @@ Author: Aaron M. Ucko Last-Update: 2012-05-10 --- a/c++/src/build-system/Makefile.app.in +++ b/c++/src/build-system/Makefile.app.in -@@ -25,8 +25,8 @@ +@@ -25,8 +25,8 @@ default_rule: all ### C/C++ source file compilation setup CPPFLAGS += -DNCBI_APP_BUILT_AS=$(APP) @@ -18,7 +18,7 @@ Last-Update: 2012-05-10 SOURCES = @UNIX_SRC@ $(SRC) ### Standard application build rules -@@ -57,7 +57,7 @@ +@@ -59,7 +59,7 @@ PROJ_TYPE = app include $(builddir)/Makefile.$(Rules) CMD_BASE = $(LINK_WRAPPER) $(LINK) -- 2.30.2