From: Michael R. Crusoe Date: Sun, 29 Sep 2019 15:33:48 +0000 (+0200) Subject: remove unused patches X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~144 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=c4459dfb2756f9a772247999b40b6a58959ddd5d;p=ncbi-blast%2B.git remove unused patches --- diff --git a/debian/patches/do_not_output_everything_to_stderr.patch b/debian/patches/do_not_output_everything_to_stderr.patch deleted file mode 100644 index 2fdcf00d..00000000 --- a/debian/patches/do_not_output_everything_to_stderr.patch +++ /dev/null @@ -1,46 +0,0 @@ -Author: Andreas Tille -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; diff --git a/debian/patches/fix_arm_mips_build b/debian/patches/fix_arm_mips_build deleted file mode 100644 index 017298a0..00000000 --- a/debian/patches/fix_arm_mips_build +++ /dev/null @@ -1,19 +0,0 @@ -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 -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 diff --git a/debian/patches/fix_checks b/debian/patches/fix_checks deleted file mode 100644 index f64ede60..00000000 --- a/debian/patches/fix_checks +++ /dev/null @@ -1,17 +0,0 @@ -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 -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 diff --git a/debian/patches/fix_gcc46_errors b/debian/patches/fix_gcc46_errors deleted file mode 100644 index a28de4ea..00000000 --- a/debian/patches/fix_gcc46_errors +++ /dev/null @@ -1,28 +0,0 @@ -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 -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 -+#include - - - // (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; diff --git a/debian/patches/fix_gcc47_errors b/debian/patches/fix_gcc47_errors deleted file mode 100644 index ba6255e2..00000000 --- a/debian/patches/fix_gcc47_errors +++ /dev/null @@ -1,320 +0,0 @@ -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 -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 - #endif -+#include - #ifdef NCBI_COMPILER_ICC - // Preemptively pull in , 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 - -+#include - - // 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 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(iter.GetContainerPtr()); - it = c->erase(it); - return it != c->end(); -@@ -511,7 +513,7 @@ - static void EraseAllElements(TTypeInfoIterator& iter) - { - Container* c = static_cast(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(iter.GetContainerPtr()); - TStlIterator erase = it++; - c->erase(erase); -@@ -551,7 +553,7 @@ - static void EraseAllElements(TTypeInfoIterator& iter) - { - Container* c = static_cast(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 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 levelIns = selectIter->second.insert(value); - - pair 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(); - } - } diff --git a/debian/patches/fix_version_extraction b/debian/patches/fix_version_extraction deleted file mode 100644 index 650370ef..00000000 --- a/debian/patches/fix_version_extraction +++ /dev/null @@ -1,35 +0,0 @@ ---- 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 --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, diff --git a/debian/patches/include_typeinfo b/debian/patches/include_typeinfo deleted file mode 100644 index e9fe46ac..00000000 --- a/debian/patches/include_typeinfo +++ /dev/null @@ -1,16 +0,0 @@ -Subject: include required by recent compiler -Description: a recent gcc version requires an include -Author: Olivier Sallou -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 - # ifdef _GLIBCXX_THROW_OR_ABORT /* using libstdc++ from GCC 4.8 or later */ -+# include - # include - # include - # endif diff --git a/debian/patches/optionally_keep_sequence b/debian/patches/optionally_keep_sequence index 3f01c1e5..2c1c0a85 100644 --- a/debian/patches/optionally_keep_sequence +++ b/debian/patches/optionally_keep_sequence @@ -1,3 +1,9 @@ +Author: Aaron M. Ucko +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 diff --git a/debian/patches/series b/debian/patches/series index 86ad827d..639f255e 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -6,11 +6,8 @@ no_multiarch_rpath 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 diff --git a/debian/patches/support_boost_1_67 b/debian/patches/support_boost_1_67 deleted file mode 100644 index 40d2a783..00000000 --- a/debian/patches/support_boost_1_67 +++ /dev/null @@ -1,274 +0,0 @@ ---- 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(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(but::runtime_config::btrt_##old_name) -+# define CONFIGURED_FILTERS RTCFG(std::vector, _, run_filters) -+# else -+# define RTCFG(type, new_name, old_name) \ -+ but::runtime_config::get(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, 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( runtime_config::RESULT_CODE ) -+ RTCFG(bool, RESULT_CODE, result_code) - #else - !runtime_config::no_result_code() - #endif diff --git a/debian/patches/support_other_cpus b/debian/patches/support_other_cpus deleted file mode 100644 index e8ae1e7e..00000000 --- a/debian/patches/support_other_cpus +++ /dev/null @@ -1,74 +0,0 @@ -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 -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:: diff --git a/debian/patches/support_recent_boost b/debian/patches/support_recent_boost deleted file mode 100644 index d223c850..00000000 --- a/debian/patches/support_recent_boost +++ /dev/null @@ -1,263 +0,0 @@ ---- 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 -- --#include --#include -- - #include "teamcity_messages.h" - --using namespace std; -+#include -+#include - --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 - #include -+#include - --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 */ diff --git a/debian/patches/wrong_path_to_touch.patch b/debian/patches/wrong_path_to_touch.patch deleted file mode 100644 index f418da73..00000000 --- a/debian/patches/wrong_path_to_touch.patch +++ /dev/null @@ -1,112 +0,0 @@ -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 -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 - #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