From 801247a1a6af0f5436e6f29920cdcb6a9a09fd6a Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Sat, 19 Sep 2020 21:15:02 -0400 Subject: [PATCH] debian/patches: Update existing patches for 2.10.1. * {hurd_fixes,run_perl_directly}: Rebase. * support_gcc10: Drop build-system portions, incorporated upstream as of this release. --- debian/changelog | 6 +- debian/patches/hurd_fixes | 18 +- debian/patches/reprobuild | 122 +++++----- debian/patches/run_perl_directly | 2 +- debian/patches/support_gcc10 | 390 ------------------------------- debian/patches/support_x32 | 6 +- 6 files changed, 79 insertions(+), 465 deletions(-) diff --git a/debian/changelog b/debian/changelog index 7ecf16eb..7df9786d 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,8 +2,12 @@ ncbi-blast+ (2.10.1-1) UNRELEASED; urgency=medium * New upstream release. (NOT RELEASED YET.) - Among other changes, "fix tblastn mt issue". (Closes: #970344.) + * debian/patches/{hurd_fixes,run_perl_directly}: Rebase. + * debian/patches/{reprobuild,support_x32}: Refresh (had fuzz). + * debian/patches/support_gcc10: Drop build-system portions, incorporated + upstream as of this release. - -- Aaron M. Ucko Sat, 19 Sep 2020 21:02:05 -0400 + -- Aaron M. Ucko Sat, 19 Sep 2020 21:15:01 -0400 ncbi-blast+ (2.10.0-3) unstable; urgency=medium diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index adb1800d..d28a3f79 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -6,26 +6,26 @@ Subject: fix portability issues that led to Hurd build failures cope with missing PATH_MAX everywhere, not just under Windows. Author: Aaron M. Ucko -Last-Update: 2011-06-10 +Last-Update: 2020-09-19 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -10017,7 +10017,7 @@ - solaris* ) +@@ -10354,7 +10354,7 @@ if test -z "$CONF_f_runpath" ; then CONF_f_runpath="-R" ;; -- linux*:[GI]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) -+ linux*:[GI]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC) + linux*:[GI]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \ +- | osf*:GCC ) ++ | osf*:GCC | gnu*:GCC ) CONF_f_runpath="-Wl,-rpath," ;; irix*:* | linux*:KCC | *:Compaq ) --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -2175,7 +2175,7 @@ - solaris* ) +@@ -2213,7 +2213,7 @@ if test -z "$CONF_f_runpath" ; then CONF_f_runpath="-R" ;; -- linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) -+ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC ) + linux*:[[GI]]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \ +- | osf*:GCC ) ++ | osf*:GCC | gnu*:GCC ) CONF_f_runpath="-Wl,-rpath," ;; irix*:* | linux*:KCC | *:Compaq ) diff --git a/debian/patches/reprobuild b/debian/patches/reprobuild index 0e659e98..6767d9ca 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 -@@ -2866,13 +2866,13 @@ +@@ -2914,13 +2914,13 @@ case "$host_os" in linux*) kver=`uname -r | sed -e 's/-.*//'` libcver=`ldd --version | awk 'NR == 1 { print $NF }'` @@ -16,11 +16,11 @@ Description: make the build more reproducible -signature_hostname=`(hostname || uname -n) 2>/dev/null \ +signature_hostname=`echo debian_build 2>/dev/null \ | sed 's/\..*//; s/-/_/g; 1q'` - signature="${signature_compiler}_${signature_compiler_version}-${release_debug}${mt_sfx}${dll_sfx}${bit64_sfx}${prof_sfx}--${verbose_host}-${signature_hostname}" + signature="${signature_compiler}_${compiler_version}-${release_debug}${mt_sfx}${dll_sfx}${bit64_sfx}${prof_sfx}--${verbose_host}-${signature_hostname}" AC_DEFINE_UNQUOTED(NCBI_SIGNATURE, "$signature", --- a/c++/include/algo/blast/core/blast_message.h +++ b/c++/include/algo/blast/core/blast_message.h -@@ -117,7 +117,7 @@ +@@ -117,7 +117,7 @@ void Blast_Perror(Blast_Message* *msg, I /** Convenient define to call the function Blast_PerrorEx. */ #define Blast_PerrorWithLocation(msg, error_code, context) \ @@ -31,7 +31,7 @@ Description: make the build more reproducible * name and line number where the error/warning occurred. This function should --- a/c++/include/connect/ncbi_util.h +++ b/c++/include/connect/ncbi_util.h -@@ -135,7 +135,7 @@ +@@ -135,7 +135,7 @@ extern NCBI_XCONNECT_EXPORT MT_LOCK CORE */ #define LOG_WRITE(lg, code, subcode, level, message) \ LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \ @@ -40,7 +40,7 @@ Description: make the build more reproducible #ifdef LOG_DATA /* AIX's defines LOG_DATA to be an integer constant; -@@ -144,7 +144,7 @@ +@@ -144,7 +144,7 @@ extern NCBI_XCONNECT_EXPORT MT_LOCK CORE #endif #define LOG_DATA(lg, code, subcode, level, data, size, message) \ LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \ @@ -62,7 +62,7 @@ Description: make the build more reproducible --- a/c++/include/corelib/ncbidiag.hpp +++ b/c++/include/corelib/ncbidiag.hpp -@@ -168,7 +168,7 @@ +@@ -168,7 +168,7 @@ NCBI_XNCBI_EXPORT const char* g_DiagUnkn /// @sa /// CDiagCompileInfo #define DIAG_COMPILE_INFO \ @@ -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 -@@ -275,7 +275,7 @@ +@@ -273,7 +273,7 @@ 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 @@ +@@ -1124,7 +1124,7 @@ void SeqDB_FileIntegrityAssert(const str #define SEQDB_FILE_ASSERT(YESNO) \ do { \ if (! (YESNO)) { \ @@ -95,7 +95,7 @@ Description: make the build more reproducible --- a/c++/include/util/ddump_viewer.hpp +++ b/c++/include/util/ddump_viewer.hpp -@@ -49,7 +49,7 @@ +@@ -49,7 +49,7 @@ BEGIN_NCBI_SCOPE // #define DEBUGDUMP_BPT(name,obj) \ @@ -106,7 +106,7 @@ Description: make the build more reproducible //--------------------------------------------------------------------------- --- a/c++/include/util/static_set.hpp +++ b/c++/include/util/static_set.hpp -@@ -886,17 +886,17 @@ +@@ -886,17 +886,17 @@ public: static const Type Var #define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array) \ @@ -167,7 +167,7 @@ Description: make the build more reproducible #else /* MBEDTLS_DEBUG_C */ --- a/c++/src/connect/ncbi_lbos_cxx.cpp +++ b/c++/src/connect/ncbi_lbos_cxx.cpp -@@ -145,7 +145,7 @@ +@@ -146,7 +146,7 @@ std::string CLBOSIpCache::HostnameResolv { /* Hostname should not be empty in any case */ if (hostname.empty()) { @@ -176,7 +176,7 @@ Description: make the build more reproducible CLBOSException::eUnknown, "Internal error in LBOS Client IP Cache. Please contact developer", eLBOS_BadRequest); -@@ -217,7 +217,7 @@ +@@ -218,7 +218,7 @@ static void s_ProcessResult(unsigned sho if (lbos_answer != NULL) { message << " " << lbos_answer; } @@ -185,7 +185,7 @@ Description: make the build more reproducible CLBOSException::s_HTTPCodeToEnum(result), message.str(), result); } -@@ -248,7 +248,7 @@ +@@ -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); @@ -194,7 +194,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, NStr::IntToString(eLBOS_InvalidArgs), eLBOS_InvalidArgs); -@@ -307,7 +307,7 @@ +@@ -308,7 +308,7 @@ void LBOS::AnnounceFromRegistry(const st port_int = NStr::StringToInt(port_str); } catch (...) { @@ -203,7 +203,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Could not parse port \"" + port_str + "\" in section \"" + reg_section + "\"", -@@ -315,7 +315,7 @@ +@@ -316,7 +316,7 @@ void LBOS::AnnounceFromRegistry(const st } if (port_int < 1 || port_int > 65535) { @@ -212,7 +212,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Invalid server port \"" + port_str + "\" in section \"" + reg_section + "\"", -@@ -623,7 +623,7 @@ +@@ -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") { @@ -221,7 +221,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "This name cannot be used for metadata", eLBOS_InvalidArgs); -@@ -679,7 +679,7 @@ +@@ -680,7 +680,7 @@ void LBOS::CMetaData::SetRate(const stri SetRate(NStr::StringToInt(rate)); } catch (const CStringException&) { @@ -230,7 +230,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Could not parse string value for SetRate", eLBOS_InvalidArgs); -@@ -706,7 +706,7 @@ +@@ -707,7 +707,7 @@ double LBOS::CMetaData::GetRate() const return NStr::StringToDouble(rate); } catch (const CStringException&) { @@ -239,7 +239,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Value in \"rate\" meta parameter cannot " "be represented as an integer", -@@ -718,7 +718,7 @@ +@@ -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) { @@ -248,7 +248,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "This convenience function throws on whitespace characters " "in \"type\" meta parameter. If you know what you are doing, " -@@ -759,7 +759,7 @@ +@@ -760,7 +760,7 @@ void LBOS::CMetaData::SetType(EHostType SetType(""); break; default: @@ -257,7 +257,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Unknown EHostType " "value. If you are sure that a correct value is " "used, please tell the developer about this issue", -@@ -793,7 +793,7 @@ +@@ -794,7 +794,7 @@ void LBOS::CMetaData::SetType(ESERV_Type SetType("FIREWALL"); break; default: @@ -266,7 +266,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Unknown ESERV_Type " "value. If you are sure that a correct value is " "used, please tell the developer about this issue", -@@ -824,7 +824,7 @@ +@@ -825,7 +825,7 @@ void LBOS::CMetaData::SetType(int host_t SetType(""); break; default: @@ -275,7 +275,7 @@ Description: make the build more reproducible CLBOSException::eInvalidArgs, "Unknown EHostType " "value. If you are sure that a correct value is " "used, please tell the developer about this issue", -@@ -870,7 +870,7 @@ +@@ -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) { @@ -286,7 +286,7 @@ Description: make the build more reproducible "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 @@ +@@ -83,7 +83,7 @@ const string kEnablField const string kSeedField = "seed"; #define PARAM_TWICE_EXCEPTION(param) \ @@ -295,7 +295,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, \ string("Parameter \"" param "\" is set " \ "twice in [") + GetSection() + "]" + \ -@@ -371,7 +371,7 @@ +@@ -371,7 +371,7 @@ static string s_RuleTypeString(EMonkeyAc case eMonkey_Send: return "write"; default: @@ -304,7 +304,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Unknown EMonkeyActionType value")); } -@@ -390,7 +390,7 @@ +@@ -390,7 +390,7 @@ static string s_SocketCallString(EMonkey case eMonkey_Connect: return "connect()"; default: @@ -313,7 +313,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Unknown EMonkeyActionType value")); } -@@ -467,7 +467,7 @@ +@@ -467,7 +467,7 @@ unsigned short CMonkeyRuleBase::GetProba { if (m_RunPos.find(sock) == m_RunPos.end()) { throw CMonkeyException( @@ -322,7 +322,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "The socket provided has not been registered with current rule"); } -@@ -511,7 +511,7 @@ +@@ -511,7 +511,7 @@ void CMonkeyRuleBase::x_ReadEIOStatus(co m_ReturnStatus = eIO_Closed; } else if (eIOStatus == "eio_invalidarg") { throw CMonkeyException( @@ -331,7 +331,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Unsupported 'return_status': ") + eIOStatus_in); } else if (eIOStatus == "eio_interrupt") { -@@ -526,7 +526,7 @@ +@@ -526,7 +526,7 @@ void CMonkeyRuleBase::x_ReadEIOStatus(co m_ReturnStatus = eIO_NotSupported; } else { throw CMonkeyException( @@ -340,7 +340,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Could not parse 'return_status': ") + eIOStatus_in); } -@@ -543,7 +543,7 @@ +@@ -543,7 +543,7 @@ void CMonkeyRuleBase::x_ReadRuns(const s split it on commas*/ vector runs_list = s_Monkey_Split(runs, ','); if (runs_list.size() == 0) @@ -349,7 +349,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Parameter \"runs\" is empty in [") + m_Section + "]" + -@@ -573,7 +573,7 @@ +@@ -573,7 +573,7 @@ void CMonkeyRuleBase::x_ReadRuns(const s if (m_RunMode == eMonkey_RunProbability) { if (*run.rbegin() != '%') { throw CMonkeyException( @@ -358,7 +358,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "Value is not percentage: " + run + ", values have to be either only percentages or " -@@ -593,7 +593,7 @@ +@@ -593,7 +593,7 @@ void CMonkeyRuleBase::x_ReadRuns(const s size_t last_step = m_Runs.size(); if (last_step == 0 && step != 1) { throw CMonkeyException( @@ -367,7 +367,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "In the string of runs: " + runs + " the first " "element MUST set value for the first run"); -@@ -610,7 +610,7 @@ +@@ -610,7 +610,7 @@ void CMonkeyRuleBase::x_ReadRuns(const s assert(run_format == eMonkey_RunSequence); if (*run.rbegin() == '%') { throw CMonkeyException( @@ -376,7 +376,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Value is percentage: ") + run + string(", values have to be either only percentages or " -@@ -619,7 +619,7 @@ +@@ -619,7 +619,7 @@ void CMonkeyRuleBase::x_ReadRuns(const s int val = NStr::StringToInt(run); if (m_Runs.size() > 0 && val <= *m_Runs.rbegin()) { throw CMonkeyException( @@ -385,7 +385,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("\"runs\" should contain values in " "increasing order")); -@@ -815,7 +815,7 @@ +@@ -815,7 +815,7 @@ CMonkeyConnectRule::CMonkeyConnectRule(s string value = name_value[1]; if (name == "allow") { if (allow_set) { @@ -394,7 +394,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Parameter \"allow\" is set " -@@ -827,7 +827,7 @@ +@@ -827,7 +827,7 @@ CMonkeyConnectRule::CMonkeyConnectRule(s } } if (!allow_set) @@ -403,7 +403,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Parameter \"allow\" not set in [") + GetSection() + "]" + -@@ -902,7 +902,7 @@ +@@ -902,7 +902,7 @@ CMonkeyPollRule::CMonkeyPollRule(string string value = name_value[1]; if (name == "ignore") { if (ignore_set) { @@ -412,7 +412,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Parameter \"ignore\" is set " -@@ -914,7 +914,7 @@ +@@ -914,7 +914,7 @@ CMonkeyPollRule::CMonkeyPollRule(string } } if (!ignore_set) { @@ -421,7 +421,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, string("Parameter \"ignore\" not set in [") + GetSection() + "]" + -@@ -1032,7 +1032,7 @@ +@@ -1032,7 +1032,7 @@ static bool s_MatchRegex(const string& t ".*" , ""); if (filtered.find_first_of("[]()+^?{}$.*\\") != string::npos) { throw CMonkeyException( @@ -430,7 +430,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, exception_message); -@@ -1051,7 +1051,7 @@ +@@ -1051,7 +1051,7 @@ static bool s_MatchRegex(const string& t } else { throw CMonkeyException( @@ -439,7 +439,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, exception_message); -@@ -1179,7 +1179,7 @@ +@@ -1179,7 +1179,7 @@ bool CMonkeyPlan::WriteRule(MONKEY_SOCKT ss << "Probability below zero for write rule in plan " << m_Name << ". Check config!"; throw CMonkeyException( @@ -448,7 +448,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, ss.str()); } -@@ -1221,7 +1221,7 @@ +@@ -1221,7 +1221,7 @@ bool CMonkeyPlan::ReadRule(MONKEY_SOCKTY stringstream ss; ss << "Probability below zero for write rule in plan " << m_Name << ". Check config!"; @@ -457,7 +457,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, ss.str()); } -@@ -1270,7 +1270,7 @@ +@@ -1270,7 +1270,7 @@ bool CMonkeyPlan::ConnectRule(MONKEY_SOC stringstream ss; ss << "Probability below zero for write rule in plan " << m_Name << ". Check config!"; @@ -466,7 +466,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, ss.str()); } -@@ -1313,7 +1313,7 @@ +@@ -1313,7 +1313,7 @@ bool CMonkeyPlan::PollRule(size_t* n ss << "Probability below zero for write rule in plan " << m_Name << ". Check config!"; throw CMonkeyException( @@ -475,7 +475,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, ss.str()); } -@@ -1372,7 +1372,7 @@ +@@ -1372,7 +1372,7 @@ CMonkey::CMonkey() : m_Probability(100), { if (sm_HookSwitch == NULL) { throw CMonkeyException( @@ -484,7 +484,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "Launch CONNECT_Init() before initializing CMonkey instance"); } -@@ -1458,7 +1458,7 @@ +@@ -1458,7 +1458,7 @@ void CMonkey::ReloadConfig(const string& prob = (int)(NStr::StringToDouble(prob_str) * 100); } if (prob < 0 || prob > 100) { @@ -493,7 +493,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "Parameter \"probability\"=" + prob_str -@@ -1469,7 +1469,7 @@ +@@ -1469,7 +1469,7 @@ void CMonkey::ReloadConfig(const string& m_Probability = (unsigned short)prob; } catch (const CStringException&) { @@ -502,7 +502,7 @@ Description: make the build more reproducible NULL, CMonkeyException::e_MonkeyInvalidArgs, "Parameter \"probability\"=" + prob_str + " for section [" + monkey_section -@@ -1757,7 +1757,7 @@ +@@ -1757,7 +1757,7 @@ bool CMonkey::RegisterThread(int token) << " has been already registered in CMonkey and cannot be used again"; if (m_RegisteredTokens.find(token) != m_RegisteredTokens.end()) { throw CMonkeyException( @@ -513,7 +513,7 @@ Description: make the build more reproducible } --- a/c++/src/connect/ncbi_priv.h +++ b/c++/src/connect/ncbi_priv.h -@@ -222,7 +222,7 @@ +@@ -222,7 +222,7 @@ extern NCBI_XCONNECT_EXPORT LOG g_CORE_L _mess.level = _xx_level; \ _mess.module = THIS_MODULE; \ _mess.func = CORE_CURRENT_FUNCTION; \ @@ -524,7 +524,7 @@ Description: make the build more reproducible _mess.raw_size = (_raw_size); \ --- a/c++/src/objects/seqfeat/BioSource.cpp +++ b/c++/src/objects/seqfeat/BioSource.cpp -@@ -941,7 +941,7 @@ +@@ -941,7 +941,7 @@ static const char* const s_IgnoreCaseQua }; typedef CStaticArraySet TCIgnoreCaseQualsSet; @@ -533,7 +533,7 @@ Description: make the build more reproducible bool s_MayIgnoreCase(const string& value) { -@@ -963,7 +963,7 @@ +@@ -963,7 +963,7 @@ static const char* const s_TaxNameElemen }; typedef CStaticArraySet TCTaxNameElementQualsSet; @@ -542,7 +542,7 @@ Description: make the build more reproducible bool s_IsTaxNameElement(const string& value) { -@@ -1367,7 +1367,7 @@ +@@ -1367,7 +1367,7 @@ static const char* const s_StopWords[] = }; typedef CStaticArraySet TCStopWordStrSet; @@ -553,7 +553,7 @@ 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 -@@ -3080,7 +3080,7 @@ +@@ -3120,7 +3120,7 @@ static const char* const s_Countries[] = "Zimbabwe" }; typedef CStaticArraySet TCStrSet; @@ -562,7 +562,7 @@ Description: make the build more reproducible // former legal country names, must be in alphabetical order (case sensitive) static const char* const s_Former_Countries[] = { -@@ -3098,7 +3098,7 @@ +@@ -3140,7 +3140,7 @@ static const char* const s_Former_Countr "Yugoslavia", "Zaire" }; @@ -573,7 +573,7 @@ Description: make the build more reproducible { --- a/c++/src/serial/datatool/classstr.cpp +++ b/c++/src/serial/datatool/classstr.cpp -@@ -850,7 +850,7 @@ +@@ -850,7 +850,7 @@ mem_simple = false; " if (!CanGet"<< mem_cName<<"()) {\n" " ThrowUnassigned("<= 3.4 */) && \ +@@ -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) -- 2.30.2