+++ /dev/null
-Author: Andreas Tille <tille@debian.org>
-Date: Wed, 21 Dec 2011 15:47:04 +0100
-Bug-Closed: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644237
-Description: Output non-erroneous messages to STDOUT instead of STDERR
-
---- ncbi-blast+-2.2.25.orig/c++/src/app/blast/update_blastdb.pl
-+++ ncbi-blast+-2.2.25/c++/src/app/blast/update_blastdb.pl
-@@ -104,7 +104,7 @@
- or die "Failed to login to " . NCBI_FTP . ": $!\n";
- $ftp->cwd(BLAST_DB_DIR);
- $ftp->binary();
-- print STDERR "Connected to NCBI\n" if $opt_verbose;
-+ print STDOUT "Connected to NCBI\n" if $opt_verbose;
- return $ftp;
- }
-
-@@ -170,14 +170,14 @@
- if ($opt_verbose and &is_multivolume_db($file)) {
- my $db_name = &extract_db_name($file);
- my $nvol = &get_num_volumes($db_name, @_);
-- print STDERR "Downloading $db_name (" . $nvol . " volumes) ...\n";
-+ print STDOUT "Downloading $db_name (" . $nvol . " volumes) ...\n";
- }
-
- download_file:
- if ($opt_force_download or
- not -f $file or
- ((stat($file))->mtime < $ftp->mdtm($file))) {
-- print STDERR "Downloading $file... " if $opt_verbose;
-+ print STDOUT "Downloading $file... " if $opt_verbose;
- $ftp->get($file);
- if ($opt_check_md5) {
- unless ($ftp->get("$file.md5")) {
-@@ -199,10 +199,10 @@
- }
- }
- }
-- print STDERR "done.\n" if $opt_verbose;
-+ print STDOUT "done.\n" if $opt_verbose;
- $retval = 1 if ($retval == 0);
- } else {
-- print STDERR "$file is up to date.\n" if $opt_verbose;
-+ print STDOUT "$file is up to date.\n" if $opt_verbose;
- }
- }
- return $retval;
+++ /dev/null
-Subject: FTBS issue on ARM and MIPS
-Descrition: switch NCBI_BIG_TYPE's baseline to Int8 from NCBI_INT8_TYPE
- to fix build failures on Linux systems with ARM or MIPS processors,
- which have inttypes.h and lack an extra-wide scalar type.
- Bug fixed upstream.
-Last-Updated: 2012-09-25
-Author: Aaron Ucko <ucko@debian.org>
-Forwarded: not-needed
---- trunk/c++/include/corelib/ncbitype.h 2012/06/01 19:13:24 54673
-+++ trunk/c++/include/corelib/ncbitype.h 2012/09/24 14:15:47 55773
-@@ -150,7 +150,7 @@
- /* BigScalar
- */
-
--#define NCBI_BIG_TYPE NCBI_INT8_TYPE
-+#define NCBI_BIG_TYPE Int8
- #define SIZEOF_NCBI_BIG 8
- #if (SIZEOF_LONG_DOUBLE > SIZEOF_NCBI_BIG)
- # undef NCBI_BIG_TYPE
+++ /dev/null
-Subject: checks misreported as absent when unpacked under /*/src/*
-
- * src/build-system/Makefile.meta.in: supply it to check_add.sh
-
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2011-05-23
---- a/c++/src/build-system/Makefile.meta.in 2011-05-23 18:48:59.000000000 -0400
-+++ b/c++/src/build-system/Makefile.meta.in 2011-05-23 18:49:20.000000000 -0400
-@@ -188,7 +188,7 @@
- expendable=false ; \
- for i in $$x_project ; do \
- if test "x$$i" = "x-" ; then expendable=true ; continue ; fi ; \
-- $(check_add) $(abs_srcdir) $$i @signature@ @exe_ext@
-+ $(check_add) $(abs_srcdir) $$i @signature@ $(subdir)
- CHECK_ADD_KET = || exit 5 ; \
- done ; \
- fi
+++ /dev/null
-Subject: GCC 4.6 compilation error due to missing def
-
- * include/corelib/ncbistre.hpp: Add stddef definition required by gcc4.6
- * src/objtools/blast/seqdb_reader/seqdbimpl.hpp: remove mutable reference
-
-Author: Olivier Sallou <olivier.sallou@irisa.fr>
-Last-Update: 2011-05-03
---- a/c++/include/corelib/ncbistre.hpp
-+++ b/c++/include/corelib/ncbistre.hpp
-@@ -116,6 +116,7 @@
- #define SEEKOFF PUBSEEKOFF
-
- #include <string>
-+#include <stddef.h>
-
-
- // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file)
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1245,7 +1245,7 @@
- CSeqDBAtlasHolder m_AtlasHolder;
-
- /// Reference to memory management layer.
-- mutable CSeqDBAtlas & m_Atlas;
-+ CSeqDBAtlas & m_Atlas;
-
- /// The list of database names provided to the constructor.
- string m_DBNames;
+++ /dev/null
-Subject: fix various GCC 4.7 compilation errors and warnings
-
- * Explicitly qualify more dependent names originating in base templates.
- * Directly #include headers as needed.
- * Use modern syntax for making protected base members public.
- * Add forward declarations as needed.
-
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2012-04-13
---- a/c++/include/connect/ncbi_conn_stream.hpp
-+++ b/c++/include/connect/ncbi_conn_stream.hpp
-@@ -259,7 +259,7 @@
- class CConn_IOStreamSetReadTimeout : protected CConn_IOStreamSetTimeout
- {
- public:
-- CConn_IOStreamSetTimeout::GetTimeout;
-+ using CConn_IOStreamSetTimeout::GetTimeout;
-
- protected:
- CConn_IOStreamSetReadTimeout(const STimeout* timeout)
-@@ -289,7 +289,7 @@
- class CConn_IOStreamSetWriteTimeout : protected CConn_IOStreamSetTimeout
- {
- public:
-- CConn_IOStreamSetTimeout::GetTimeout;
-+ using CConn_IOStreamSetTimeout::GetTimeout;
-
- protected:
- CConn_IOStreamSetWriteTimeout(const STimeout* timeout)
---- a/c++/include/corelib/ncbiexpt.hpp
-+++ b/c++/include/corelib/ncbiexpt.hpp
-@@ -852,7 +852,7 @@
- exception_class(const exception_class& other) \
- : base_class(other) \
- { \
-- x_Assign(other); \
-+ this->x_Assign(other); \
- } \
- public: \
- virtual ~exception_class(void) throw() {} \
-@@ -1172,7 +1172,7 @@
- : TBase( other)
- {
- m_Errno = other.m_Errno;
-- x_Assign(other);
-+ this->x_Assign(other);
- }
-
- /// Destructor.
---- a/c++/include/corelib/ncbimisc.hpp
-+++ b/c++/include/corelib/ncbimisc.hpp
-@@ -39,6 +39,7 @@
- #ifdef HAVE_SYS_TYPES_H
- # include <sys/types.h>
- #endif
-+#include <cstdlib>
- #ifdef NCBI_COMPILER_ICC
- // Preemptively pull in <cctype>, which breaks if we've already
- // repointed is* at NCBI_is*.
---- a/c++/include/corelib/ncbistl.hpp
-+++ b/c++/include/corelib/ncbistl.hpp
-@@ -37,6 +37,7 @@
-
- #include <common/ncbi_export.h>
-
-+#include <algorithm>
-
- // Get rid of some warnings in MSVC++
- #if (_MSC_VER >= 1200)
---- a/c++/include/corelib/ncbistr.hpp
-+++ b/c++/include/corelib/ncbistr.hpp
-@@ -3039,7 +3039,7 @@
- : TBase(other)
- {
- m_Pos = other.m_Pos;
-- x_Assign(other);
-+ this->x_Assign(other);
- }
-
- /// Destructor.
---- a/c++/include/serial/impl/stltypes.hpp
-+++ b/c++/include/serial/impl/stltypes.hpp
-@@ -412,6 +412,7 @@
- typedef StlIterator TStlIterator;
- typedef TypeInfoIterator TTypeInfoIterator;
- typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
-+ typedef CStlClassInfoFunctions<Container> CParent;
-
- static TStlIterator& It(TTypeInfoIterator& iter)
- {
-@@ -437,7 +438,8 @@
- }
- static bool InitIterator(TTypeInfoIterator& iter)
- {
-- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
-+ TStlIterator stl_iter
-+ = CParent::Get(iter.GetContainerPtr()).begin();
- if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
- void* data = &iter.m_IteratorData;
- new (data) TStlIterator(stl_iter);
-@@ -445,7 +447,7 @@
- else {
- iter.m_IteratorData = new TStlIterator(stl_iter);
- }
-- return stl_iter != Get(iter.GetContainerPtr()).end();
-+ return stl_iter != CParent::Get(iter.GetContainerPtr()).end();
- }
- static void ReleaseIterator(TTypeInfoIterator& iter)
- {
-@@ -466,7 +468,7 @@
-
- static bool NextElement(TTypeInfoIterator& iter)
- {
-- return ++It(iter) != Get(iter.GetContainerPtr()).end();
-+ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end();
- }
- static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
- {
-@@ -503,7 +505,7 @@
-
- static bool EraseElement(TTypeInfoIterator& iter)
- {
-- TStlIterator& it = It(iter);
-+ TStlIterator& it = CParent::It(iter);
- Container* c = static_cast<Container*>(iter.GetContainerPtr());
- it = c->erase(it);
- return it != c->end();
-@@ -511,7 +513,7 @@
- static void EraseAllElements(TTypeInfoIterator& iter)
- {
- Container* c = static_cast<Container*>(iter.GetContainerPtr());
-- c->erase(It(iter), c->end());
-+ c->erase(CParent::It(iter), c->end());
- }
-
- static void SetIteratorFunctions(CStlOneArgTemplate* info)
-@@ -542,7 +544,7 @@
- }
- static bool EraseElement(TTypeInfoIterator& iter)
- {
-- TStlIterator& it = It(iter);
-+ TStlIterator& it = CParent::It(iter);
- Container* c = static_cast<Container*>(iter.GetContainerPtr());
- TStlIterator erase = it++;
- c->erase(erase);
-@@ -551,7 +553,7 @@
- static void EraseAllElements(TTypeInfoIterator& iter)
- {
- Container* c = static_cast<Container*>(iter.GetContainerPtr());
-- c->erase(It(iter), c->end());
-+ c->erase(CParent::It(iter), c->end());
- }
-
- static void SetIteratorFunctions(CStlOneArgTemplate* info)
---- a/c++/include/serial/iterator.hpp
-+++ b/c++/include/serial/iterator.hpp
-@@ -520,13 +520,13 @@
- CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo)
- : m_NeedType(needType)
- {
-- Init(beginInfo);
-+ this->Init(beginInfo);
- }
- CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo,
- const string& filter)
- : m_NeedType(needType)
- {
-- Init(beginInfo, filter);
-+ this->Init(beginInfo, filter);
- }
-
- virtual bool CanSelect(const CConstObjectInfo& object)
---- a/c++/include/util/bitset/bmfunc.h
-+++ b/c++/include/util/bitset/bmfunc.h
-@@ -39,6 +39,13 @@
- namespace bm
- {
-
-+bm::id_t bit_block_any_range(const bm::word_t* block,
-+ bm::word_t left,
-+ bm::word_t right);
-+
-+bm::id_t bit_block_calc_count_range(const bm::word_t* block,
-+ bm::word_t left,
-+ bm::word_t right);
-
- /*!
- @brief Structure with statistical information about bitset's memory
---- a/c++/include/util/bitset/bmserial.h
-+++ b/c++/include/util/bitset/bmserial.h
-@@ -1381,7 +1381,7 @@
- case set_block_arrgap:
- case set_block_arrgap_egamma:
- {
-- unsigned arr_len = read_id_list(dec, btype, this->id_array_);
-+ unsigned arr_len = this->read_id_list(dec, btype, this->id_array_);
- gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len);
- break;
- }
-@@ -1390,7 +1390,7 @@
- (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32());
- case set_block_arrgap_egamma_inv:
- case set_block_arrgap_inv:
-- gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head);
-+ gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head);
- break;
- default:
- BM_ASSERT(0);
---- a/c++/include/util/linkedset.hpp
-+++ b/c++/include/util/linkedset.hpp
-@@ -268,10 +268,10 @@
- pair<iterator, bool> ins = m_Container.insert(value);
- if ( ins.second ) {
- if ( ins.first == begin() )
-- insertToStart(*ins.first);
-+ this->insertToStart(*ins.first);
- else {
- iterator prev = ins.first;
-- insertAfter(*--prev, *ins.first);
-+ this->insertAfter(*--prev, *ins.first);
- }
- }
- return ins;
-@@ -280,10 +280,10 @@
- void erase(iterator iter)
- {
- if ( iter == begin() )
-- removeFromStart(*iter);
-+ this->removeFromStart(*iter);
- else {
- iterator prev = iter;
-- removeAfter(*--prev, *iter);
-+ this->removeAfter(*--prev, *iter);
- }
- m_Container.erase(iter);
- }
-@@ -422,10 +422,10 @@
- {
- iterator iter = m_Container.insert(value);
- if ( iter == begin() )
-- insertToStart(get(iter));
-+ this->insertToStart(get(iter));
- else {
- iterator prev = iter;
-- insertAfter(get(--prev), get(iter));
-+ this->insertAfter(get(--prev), get(iter));
- }
- return iter;
- }
-@@ -433,10 +433,10 @@
- void erase(iterator iter)
- {
- if ( iter == begin() )
-- removeFromStart(get(iter));
-+ this->removeFromStart(get(iter));
- else {
- iterator prev = iter;
-- removeAfter(get(--prev), get(iter));
-+ this->removeAfter(get(--prev), get(iter));
- }
- m_Container.erase(iter);
- }
---- a/c++/include/util/rangemap.hpp
-+++ b/c++/include/util/rangemap.hpp
-@@ -578,7 +578,7 @@
- // get level
-
- // insert element
-- TSelectMapI selectIter = insertLevel(selectKey);
-+ TSelectMapI selectIter = this->insertLevel(selectKey);
- pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value);
-
- pair<iterator, bool> ret;
-@@ -640,7 +640,7 @@
- // insert element
- iterator ret;
- ret.m_Range = range_type::GetWhole();
-- ret.m_SelectIter = insertLevel(selectKey);
-+ ret.m_SelectIter = this->insertLevel(selectKey);
- ret.m_SelectIterEnd = this->m_SelectMap.end();
- ret.m_LevelIter = ret.m_SelectIter->second.insert(value);
- return ret;
---- a/c++/src/serial/stdtypes.cpp
-+++ b/c++/src/serial/stdtypes.cpp
-@@ -720,7 +720,7 @@
- if ( IsSigned() ) {
- // signed -> unsigned
- // check for negative value
-- if ( IsNegative(value) )
-+ if ( CParent::IsNegative(value) )
- ThrowIntegerOverflow();
- }
- if ( sizeof(value) > sizeof(result) ) {
-@@ -751,7 +751,7 @@
- // unsigned -> signed
- if ( sizeof(value) == sizeof(result) ) {
- // same size - check for sign change only
-- if ( IsNegative(result) )
-+ if ( CParent::IsNegative(result) )
- ThrowIntegerOverflow();
- }
- }
-@@ -786,7 +786,7 @@
- if ( IsSigned() ) {
- // signed -> unsigned
- // check for negative value
-- if ( IsNegative(value) )
-+ if ( CParent::IsNegative(value) )
- ThrowIntegerOverflow();
- }
- if ( sizeof(value) > sizeof(result) ) {
-@@ -817,7 +817,7 @@
- // unsigned -> signed
- if ( sizeof(value) == sizeof(result) ) {
- // same size - check for sign change only
-- if ( IsNegative(result) )
-+ if ( CParent::IsNegative(result) )
- ThrowIntegerOverflow();
- }
- }
+++ /dev/null
---- a/c++/src/build-system/configure.ac
-+++ b/c++/src/build-system/configure.ac
-@@ -5181,15 +5187,26 @@ if test "$with_boost" != "no"; then
- AC_CACHE_CHECK([Boost version],
- ncbi_cv_lib_boost_version,
- [AC_LANG_CONFTEST([AC_LANG_SOURCE([[
-+cat >/dev/null <<_NCBI_EOF
- #include <boost/version.hpp>
--ncbi_cv_lib_boost_version_num=BOOST_VERSION
--ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
-+_NCBI_EOF
-+get_BOOST_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+BOOST_VERSION
-+_NCBI_EOF
-+}
-+get_BOOST_LIB_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+BOOST_LIB_VERSION
-+_NCBI_EOF
-+}
-+ncbi_cv_lib_boost_version_num=\`get_BOOST_VERSION\`
-+ncbi_cv_lib_boost_version=\`get_BOOST_LIB_VERSION | tr -d '"'\`
- ]])])
-- eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" \
-- 2>&AS_MESSAGE_LOG_FD | grep '^ncbi_cv_' \
-- | tr -d "$wschars" > conftest.sh
-+ eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" > conftest.sh \
-+ 2>&AS_MESSAGE_LOG_FD
- . ./conftest.sh
-- rm -f contest*
-+ rm -f conftest*
- ])
- AC_DEFINE_UNQUOTED(NCBI_EXPECTED_BOOST_VERSION,
- $ncbi_cv_lib_boost_version_num,
+++ /dev/null
-Subject: include required by recent compiler
-Description: a recent gcc version requires an include
-Author: Olivier Sallou <osallou@debian.org>
-Forwarded: yes
-Bug: sent by mail
-Last-Updated: 2014-06-30
---- a/c++/include/corelib/ncbistl.hpp
-+++ b/c++/include/corelib/ncbistl.hpp
-@@ -215,6 +215,7 @@ END_NCBI_SCOPE
- # elif defined(_GLIBCXX_DEPRECATED)
- # include <ext/concurrence.h>
- # ifdef _GLIBCXX_THROW_OR_ABORT /* using libstdc++ from GCC 4.8 or later */
-+# include <typeinfo>
- # include <bits/unique_ptr.h>
- # include <bits/shared_ptr.h>
- # endif
+Author: Aaron M. Ucko <ucko@debian.org>
+Date: Wed Dec 14 22:44:19 2016 -0500
+Description: Hang on to sequence data even if -parse_deflines recognized a non-local ID,
+ on the condition that the environment variable BLAST_ALWAYS_KEEP_SEQUENCE
+ (or configuration parameter [BLAST] always_keep_sequence) is set to a
+ "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
@@ -495,6 +495,11 @@ void CExportStrategy::x_Process_Pssm(CRe
use_pie_for_apps
skip_services_unit_test
fix_configure
-#fix_version_extraction
-#support_recent_boost
support_x32
suppress_gnutls_version_check
optionally_keep_sequence
fix_unit_tests
-#support_boost_1_67
system_mbedtls_only
+++ /dev/null
---- a/c++/include/corelib/teamcity_messages.h
-+++ b/c++/include/corelib/teamcity_messages.h
-@@ -33,9 +33,9 @@ protected:
- std::ostream *m_out;
-
- public:
-- std::string escape(std::string s);
-+ std::string escape(const std::string &s);
- void openMsg(const std::string &name);
-- void writeProperty(std::string name, std::string value);
-+ void writeProperty(const std::string &name, const std::string &value);
- void closeMsg();
-
- public:
-@@ -46,14 +46,14 @@ public:
-
- void setOutput(std::ostream &);
-
-- void suiteStarted(std::string name, std::string flowid = std::string());
-- void suiteFinished(std::string name, std::string flowid = std::string());
-+ void suiteStarted(const std::string &name, const std::string &flowid = std::string());
-+ void suiteFinished(const std::string &name, const std::string &flowid = std::string());
-
-- void testStarted(std::string name, std::string flowid = std::string(), bool captureStandardOutput = false);
-- void testFailed(std::string name, std::string message, std::string details, std::string flowid = std::string());
-- void testIgnored(std::string name, std::string message, std::string flowid = std::string());
-- void testOutput(std::string name, std::string output, std::string flowid, bool isStdErr = StdOut);
-- void testFinished(std::string name, int durationMs = -1, std::string flowid = std::string());
-+ void testStarted(const std::string &name, const std::string &flowid = std::string(), bool captureStandardOutput = false);
-+ void testFailed(const std::string &name, const std::string &message, const std::string &details, const std::string &flowid = std::string());
-+ void testIgnored(const std::string &name, const std::string &message, const std::string &flowid = std::string());
-+ void testOutput(const std::string &name, const std::string &output, const std::string &flowid, bool isStdErr = StdOut);
-+ void testFinished(const std::string &name, int durationMs = -1, const std::string &flowid = std::string());
- };
-
- }
---- a/c++/src/corelib/teamcity_boost.cpp
-+++ b/c++/src/corelib/teamcity_boost.cpp
-@@ -83,6 +83,17 @@ public:
- virtual void entry_context_start(std::ostream&, boost::unit_test::log_level);
- virtual void log_entry_context(std::ostream&, boost::unit_test::const_string);
- virtual void entry_context_finish(std::ostream&);
-+
-+#if BOOST_VERSION >= 106500
-+ // Since v1.65.0 the log level is passed to the formatters for the contexts
-+ // See boostorg/test.git:fcb302b66ea09c25f0682588d22fbfdf59eac0f7
-+ void log_entry_context(std::ostream& os, boost::unit_test::log_level, boost::unit_test::const_string ctx) override {
-+ log_entry_context(os, ctx);
-+ }
-+ void entry_context_finish(std::ostream& os, boost::unit_test::log_level) override {
-+ entry_context_finish(os);
-+ }
-+#endif
- };
-
- // Fake fixture to register formatter
-@@ -90,14 +101,17 @@ struct TeamcityFormatterRegistrar {
- TeamcityFormatterRegistrar() {
- if (underTeamcity()) {
- boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter());
-- boost::unit_test::unit_test_log.set_threshold_level
-- (RTCFG(but::log_level, LOG_LEVEL, log_level));
-+ boost::unit_test::unit_test_log.set_threshold_level(boost::unit_test::log_test_units);
- }
- }
- };
-
- BOOST_GLOBAL_FIXTURE(TeamcityFormatterRegistrar);
-
-+// Dummy method used to keep object file in case of static library linking
-+// See README.md and https://github.com/JetBrains/teamcity-cpp/pull/19
-+void TeamcityGlobalFixture() {}
-+
- // Formatter implementation
- static std::string toString(boost::unit_test::const_string bstr) {
- std::stringstream ss;
---- a/c++/src/corelib/teamcity_messages.cpp
-+++ b/c++/src/corelib/teamcity_messages.cpp
-@@ -26,7 +26,7 @@ namespace jetbrains {
- namespace teamcity {
-
- std::string getFlowIdFromEnvironment() {
--#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)) && 0
-+#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32)) && !defined(__CYGWIN__) && !defined(__MINGW32__) && 0
- char *flowId = NULL;
- size_t sz = 0;
- std::string result;
-@@ -43,7 +43,7 @@ std::string getFlowIdFromEnvironment() {
- }
-
- bool underTeamcity() {
--#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)) && 0
-+#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32)) && !defined(__CYGWIN__) && !defined(__MINGW32__) && 0
- char *teamCityProjectName = 0;
- size_t sz = 0;
- bool result = false;
-@@ -66,8 +66,9 @@ void TeamcityMessages::setOutput(std::os
- m_out = &out;
- }
-
--std::string TeamcityMessages::escape(std::string s) {
-+std::string TeamcityMessages::escape(const std::string &s) {
- std::string result;
-+ result.reserve(s.length());
-
- for (size_t i = 0; i < s.length(); i++) {
- char c = s[i];
-@@ -86,8 +87,7 @@ std::string TeamcityMessages::escape(std
- }
-
- void TeamcityMessages::openMsg(const std::string &name) {
-- // endl for http://jetbrains.net/tracker/issue/TW-4412
-- *m_out << std::endl << "##teamcity[" << name;
-+ *m_out << "##teamcity[" << name;
- }
-
- void TeamcityMessages::closeMsg() {
-@@ -96,11 +96,11 @@ void TeamcityMessages::closeMsg() {
- *m_out << std::endl;
- }
-
--void TeamcityMessages::writeProperty(std::string name, std::string value) {
-+void TeamcityMessages::writeProperty(const std::string &name, const std::string &value) {
- *m_out << " " << name << "='" << escape(value) << "'";
- }
-
--void TeamcityMessages::suiteStarted(std::string name, std::string flowid) {
-+void TeamcityMessages::suiteStarted(const std::string &name, const std::string &flowid) {
- openMsg("testSuiteStarted");
- writeProperty("name", name);
- if(flowid.length() > 0) {
-@@ -110,7 +110,7 @@ void TeamcityMessages::suiteStarted(std:
- closeMsg();
- }
-
--void TeamcityMessages::suiteFinished(std::string name, std::string flowid) {
-+void TeamcityMessages::suiteFinished(const std::string &name, const std::string &flowid) {
- openMsg("testSuiteFinished");
- writeProperty("name", name);
- if(flowid.length() > 0) {
-@@ -120,7 +120,7 @@ void TeamcityMessages::suiteFinished(std
- closeMsg();
- }
-
--void TeamcityMessages::testStarted(std::string name, std::string flowid, bool captureStandardOutput) {
-+void TeamcityMessages::testStarted(const std::string &name, const std::string &flowid, bool captureStandardOutput) {
- openMsg("testStarted");
- writeProperty("name", name);
- if(flowid.length() > 0) {
-@@ -134,7 +134,7 @@ void TeamcityMessages::testStarted(std::
- closeMsg();
- }
-
--void TeamcityMessages::testFinished(std::string name, int durationMs, std::string flowid) {
-+void TeamcityMessages::testFinished(const std::string &name, int durationMs, const std::string &flowid) {
- openMsg("testFinished");
-
- writeProperty("name", name);
-@@ -152,7 +152,7 @@ void TeamcityMessages::testFinished(std:
- closeMsg();
- }
-
--void TeamcityMessages::testFailed(std::string name, std::string message, std::string details, std::string flowid) {
-+void TeamcityMessages::testFailed(const std::string &name, const std::string &message, const std::string &details, const std::string &flowid) {
- openMsg("testFailed");
- writeProperty("name", name);
- writeProperty("message", message);
-@@ -164,7 +164,7 @@ void TeamcityMessages::testFailed(std::s
- closeMsg();
- }
-
--void TeamcityMessages::testIgnored(std::string name, std::string message, std::string flowid) {
-+void TeamcityMessages::testIgnored(const std::string &name, const std::string &message, const std::string &flowid) {
- openMsg("testIgnored");
- writeProperty("name", name);
- writeProperty("message", message);
-@@ -175,7 +175,7 @@ void TeamcityMessages::testIgnored(std::
- closeMsg();
- }
-
--void TeamcityMessages::testOutput(std::string name, std::string output, std::string flowid, bool isStdError) {
-+void TeamcityMessages::testOutput(const std::string &name, const std::string &output, const std::string &flowid, bool isStdError) {
- openMsg(isStdError ? "testStdErr" : "testStdOut");
- writeProperty("name", name);
- writeProperty("out", output);
---- a/c++/src/corelib/test_boost.cpp
-+++ b/c++/src/corelib/test_boost.cpp
-@@ -95,8 +95,15 @@
-
- #if BOOST_VERSION >= 106000
- # define attr_value utils::attr_value
--# define RTCFG(type, new_name, old_name) \
-- but::runtime_config::get<type >(but::runtime_config::new_name)
-+# if BOOST_VERSION >= 106400
-+ // Everything old is new again, apparently...
-+# define RTCFG(type, new_name, old_name) \
-+ but::runtime_config::get<type >(but::runtime_config::btrt_##old_name)
-+# define CONFIGURED_FILTERS RTCFG(std::vector<std::string>, _, run_filters)
-+# else
-+# define RTCFG(type, new_name, old_name) \
-+ but::runtime_config::get<type >(but::runtime_config::new_name)
-+# endif
- #else
- # define RTCFG(type, new_name, old_name) but::runtime_config::old_name()
- # if BOOST_VERSION >= 105900
-@@ -112,8 +119,10 @@
- # endif
- #endif
-
--#define CONFIGURED_FILTERS \
-+#ifndef CONFIGURED_FILTERS
-+ #define CONFIGURED_FILTERS \
- RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run)
-+#endif
-
- #ifdef NCBI_COMPILER_MSVC
- # pragma warning(pop)
-@@ -278,11 +287,19 @@ public:
- virtual
- void entry_context_start(ostream& ostr, but::log_level l);
-
-+# if BOOST_VERSION >= 106500
-+ virtual
-+ void log_entry_context(ostream& os, but::log_level l, but::const_string v);
-+
-+ virtual
-+ void entry_context_finish(ostream& os, but::log_level l);
-+# else
- virtual
- void log_entry_context(ostream& ostr, but::const_string value);
-
- virtual
- void entry_context_finish (ostream& ostr);
-+# endif
- #endif
-
- private:
-@@ -2124,6 +2141,19 @@ void CNcbiBoostLogger::entry_context_sta
- m_Upper->entry_context_start(ostr, l);
- }
-
-+# if BOOST_VERSION >= 106500
-+void CNcbiBoostLogger::log_entry_context(ostream& ostr,
-+ but::log_level l,
-+ but::const_string value)
-+{
-+ m_Upper->log_entry_context(ostr, l, value);
-+}
-+
-+void CNcbiBoostLogger::entry_context_finish(ostream& ostr, but::log_level l)
-+{
-+ m_Upper->entry_context_finish(ostr, l);
-+}
-+# else
- void CNcbiBoostLogger::log_entry_context(ostream& ostr,
- but::const_string value)
- {
-@@ -2134,6 +2164,7 @@ void CNcbiBoostLogger::entry_context_fin
- {
- m_Upper->entry_context_finish(ostr);
- }
-+# endif
- #endif
-
- void
-@@ -2316,7 +2347,7 @@ main(int argc, char* argv[])
-
- if (
- #if BOOST_VERSION >= 106000
-- runtime_config::get<bool>( runtime_config::RESULT_CODE )
-+ RTCFG(bool, RESULT_CODE, result_code)
- #else
- !runtime_config::no_result_code()
- #endif
+++ /dev/null
-Subject: build correctly on architectures that wound up w/NCBI_SLOW_ATOMIC_SWAP
-
-* include/corelib/impl/ncbi_atomic_defs.h, include/corelib/ncbiatomic.h:
- fix powerpc detection, which previously only worked under Darwin.
-* src/objects/seq/seq_id_*.hpp: move sx_GetSeqIdMutex to join its users.
-
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2011-06-08
-Index: b/c++/include/corelib/impl/ncbi_atomic_defs.h
-===================================================================
---- a/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:26:07.000000000 -0400
-+++ b/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:29:25.000000000 -0400
-@@ -259,7 +259,7 @@
- # endif
- #endif
-
--#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
-+#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__powerpc__) && !defined(__powerpc64__) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
- # define NCBI_SWAP_POINTERS_EXTERN 1
- # define NCBI_SLOW_ATOMIC_SWAP 1
- #endif
-Index: b/c++/include/corelib/ncbiatomic.h
-===================================================================
---- a/c++/include/corelib/ncbiatomic.h 2011-06-08 20:26:00.000000000 -0400
-+++ b/c++/include/corelib/ncbiatomic.h 2011-06-08 20:30:34.000000000 -0400
-@@ -121,14 +121,14 @@
- asm volatile("swap [%2], %1" : "=m" (*nv_loc), "=r" (old_value)
- : "r" (nv_loc), "1" (new_value), "m" (*nv_loc));
- return old_value;
--# elif defined(__ppc__) || defined(__ppc64__)
-+# elif defined(__powerpc__) || defined(__powerpc64__) || defined(__ppc__) || defined(__ppc64__)
- void* old_value;
- int swapped = 0;
- NCBI_SCHED_SPIN_INIT();
- while ( !swapped ) {
- swapped = 0;
- asm volatile(
--#ifdef __ppc64__
-+#if defined(__powerpc64__) || defined(__ppc64__)
- "ldarx %1,0,%4\n\tstdcx. %3,0,%4"
- #else
- "lwarx %1,0,%4\n\tstwcx. %3,0,%4"
-Index: b/c++/src/objects/seq/seq_id_handle.cpp
-===================================================================
---- a/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:26:34.000000000 -0400
-+++ b/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:28:43.000000000 -0400
-@@ -47,11 +47,6 @@
- // CSeq_id_Info
- //
-
--//#define NCBI_SLOW_ATOMIC_SWAP
--#ifdef NCBI_SLOW_ATOMIC_SWAP
--DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
--#endif
--
-
- CSeq_id_Info::CSeq_id_Info(CSeq_id::E_Choice type,
- CSeq_id_Mapper* mapper)
-Index: b/c++/src/objects/seq/seq_id_tree.cpp
-===================================================================
---- a/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:26:34.000000000 -0400
-+++ b/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:28:53.000000000 -0400
-@@ -42,6 +42,11 @@
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
-
-+//#define NCBI_SLOW_ATOMIC_SWAP
-+#ifdef NCBI_SLOW_ATOMIC_SWAP
-+DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
-+#endif
-+
- ////////////////////////////////////////////////////////////////////
- //
- // CSeq_id_***_Tree::
+++ /dev/null
---- a/c++/src/corelib/teamcity_messages.cpp
-+++ b/c++/src/corelib/teamcity_messages.cpp
-@@ -15,40 +15,61 @@
- * $Id: teamcity_messages.cpp 435791 2014-05-20 18:47:58Z camacho $
- */
-
--#include <ncbi_pch.hpp>
--
--#include <stdlib.h>
--#include <sstream>
--
- #include "teamcity_messages.h"
-
--using namespace std;
-+#include <cstdlib>
-+#include <sstream>
-
--namespace JetBrains {
-+namespace jetbrains {
-+namespace teamcity {
-
- std::string getFlowIdFromEnvironment() {
-+#if defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)
-+ char *flowId = NULL;
-+ size_t sz = 0;
-+ std::string result;
-+ if(!_dupenv_s(&flowId, &sz,"TEAMCITY_PROCESS_FLOW_ID")) {
-+ result = flowId != NULL ? flowId : "";
-+ free(flowId);
-+ }
-+
-+ return result;
-+#else
- const char *flowId = getenv("TEAMCITY_PROCESS_FLOW_ID");
- return flowId == NULL ? "" : flowId;
-+#endif
- }
-
- bool underTeamcity() {
-+#if defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)
-+ char *teamCityProjectName = 0;
-+ size_t sz = 0;
-+ bool result = false;
-+ if(!_dupenv_s(&teamCityProjectName, &sz, "TEAMCITY_PROJECT_NAME")) {
-+ result = teamCityProjectName != NULL;
-+ free(teamCityProjectName);
-+ }
-+
-+ return result;
-+#else
- return getenv("TEAMCITY_PROJECT_NAME") != NULL;
-+#endif
- }
-
- TeamcityMessages::TeamcityMessages()
--: m_out(&cout)
-+: m_out(&std::cout)
- {}
-
--void TeamcityMessages::setOutput(ostream &out) {
-+void TeamcityMessages::setOutput(std::ostream &out) {
- m_out = &out;
- }
-
--string TeamcityMessages::escape(string s) {
-- string result;
--
-+std::string TeamcityMessages::escape(std::string s) {
-+ std::string result;
-+
- for (size_t i = 0; i < s.length(); i++) {
- char c = s[i];
--
-+
- switch (c) {
- case '\n': result.append("|n"); break;
- case '\r': result.append("|r"); break;
-@@ -58,56 +79,60 @@ string TeamcityMessages::escape(string s
- default: result.append(&c, 1);
- }
- }
--
-+
- return result;
- }
-
--void TeamcityMessages::openMsg(const string &name) {
-- *m_out << "##teamcity[" << name;
-+void TeamcityMessages::openMsg(const std::string &name) {
-+ // endl for http://jetbrains.net/tracker/issue/TW-4412
-+ *m_out << std::endl << "##teamcity[" << name;
- }
-
- void TeamcityMessages::closeMsg() {
- *m_out << "]";
- // endl for http://jetbrains.net/tracker/issue/TW-4412
-- *m_out << endl;
-- m_out->flush();
-+ *m_out << std::endl;
- }
-
--void TeamcityMessages::writeProperty(string name, string value) {
-+void TeamcityMessages::writeProperty(std::string name, std::string value) {
- *m_out << " " << name << "='" << escape(value) << "'";
- }
-
--void TeamcityMessages::suiteStarted(string name, string flowid) {
-+void TeamcityMessages::suiteStarted(std::string name, std::string flowid) {
- openMsg("testSuiteStarted");
- writeProperty("name", name);
- if(flowid.length() > 0) {
- writeProperty("flowId", flowid);
- }
--
-+
- closeMsg();
- }
-
--void TeamcityMessages::suiteFinished(string name, string flowid) {
-+void TeamcityMessages::suiteFinished(std::string name, std::string flowid) {
- openMsg("testSuiteFinished");
- writeProperty("name", name);
- if(flowid.length() > 0) {
- writeProperty("flowId", flowid);
- }
--
-+
- closeMsg();
- }
-
--void TeamcityMessages::testStarted(string name, string flowid) {
-+void TeamcityMessages::testStarted(std::string name, std::string flowid, bool captureStandardOutput) {
- openMsg("testStarted");
- writeProperty("name", name);
- if(flowid.length() > 0) {
- writeProperty("flowId", flowid);
- }
--
-+
-+ if(captureStandardOutput) {
-+ writeProperty("captureStandardOutput", "true"); // false by default
-+ }
-+
- closeMsg();
- }
-
--void TeamcityMessages::testFinished(string name, int durationMs, string flowid) {
-+void TeamcityMessages::testFinished(std::string name, int durationMs, std::string flowid) {
- openMsg("testFinished");
-
- writeProperty("name", name);
-@@ -117,15 +142,15 @@ void TeamcityMessages::testFinished(stri
- }
-
- if(durationMs >= 0) {
-- stringstream out;
-+ std::stringstream out(std::ios_base::out);
- out << durationMs;
- writeProperty("duration", out.str());
- }
--
-+
- closeMsg();
- }
-
--void TeamcityMessages::testFailed(string name, string message, string details, string flowid) {
-+void TeamcityMessages::testFailed(std::string name, std::string message, std::string details, std::string flowid) {
- openMsg("testFailed");
- writeProperty("name", name);
- writeProperty("message", message);
-@@ -133,19 +158,31 @@ void TeamcityMessages::testFailed(string
- if(flowid.length() > 0) {
- writeProperty("flowId", flowid);
- }
--
-+
- closeMsg();
- }
-
--void TeamcityMessages::testIgnored(std::string name, std::string message, string flowid) {
-+void TeamcityMessages::testIgnored(std::string name, std::string message, std::string flowid) {
- openMsg("testIgnored");
- writeProperty("name", name);
- writeProperty("message", message);
- if(flowid.length() > 0) {
- writeProperty("flowId", flowid);
- }
--
-+
- closeMsg();
- }
-
-+void TeamcityMessages::testOutput(std::string name, std::string output, std::string flowid, bool isStdError) {
-+ openMsg(isStdError ? "testStdErr" : "testStdOut");
-+ writeProperty("name", name);
-+ writeProperty("out", output);
-+ if(flowid.length() > 0) {
-+ writeProperty("flowId", flowid);
-+ }
-+
-+ closeMsg();
-+}
-+
-+}
- }
---- a/c++/src/corelib/teamcity_messages.h
-+++ b/c++/src/corelib/teamcity_messages.h
-@@ -18,17 +18,18 @@
- #ifndef H_TEAMCITY_MESSAGES
- #define H_TEAMCITY_MESSAGES
-
--#include <string>
- #include <iostream>
-+#include <string>
-
--namespace JetBrains {
-+namespace jetbrains {
-+namespace teamcity {
-
- std::string getFlowIdFromEnvironment();
- bool underTeamcity();
-
- class TeamcityMessages {
- std::ostream *m_out;
--
-+
- protected:
- std::string escape(std::string s);
-
-@@ -37,19 +38,24 @@ protected:
- void closeMsg();
-
- public:
-+ static const bool StdErr = true;
-+ static const bool StdOut = false;
-+
- TeamcityMessages();
--
-+
- void setOutput(std::ostream &);
--
-- void suiteStarted(std::string name, std::string flowid = "");
-- void suiteFinished(std::string name, std::string flowid = "");
--
-- void testStarted(std::string name, std::string flowid = "");
-- void testFailed(std::string name, std::string message, std::string details, std::string flowid = "");
-- void testIgnored(std::string name, std::string message, std::string flowid = "");
-- void testFinished(std::string name, int durationMs = -1, std::string flowid = "");
-+
-+ void suiteStarted(std::string name, std::string flowid = std::string());
-+ void suiteFinished(std::string name, std::string flowid = std::string());
-+
-+ void testStarted(std::string name, std::string flowid = std::string(), bool captureStandardOutput = false);
-+ void testFailed(std::string name, std::string message, std::string details, std::string flowid = std::string());
-+ void testIgnored(std::string name, std::string message, std::string flowid = std::string());
-+ void testOutput(std::string name, std::string output, std::string flowid, bool isStdErr = StdOut);
-+ void testFinished(std::string name, int durationMs = -1, std::string flowid = std::string());
- };
-
- }
-+}
-
- #endif /* H_TEAMCITY_MESSAGES */
+++ /dev/null
-Subject: upstream bug using hard path for touch
-Description: upstream makes use of a hard path that
-does not match on hurd systems. Patch comes from upstream
- and will be included in next release
-Author: Olivier Sallou <osallou@debian.org>
-Last-Updated: 12/03/2012
---- a/c++/src/build-system/Makefile.meta.in
-+++ b/c++/src/build-system/Makefile.meta.in
-@@ -28,7 +28,7 @@
-
- @make_shell@
- RM = /bin/rm
--TOUCH = /usr/bin/touch
-+TOUCH = @TOUCH@
- MKDIR = /bin/mkdir
-
- signature = @signature@
---- a/c++/src/build-system/Makefile.mk.in
-+++ b/c++/src/build-system/Makefile.mk.in
-@@ -54,7 +54,7 @@
- RMDIR = /bin/rm -rf
- COPY = /bin/cp -p
- BINCOPY = @BINCOPY@
--TOUCH = /usr/bin/touch
-+TOUCH = @TOUCH@
- MKDIR = /bin/mkdir
- BINTOUCH = $(TOUCH)
- LN_S = @LN_S@
---- a/c++/src/build-system/NEWS
-+++ b/c++/src/build-system/NEWS
-@@ -8,3 +8,5 @@
- 2011-05-17: new @ncbi_java@ variable for --with-jni builds.
-
- 2011-10-05: new @FEATURES@ variable for the unit test framework.
-+
-+2012-02-27: new @TOUCH@ variable to avoid hard-coded paths.
---- a/c++/src/build-system/configure.ac
-+++ b/c++/src/build-system/configure.ac
-@@ -1965,6 +1965,7 @@
- AC_MSG_RESULT(no)
- fi
-
-+AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -318,7 +318,7 @@
- # include <unistd.h>
- #endif"
-
--ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
-+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL TOUCH EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
- ac_subst_files=''
-
- # Initialize some variables set by options.
-@@ -6615,6 +6615,46 @@
- echo "${ECHO_T}no" >&6
- fi
-
-+# Extract the first word of "touch", so it can be a program name with args.
-+set dummy touch; ac_word=$2
-+echo "$as_me:$LINENO: checking for $ac_word" >&5
-+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-+if test "${ac_cv_path_TOUCH+set}" = set; then
-+ echo $ECHO_N "(cached) $ECHO_C" >&6
-+else
-+ case $TOUCH in
-+ [\\/]* | ?:[\\/]*)
-+ ac_cv_path_TOUCH="$TOUCH" # Let the user override the test with a path.
-+ ;;
-+ *)
-+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+as_dummy="/bin:/usr/bin:$PATH"
-+for as_dir in $as_dummy
-+do
-+ IFS=$as_save_IFS
-+ test -z "$as_dir" && as_dir=.
-+ for ac_exec_ext in '' $ac_executable_extensions; do
-+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
-+ ac_cv_path_TOUCH="$as_dir/$ac_word$ac_exec_ext"
-+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ break 2
-+ fi
-+done
-+done
-+
-+ ;;
-+esac
-+fi
-+TOUCH=$ac_cv_path_TOUCH
-+
-+if test -n "$TOUCH"; then
-+ echo "$as_me:$LINENO: result: $TOUCH" >&5
-+echo "${ECHO_T}$TOUCH" >&6
-+else
-+ echo "$as_me:$LINENO: result: no" >&5
-+echo "${ECHO_T}no" >&6
-+fi
-+
- echo "$as_me:$LINENO: checking for egrep" >&5
- echo $ECHO_N "checking for egrep... $ECHO_C" >&6
- if test "${ac_cv_prog_egrep+set}" = set; then
-@@ -33848,6 +33888,7 @@
- s,@DISTCC@,$DISTCC,;t t
- s,@CCACHE@,$CCACHE,;t t
- s,@TAIL@,$TAIL,;t t
-+s,@TOUCH@,$TOUCH,;t t
- s,@EGREP@,$EGREP,;t t
- s,@VALGRIND_PATH@,$VALGRIND_PATH,;t t
- s,@CXXCPP@,$CXXCPP,;t t
projects / ncbi-blast+.git / commitdiff