debian/changelog

+ncbi-blast+ (2.9.0-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Drop transitional blast2 package. (Closes: #940742).
+  * debian/copyright: refreshed
+  * debhelper-compat 12
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/changelog
+  * Use secure URI in Homepage field.
+  * Move source package lintian overrides to debian/source.
+  * Set upstream metadata fields: Contact, Name.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 29 Sep 2019 13:29:30 +0200
+
 ncbi-blast+ (2.9.0-2) unstable; urgency=medium
 
   * debian/control: Standards-Version: 4.4.1 (already compliant).

debian/compat

-11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
 	   Aaron M. Ucko <ucko@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
+Build-Depends: debhelper-compat (= 12)
 Build-Depends-Arch: 2to3,
                libboost-test-dev,
                libbz2-dev,
@@ -19,7 +19,7 @@ Build-Depends-Arch: 2to3,
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
 Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
-Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
+Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
 Rules-Requires-Root: no
 
 Package: ncbi-blast+
@@ -56,14 +56,3 @@ Description: NCBI Blast legacy call script
  This package adds some fake scripts to call NCBI+ programs
  with the NCBI blast command line. It makes use of the
  legacy_blast script in ncbi-blast+ package.
-
-Package: blast2
-Architecture: all
-Multi-Arch: foreign
-Section: oldlibs
-Priority: optional
-Depends: ncbi-blast+-legacy,
-         ${misc:Depends}
-Description: transitional dummy package to ncbi-blast+-legacy
- This is a transitional dummy package for ncbi-blast+-legacy.
- It can safely be removed.

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ncbi-blast+
 Upstream-Contact: blastsoft@ncbi.nlm.nih.gov
 
+Files: c++/*
+Copyright: NCBI
+License: PD
+                                  PUBLIC DOMAIN NOTICE
+                     National Center for Biotechnology Information
+ .
+        This software/database is a "United States Government Work" under the
+        terms of the United States Copyright Act.  It was written as part of
+        the author's official duties as a United States Government employee and
+        thus cannot be copyrighted.  This software/database is freely available
+        to the public for use. The National Library of Medicine and the U.S.
+        Government have not placed any restriction on its use or reproduction.
+ .
+        Although all reasonable efforts have been taken to ensure the accuracy
+        and reliability of the software and data, the NLM and the U.S.
+        Government do not and cannot warrant the performance or results that
+        may be obtained by using this software or data. The NLM and the U.S.
+        Government disclaim all warranties, express or implied, including
+        warranties of performance, merchantability or fitness for any particular
+        purpose.
+ .
+        Please cite the author in any work or product based on this material.
+
 Files: c++/src/connect/mbedtls/*
 Copyright: 2006-2015, ARM Limited, All Rights Reserved
 License: Apache-2.0
@@ -27,29 +50,6 @@ License: Netscape
  software provided that this copyright notice appears on all copies.
  This software is provided "AS IS," without a warranty of any kind.
 
-Files: c++/*
-Copyright: NCBI
-License: PD
-                                  PUBLIC DOMAIN NOTICE
-                     National Center for Biotechnology Information
- .
-        This software/database is a "United States Government Work" under the
-        terms of the United States Copyright Act.  It was written as part of
-        the author's official duties as a United States Government employee and
-        thus cannot be copyrighted.  This software/database is freely available
-        to the public for use. The National Library of Medicine and the U.S.
-        Government have not placed any restriction on its use or reproduction.
- .
-        Although all reasonable efforts have been taken to ensure the accuracy
-        and reliability of the software and data, the NLM and the U.S.
-        Government do not and cannot warrant the performance or results that
-        may be obtained by using this software or data. The NLM and the U.S.
-        Government disclaim all warranties, express or implied, including
-        warranties of performance, merchantability or fitness for any particular
-        purpose.
- .
-        Please cite the author in any work or product based on this material.
-
 Files: c++/*/util/compress/zlib/*
 Copyright: 1995-2004 Jean-loup Gailly and Mark Adler
 License: BSD-3-clause
@@ -106,11 +106,11 @@ License: BSD-4-clause
  NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-Files: c++/src/build-system/config.*s* c++/src/util/regexp/missing
+Files: c++/src/build-system/config.*s*
 Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc
 License: GPL-2
 
-Files: c++/src/build-system/ax_jni_include_dir.m4
+Files: c++/src/build-system/m4/ax_jni_include_dir.m4
 Copyright: 2008 Don Anderson <dda@sleepycat.com>
 License: as_is
    Copying and distribution of this file, with or without modification, are

debian/patches/do_not_output_everything_to_stderr.patch

-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;

debian/patches/fix_arm_mips_build

-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

debian/patches/fix_checks

-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

debian/patches/fix_gcc46_errors

-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;

debian/patches/fix_gcc47_errors

-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();
-                 }
-             }

debian/patches/fix_version_extraction

---- 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,

debian/patches/include_typeinfo

-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

debian/patches/optionally_keep_sequence

+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

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

debian/patches/support_boost_1_67

---- 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

debian/patches/support_other_cpus

-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::

debian/patches/support_recent_boost

---- 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 */

debian/patches/support_x32

+Author: Aaron M. Ucko <ucko@debian.org>
+Date:   Fri Aug 5 19:42:47 2016 -0400
+Description: Support x32
+
+Avoid picking up wrong inline assembly.
 --- a/c++/include/corelib/impl/ncbi_atomic_defs.h
 +++ b/c++/include/corelib/impl/ncbi_atomic_defs.h
 @@ -117,7 +117,7 @@

debian/patches/suppress_gnutls_version_check

+Author: Aaron M. Ucko <ucko@debian.org>
+Date:   Wed Dec 7 21:34:44 2016 -0500
+Description: suppress gnutls version check
+    
+    Prevent bailing when the exact compile-time and runtime GNU TLS versions
+    differ; trust dpkg to disallow combinations that are actually incompatible.
+
 --- a/c++/src/connect/ncbi_gnutls.c
 +++ b/c++/src/connect/ncbi_gnutls.c
 @@ -660,6 +660,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull

debian/patches/system_mbedtls_only

+Author: Aaron M. Ucko <amu@ucko.debian.net>
+Date:   Sun Feb 3 21:43:23 2019 -0500
+Subject: Omit convenience mbed TLS copy
 --- a/c++/src/connect/Makefile.connssl.lib
 +++ b/c++/src/connect/Makefile.connssl.lib
 @@ -2,7 +2,9 @@

debian/patches/wrong_path_to_touch.patch

-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