[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/

[Martin Mokrejs]

commit:     cb7af5375a7fbfdfaeddf149fed723aa81e1827e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 23 20:38:29 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 23 20:38:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cb7af537

dropped the duplicate part from the patch

---
 .../files/ncbi-tools++-12.0.0-configure.patch      | 1660 --------------------
 1 file changed, 1660 deletions(-)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
index 0d4bd39..4c77991 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
@@ -1,1663 +1,3 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori	2014-06-23 17:35:47.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac	2014-06-23 17:36:41.000000000 +0200
-@@ -1,5 +1,5 @@
- #############################################################################
--#  $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $
-+#  $Id$
- #  Derived from configure.in version 1.173.
- # ==========================================================================
- #
-@@ -38,7 +38,7 @@
- #
- #############################################################################
- 
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
- 
- dnl Early setup, most crucially for locking.  The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -71,7 +71,7 @@
-                      python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
-                      sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
-                      oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
--                     magic, curl],
-+                     magic, curl, gsoap, mongodb],
-         [if test "${[with_]X-no}" != "no"; then
-             AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
-          else
-@@ -143,6 +143,8 @@
-    [ --with-bin-release      build executables suitable for public release])
- AC_ARG_WITH(mt,
-    [ --with-mt               compile in a MultiThread-safe manner])
-+AC_ARG_WITH(openmp,
-+   [ --with-openmp           enable OpenMP extensions for all projects])
- AC_ARG_WITH(64,
-    [ --with-64               compile to 64-bit code])
- AC_ARG_WITH(universal,
-@@ -220,11 +222,15 @@
- 
- ## NCBI packages
- AC_ARG_WITH(ncbi-c,
-+   [ --with-ncbi-c=DIR       use NCBI C Toolkit installation in DIR])
-+AC_ARG_WITH(ncbi-c2,
-    [ --without-ncbi-c        do not use NCBI C Toolkit])
- AC_ARG_WITH(sss,
-+   [ --with-sss=DIR          use NCBI SSS installation in DIR])
-+AC_ARG_WITH(sss2,
-    [ --without-sss           do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
--   [ --without-sssutils      do not use NCBI SSS UTIL library])
-+   [ --without-utils         do not use NCBI SSS UTIL library])
- AC_ARG_WITH(sssdb,
-    [ --without-sssdb         do not use NCBI SSS DB library])
- AC_ARG_WITH(included-sss,
-@@ -439,6 +445,14 @@
-    [ --with-mimetic=DIR      use libmimetic installation in DIR])
- AC_ARG_WITH(mimetic2,
-    [ --without-mimetic       do not use libmimetic])
-+AC_ARG_WITH(gsoap,
-+   [ --with-gsoap=DIR        use gSOAP++ installation in DIR])
-+AC_ARG_WITH(gsoap2,
-+   [ --without-gsoap         do not use gSOAP++])
-+AC_ARG_WITH(mongodb,
-+   [ --with-mongodb=DIR      use MongoDB installation in DIR])
-+AC_ARG_WITH(mongodb2,
-+   [ --without-mongodb       do not use MongoDB])
- AC_ARG_WITH(3psw,
-    [ --with-3psw=std:netopt  favor standard (system) builds of the above pkgs.])
- AC_ARG_WITH(3psw2,
-@@ -479,24 +493,28 @@
-    [***** See also HTML documentation in ./doc/index.html *****])
- 
- 
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
- plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
--lfs limited-linker \
-+lfs limited-linker openmp \
- autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
- deactivation makefile-auto-update projects flat-makefile configure-dialog \
- check ncbi-public strip pch caution ccache distcc \
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
--gif jpeg tiff png xpm magic curl mimetic 3psw \
-+gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench x"
-+serial objects dbapi app ctools gui algo internal gbench"
- 
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,7 +540,6 @@
-    case "$x_arg" in
-       --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
-       | --cache-file= | --build= | --host= | --target= | --with-runpath= \
--      | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
-       | --with-relative-runpath= | --x-includes= | --x-libraries= )
-       AC_MSG_ERROR([$x_arg:  requires value;  use --help to show usage])
-       ;;
-@@ -533,12 +550,11 @@
-       | --with-universal=* | --with-tcheck=* \
-       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
-       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
--      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
-       | [[A-Z]*=*] \
-       | --with-z=* | --with-bz2=* | --with-lzo=* \
--      | --with-pcre=* \
-+      | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
-       | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \
--      | --with-krb5=* | --with-curl=* \
-+      | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \
-       | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
-       | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
-       | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
-@@ -552,7 +568,7 @@
-       | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
-       | --x-includes=* | --x-libraries=* | --with-3psw=* \
-       | --target=* | --with-runpath=* | --with-relative-runpath=* \
--      | --no-create | --no-recursion)
-+      | --help | --no-create | --no-recursion)
-       ;;
- 
-       * )
-@@ -560,6 +576,8 @@
-       ;;
-    esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
- 
- 
- if test "$with_gbench" = "yes" ; then
-@@ -604,6 +622,13 @@
-     : ${with_optimization=no}
- fi
- 
-+if test "$with_openmp" = yes; then
-+   if test "$with_mt" = no; then
-+      AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp])
-+   fi
-+   : ${with_mt=yes} 
-+fi
-+
- #### Check for special options
- if test "$with_extra_action" = "yes" ; then
-    AC_MSG_ERROR([--with-extra-action must have a value after =])
-@@ -649,15 +674,10 @@
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
--if test -n "$with_projects"; then
--   case "$with_projects" in
--      /* ) abs_projects=$with_projects         ;;
--      yes) abs_projects=$srcdir/projects       ;;
--      *  ) abs_projects=$srcdir/$with_projects ;;
--   esac
--   test -r "$abs_projects"  ||  \
--      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
--fi
-+# Generally save any originally specified flags.
-+USER_CFLAGS=$CFLAGS
-+USER_CXXFLAGS=$CXXFLAGS
-+USER_LDFLAGS=$LDFLAGS
- 
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -675,6 +695,23 @@
- #### Make some provisions for traditional operation
- AC_PROG_INSTALL
- 
-+#### Point ICC at a suitable GCC version ASAP.
-+case "/$CXX" in
-+   */icpc )
-+      if test -d /usr/local/gcc; then
-+         case "`$CXX -dumpversion`:$host_cpu" in
-+            *:i?86)           v=4.4.5 ;;
-+            ?.* | 1[[01]].* ) v=4.0.1 ;;
-+            *)                v=4.4.2 ;;
-+         esac
-+         gcc=/usr/local/gcc/$v/bin/gcc
-+         if test -x $gcc; then
-+            CC="$CC -gcc-name=$gcc"
-+            CXX="$CXX -gcc-name=$gcc"
-+         fi
-+      fi
-+      ;;
-+esac
- 
- #### C and C++ compilers
- AC_LANG(C++)
-@@ -987,6 +1024,30 @@
-         ;;
-      * ) NCBIATOMIC_LIB=xncbi ;;
-    esac
-+   case "$compiler" in
-+      GCC )
-+         if $CC -v | grep clang >/dev/null; then
-+            :
-+            # Will allegedly support -openmp at some point, but as of 3.4,
-+            # just parses it as specifying an output filename: -o penmp.
-+         else
-+            case "$compiler_version" in
-+               [[123]]?? | 4[[01]]? ) ;;
-+               * ) : ${OPENMP_FLAGS=-fopenmp} ;;
-+            esac
-+         fi
-+         ;;
-+      ICC )
-+         : ${OPENMP_FLAGS=-openmp}
-+         ;;
-+      WorkShop* )
-+         : ${OPENMP_FLAGS=-xopenmp=parallel}
-+         ;;
-+   esac
-+   if test "$with_openmp" = yes; then
-+      MT_FLAG="$MT_FLAG $OPENMP_FLAGS"
-+      OPENMP_FLAGS=
-+   fi
-    mt_sfx="MT"
-    NCBI_FEATURE(MT)
- else
-@@ -994,6 +1055,7 @@
-    MT_FLAG=
-    THREAD_LIBS=
-    NCBIATOMIC_LIB=
-+   OPENMP_FLAGS=
-    mt_sfx=""
- fi
- MT_SFX="${mt_sfx}"
-@@ -1006,6 +1068,9 @@
- APP_LDFLAGS=
- DLL_LDFLAGS=
- 
-+### Should go before any test compiler runs
-+AC_GNU_SOURCE
-+
- case "$host_os:$compiler" in
-    darwin*:GCC )
-       AC_CACHE_CHECK([whether $CC supports -Wl,-rpath],
-@@ -1047,6 +1112,47 @@
-       ;;
- esac
- 
-+case "$compiler:$compiler_version" in
-+   GCC:4[[0-6]]? | ICC:1[[01]]?? )
-+     ncbi_cv_prog_cxx_11=no
-+     ncbi_cv_prog_c_99=no
-+     ;;
-+   ICC:* )
-+     ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline'
-+     ;;
-+esac
-+
-+AC_CACHE_CHECK([how to enable C++ '11 features in $CXX],
-+   ncbi_cv_prog_cxx_11,
-+   [orig_CXX=$CXX
-+    ncbi_cv_prog_cxx_11=no
-+    for x in -std=gnu++11 -std=gnu++0x; do
-+       CXX="$orig_CXX $x"
-+       AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+          [ncbi_cv_prog_cxx_11=$x])
-+          test "x$ncbi_cv_prog_cxx_11" = "xno"  ||  break
-+       done
-+       CXX=$orig_CXX])
-+test "$ncbi_cv_prog_cxx_11" = no  ||  CXX="$CXX $ncbi_cv_prog_cxx_11"
-+
-+AC_LANG_PUSH(C)
-+AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC],
-+   ncbi_cv_prog_c_99,
-+   [orig_CC=$CC
-+    ncbi_cv_prog_c_99=no
-+    for x in -xc99=all "-std=gnu11 -fgnu89-inline" \
-+             "-std=gnu1x -fgnu89-inline" \
-+             "-std=gnu99 -fgnu89-inline" \
-+             "-std=gnu9x -fgnu89-inline"; do
-+       CC="$orig_CC $x"
-+       AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+          [ncbi_cv_prog_c_99=$x])
-+          test "x$ncbi_cv_prog_c_99" = "xno"  ||  break
-+       done
-+       CC=$orig_CC])
-+AC_LANG_POP(C)
-+test "$ncbi_cv_prog_c_99" = no  ||  CC="$CC $ncbi_cv_prog_c_99"
-+
- #### Provide default environment setup for known platforms/compilers
- DEPFLAGS="-M"
- DEPFLAGS_POST="" # Needed for VisualAge
-@@ -1059,7 +1165,15 @@
-    ;;
- 
-  solaris*:GCC )
--   CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS"
-+   # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only
-+   # in C++ mode.  Set it for C code as well to ensure consistent
-+   # header behavior, taking care to match the C standard version
-+   # (as enforced by <sys/feature_tests.h>).
-+   case "$ncbi_cv_prog_c_99" in
-+      no) CC="$CC -D_XOPEN_SOURCE=500" ;;
-+      *)  CC="$CC -D_XOPEN_SOURCE=600" ;;
-+   esac
-+
-    STRIP="@:"
-    ;;
- 
-@@ -1202,11 +1316,19 @@
-       LDFLAGS="-flat_namespace $LDFLAGS"
- 
-       if test "$with_ncbi_public" = yes; then
-+         sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
-+         case "$host_os" in
-+            darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older
-          TARGET='-mmacosx-version-min=10.5'
--         sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk'
-+               sdks="/Developer/SDKs/MacOSX10.6.sdk"
-          if test "$with_64:${with_universal-no}" != "yes:no"; then
-             sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks"
-          fi
-+               ;;
-+            * )
-+               TARGET='-mmacosx-version-min=10.7'
-+               ;;
-+         esac
-          for sdk in $sdks; do
-             if test -d "$sdk"; then 
-                TARGET="-isysroot $sdk $TARGET"
-@@ -1487,8 +1609,8 @@
-         ;;
-       GCC:* )
-         DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
--        case "$host_os" in
--           freebsd* ) ;;
-+        case "$host_os:$host_cpu:$compiler_version" in
-+           freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
-            * )        DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
-         esac
-         if test "$with_profiling" != "yes"; then
-@@ -1587,13 +1709,9 @@
-     solaris* )
-       CONF_f_runpath="-R"
-       ;;
--    linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+    linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-       CONF_f_runpath="-Wl,-rpath,"
-       ;;
--    linux*:ICC )
--      # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop
--      CONF_f_runpath="-Xlinker -rpath -Xlinker "
--      ;;
-     irix*:* | linux*:KCC | *:Compaq )
-       CONF_f_runpath="-rpath "
-       ;;
-@@ -1697,8 +1815,11 @@
-     LINK="$LINK -Kc++"
-     ;;
-   ICC:1???:* )
--    APP_LDFLAGS="-static-intel $APP_LDFLAGS"
--    DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS"
-+    # Suppress "warning #10237: -lcilkrts linked in dynamically, static
-+    # library not available" which is not a problem in practice due to
-+    # as-needed linkage.
-+    APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS"
-+    DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS"
-     # Redundant for apps, but necessary for plugins to be adequately
-     # self-contained, at least on 32-bit Linux.
-     LIBS="$LIBS -lstdc++"
-@@ -1817,18 +1938,6 @@
- 
- #### Intel compiler::  common flags and definitions
- if test "$compiler" = "ICC" ; then
--   if test -d /usr/local/gcc; then
--      case "$compiler_version:$HOST_CPU" in
--         *:i?86)               v=4.4.5 ;;
--         ???:* | 1[[01]]??:* ) v=4.0.1 ;;
--         *)                    v=4.4.2 ;;
--      esac
--      gcc=/usr/local/gcc/$v/bin/gcc
--      if test -x $gcc; then
--         CC="$CC -gcc-name=$gcc"
--         CXX="$CXX -gcc-name=$gcc"
--      fi
--   fi
-    if test -n "$icc_license" ; then
-       icc_CC="$CC"
-       icc_CXX="$CXX"
-@@ -2073,6 +2182,7 @@
- fi
- 
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
-@@ -2086,6 +2196,16 @@
- 
- AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind)
- 
-+AC_PATH_PROG(LDD, ldd)
-+if test -n "$LDD"; then
-+   AC_MSG_CHECKING([whether $LDD accepts -r])
-+   if $LDD -r /bin/ls >/dev/null 2>&1; then
-+      AC_MSG_RESULT(yes)
-+      LDD_R="$LDD -r"
-+   else
-+      AC_MSG_RESULT(no)
-+   fi
-+fi
- 
- #### Check if "${build_root}" is defined;  provide a default one
- if test -n "${with_build_root}" ; then
-@@ -2170,9 +2290,6 @@
- fi
- 
- 
--### Should go before any test compiler runs
--AC_GNU_SOURCE
--
- #### Determine whether this is implicitly a 64-bit platform
- AC_TYPE_SIZE_T
- if test "${with_universal-no}" = "no"; then
-@@ -2342,7 +2459,7 @@
-       fi
-       ;;
-     *:ICC )
--      runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)"
-+      runpath="$runpath -Wl,-rpath-link,\$(libdir)"
-       ;;
-    esac
- elif test "$with_runpath" = "yes"  -o  "$with_dll" != "no" ; then
-@@ -2658,15 +2775,30 @@
-    dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
-    dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
-    optrx="$wsrx-x*O[0-9s]*$wsrx"
-+   NDEB_CFLAGS=`  echo " $CFLAGS "   | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+   NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+   NDEB_LDFLAGS=` echo " $LDFLAGS "  | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-    if test "$with_symbols" = "no" ; then
--      CFLAGS=`  echo " $CFLAGS "   | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
--      CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
--      LDFLAGS=` echo " $LDFLAGS "  | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+      CFLAGS=$NDEB_CFLAGS
-+      CXXFLAGS=$NDEB_CXXFLAGS
-+      LDFLAGS=$NDEB_LDFLAGS
-    else
-       echo " $CFLAGS "  | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g"
-       echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g" 
-       echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
-       STRIP="@:"
-+      case "$compiler:$compiler_version" in
-+         GCC:4[89]? | GCC:[5-9]? | GCC:???? )
-+            # GCC 4.8 defaults to DWARF 4, which Totalview for one
-+            # can't handle; roll back to version 3 by default.
-+            echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+               CFLAGS="$NDEB_CFLAGS -gdwarf-3"
-+            echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+               CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3"
-+            echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+               LDFLAGS="$NDEB_LDFLAGS -gdwarf-3"
-+            ;;
-+      esac
-    fi
- 
-    NOPT_CFLAGS=`  echo " $CFLAGS "    | sed "s/$optrx/ /g"`
-@@ -3024,9 +3156,9 @@
- ### Check for other standard library functions
- 
- AC_FUNC_VPRINTF
--AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \
--               getpass getpassphrase getpwuid getrusage gettimeofday \
--               getuid memrchr readpassphrase readv usleep \
-+AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \
-+               getpagesize getpass getpassphrase getpwuid getrusage \
-+               gettimeofday getuid memrchr readpassphrase readv usleep \
-                asprintf vasprintf vsnprintf select statfs statvfs \
-                strcasecmp strlcat strlcpy strdup strndup strtok_r \
-                sysmp timegm utimes lutimes writev)
-@@ -3253,17 +3385,6 @@
- fi
- 
- 
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
--       [[#include <algorithm>]],
--       [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
--       [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
--   AC_DEFINE(HAVE_IS_SORTED, 1,
--             [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
- 
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
-    AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3400,7 +3521,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
-    ncbi_cv_c_restrict,
-    [ncbi_cv_c_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_c_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_c_restrict=$restrict], [])
-@@ -3420,7 +3541,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
-    ncbi_cv_cxx_restrict,
-    [ncbi_cv_cxx_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_cxx_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3525,14 +3646,6 @@
-               unaligned addresses.])
- fi
- 
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
--       [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
--   AC_DEFINE(HAVE_NULLPTR, 1,
--      [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
- 
-@@ -3630,7 +3743,16 @@
- dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop)
- AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)])
- LIBS=$orig_LIBS
-+# Temporarily drop OpenMP flags for this test, as some toolchains count
-+# its support library's indirect use of librt when building applications
-+# but not when building shared libraries with --no-undefined.
-+orig_CXXFLAGS=$CXXFLAGS
-+orig_LDFLAGS=$LDFLAGS
-+CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
-+LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
- NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime)
-+CXXFLAGS=$orig_CXXFLAGS
-+LDFLAGS=$orig_LDFLAGS
- NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle)
- # Add to (orig_)LIBS if present for the sake of corelib and the
- # following call to AC_CHECK_FUNCS.
-@@ -3734,7 +3856,6 @@
-    NCBI_PACKAGE(LocalBZ2)
- fi
- 
--: ${LZO_PATH=$NCBI/lzo2}
- if test -d "$LZO_PATH"; then
-    NCBI_FIX_DIR(LZO_PATH)
- fi
-@@ -3767,7 +3888,7 @@
- ## SSL/TLS libraries
- case "$with_gcrypt" in
-    no )       ac_cv_path_LIBGCRYPT_CONFIG=no ;;
--   yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt}  ;;
-+   yes | '' )                                ;;
-    * )        GCRYPT_PATH=$with_gcrypt       ;;
- esac
- if test -d "$GCRYPT_PATH"; then
-@@ -3802,13 +3923,16 @@
- 
- case "$with_gnutls" in
-    no )       ac_cv_path_LIBGNUTLS_CONFIG=no ;;
--   yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls}  ;;
-+   yes | '' )                                ;;
-    * )        GNUTLS_PATH=$with_gnutls       ;;
- esac
- if test -d "$GNUTLS_PATH"; then
-    NCBI_FIX_DIR(GNUTLS_PATH)
-+   gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin
-+else
-+   gnutls_config_path=$PATH
- fi
--AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin:$PATH])
-+AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
- 
- if test "x$with_gnutls" != xno; then
-    if test -x "$LIBGNUTLS_CONFIG"; then
-@@ -3817,7 +3941,7 @@
-          test "x$p" = "x/usr"  ||  GNUTLS_PATH=$p
-       fi
-    else
--      LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls"
-+      LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
-       $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 ||  LIBGNUTLS_CONFIG=no
-    fi
-    case "$LIBGNUTLS_CONFIG" in
-@@ -3846,6 +3970,10 @@
-  $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS)
- if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
-    NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib])
-+   # Conservatively build against gcrypt if available even when gnutls
-+   # uses nettle instead, because gcrypt needs explicit initialization
-+   # to be thread-safe, but gnutls's headers don't indicate which
-+   # underlying crypto library it's actually using.
-    case "$GNUTLS_INCLUDE" in
-        *$GCRYPT_INCLUDE* ) ;;
-        *                 ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;;
-@@ -4108,7 +4236,8 @@
-    SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
-    SYBASE_DLLS="$SYBASE_DLLLIST"
- 
--   AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase,
-+   AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}],
-+      ncbi_cv_lib_sybase,
-       [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
-        LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS"
-        AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4216,7 +4345,8 @@
-       AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH])
-    else
-       FTDS_LIBS="$FTDS_CTLIBS"
--      AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds,
-+      AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}],
-+         ncbi_cv_lib_freetds,
-          [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS"
-           LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS"
-           AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4281,7 +4411,7 @@
-       # Kill off single quotes, due to later requoting
-       : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`}
-       NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r},
--         [s/'//g; ])
-+         [s/'//g; $no_usr_lib])
-       AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql,
-          [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS"
-           LIBS="$MYSQL_LIBS $orig_LIBS"
-@@ -4310,7 +4440,6 @@
- if test "$with_bdb" != "no" ; then
-    case "$with_bdb" in
-       yes | "" )
--         : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"}
-          ;;
-       */*)
-           BERKELEYDB_PATH=$with_bdb
-@@ -4351,7 +4480,8 @@
-    else
-       BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS}
-    fi
--   AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH],
-+   AC_CACHE_CHECK(
-+      [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}],
-       ncbi_cv_lib_berkeley_db,
-       [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS"
-        LIBS="$BERKELEYDB_LIBS $orig_LIBS"
-@@ -4450,7 +4580,8 @@
-    NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst])
-    CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS"
-    LIBS="$ODBC_LIBS $orig_LIBS"
--   AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc,
-+   AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}],
-+      ncbi_cv_lib_odbc,
-       [AC_LINK_IFELSE([AC_LANG_PROGRAM(
-           [[#include <sql.h>]],
-           [[SQLHDBC hdbc;  SQLCHAR* cp = (SQLCHAR*) "x";
-@@ -4542,7 +4673,7 @@
-    AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH])
-    if test -x "$PERL"; then
-       PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'`
--      PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'`
-+      PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'`
-       PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS"
-       PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'`
-       NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS])
-@@ -4603,9 +4734,7 @@
- 
- ## Boost
- if test "$with_boost" != "no"; then
--   if test "${with_boost-yes}" = yes; then
--      : ${BOOST_PATH=$NCBI/boost}
--   else
-+   if test "${with_boost-yes}" != yes; then
-       BOOST_PATH=$with_boost
-    fi
-    if test -d "$BOOST_PATH"; then
-@@ -4644,17 +4773,22 @@
-    if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
-       BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
-    fi
--   case "$ncbi_compiler" in
--      MIPSPRO)
-+   case "$compiler:$ncbi_compiler_ver" in
-+      MIPSpro*)
-          BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers"
-          ;;
--      WORKSHOP)
-+      WorkShop*)
-          # Boost.Test's macros yield a *lot* of spurious "should not initialize
-          # a non-const reference with a temporary" warnings, to the point of
-          # overwhelming the compiler in some cases; turn them off altogether
-          # when using Boost at all.
-          BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
-          ;;
-+      GCC*:4[[7-9]]* | GCC*:5*)
-+         # Some portions of Boost also have a lot of "unused" typedefs
-+         # from concept checking.
-+         BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
-+         ;;
-    esac
-    case "$ncbi_cv_lib_boost_version" in
-       0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;;
-@@ -4666,7 +4800,7 @@
-          fi
-          with_boost=no
-          ;;
--      1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;;
-+      1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
-       '' ) with_boost=no ;;
-       * )
-          AC_MSG_WARN(
-@@ -4751,7 +4885,9 @@
-        BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS
-    fi
- 
--   AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex,
-+   in_path=${BOOST_PATH:+ in $BOOST_PATH}
-+
-+   AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex,
-       CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-       LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS"
-       [AC_LINK_IFELSE(
-@@ -4759,7 +4895,7 @@
-               [[throw boost::regex_error(boost::regex_constants::error_stack);]])],
-           [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])])
- 
--   AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit,
-+   AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit,
-       CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-       LIBS="$RT_LIBS $orig_LIBS"
-       [AC_LINK_IFELSE(
-@@ -4774,7 +4910,7 @@
-        BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS
-    fi
- 
--   AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system,
-+   AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system,
-       CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-       LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS"
-       [AC_LINK_IFELSE(
-@@ -4785,6 +4921,24 @@
-            BOOST_SYSTEM_LIBS=
-            BOOST_SYSTEM_STATIC_LIBS=])])
- 
-+   boost_fs_lib=-lboost_filesystem${BOOST_TAG}
-+   if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then
-+       boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static
-+   else
-+       boost_fs_static_lib=$boost_fs_lib
-+   fi
-+   BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS"
-+   BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS"
-+
-+   AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem,
-+      CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-+      LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS"
-+      [AC_LINK_IFELSE(
-+          [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]],
-+              [[return boost::filesystem::portable_name("foo");]])],
-+          [ncbi_cv_lib_boost_filesystem=yes],
-+          [ncbi_cv_lib_boost_filesystem=no])])
-+
-    BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}
-    if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then
-        BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static
-@@ -4813,7 +4967,7 @@
-    BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS
-    BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS
- 
--   AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test,
-+   AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test,
-       CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-       LIBS="$RT_LIBS $orig_LIBS"
-       found=
-@@ -4853,7 +5007,7 @@
-        BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
-    fi
- 
--   AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread,
-+   AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
-       CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-       LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
-       [AC_LINK_IFELSE(
-@@ -4864,12 +5018,25 @@
-    BOOST_INCLUDE=
-    BOOST_LIBPATH=
-    BOOST_TAG=
-+   ncbi_cv_lib_boost_filesystem=no
-    ncbi_cv_lib_boost_regex=no
-    ncbi_cv_lib_boost_spirit=no
-+   ncbi_cv_lib_boost_system=no
-    ncbi_cv_lib_boost_test=no
-    ncbi_cv_lib_boost_thread=no
- fi
- 
-+if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
-+   dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
-+   dnl           [Define to 1 if the `Boost.Filesystem' library is available.])
-+   NCBI_PACKAGE(Boost.Filesystem)
-+else
-+   boost_fs_lib=
-+   boost_fs_static_lib=
-+   BOOST_FILESYSTEM_LIBS=
-+   BOOST_FILESYSTEM_STATIC_LIBS=
-+fi
-+
- if test "$ncbi_cv_lib_boost_regex" != "no"; then
-    AC_DEFINE(HAVE_BOOST_REGEX, 1,
-              [Define to 1 if the `Boost.Regex' library is available.])
-@@ -4927,7 +5094,10 @@
- 
- ## NCBI C Toolkit
- if test "$with_ncbi_c" != "no" ; then
--   NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
-+   if test "${with_ncbi_c-yes}" != yes; then
-+      NCBI_C_PATH=$with_ncbi_c
-+   fi
-+   : ${NCBI_C_PATH="$NCBI"}
-    if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
-       NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
-    fi
-@@ -4949,7 +5119,8 @@
-      NCBI_C_ncbi="-lncbi"
-    fi
-    NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH"
--   AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools,
-+   AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}],
-+      ncbi_cv_lib_ctools,
-       [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS"
-        LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS"
-        AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5000,11 +5171,7 @@
- 
- ## OpenGL
- if test "$with_opengl" != "no"; then
--   if test "${with_opengl-yes}" = yes; then
--      if test -d $NCBI/MesaGL; then
--         : ${OPENGL_PATH=$NCBI/MesaGL}
--      fi
--   else
-+   if test "${with_opengl-yes}" != yes; then
-       OPENGL_PATH=$with_opengl
-    fi
-    if test -d "$OPENGL_PATH"; then
-@@ -5101,7 +5268,6 @@
-    else
-       OSMESA_STATIC_LIBS=$OSMESA_LIBS
-    fi
--   : ${GLUT_PATH=$NCBI/glut}
-    if test "$with_glut" != "no"; then
-       if test "${with_glut-yes}" != "yes"; then
-          GLUT_PATH=$with_glut
-@@ -5121,7 +5287,6 @@
-          NCBI_MISSING_PACKAGE(glut)
-       fi
-    fi
--   : ${GLEW_PATH=$NCBI/glew}
-    if test "$with_glew" != "no"; then
-       if test "${with_glew-yes}" != "yes"; then
-          GLEW_PATH=$with_glew
-@@ -5214,7 +5379,7 @@
- : ${with_wxwidgets_ucs=no}
- if test "$with_wxwidgets" != "no" ; then
-    case "$with_wxwidgets" in
--      yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;;
-+      yes | "" ) ;;
-       *        ) WXWIDGETS_PATH=$with_wxwidgets ;;
-    esac
-    if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-@@ -5283,12 +5448,13 @@
-          libsed=$basesed
-          ;;
-    esac
--   AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH],
-+   AC_CACHE_CHECK(
-+      [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
-       ncbi_cv_lib_wxwidgets,
-       [if test -x "$wxconf" ; then
-           WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
-           NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
--             [$libsed; ])
-+             [$libsed; s/ -lm / /g;])
- 
-           CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
-           LIBS="$WXWIDGETS_LIBS $orig_LIBS"
-@@ -5315,12 +5481,12 @@
- else
-    NCBI_PACKAGE(wxWidgets)
-    case "`"$wxconf" $wxcfflags --version`" in
--      2.[[89]].* | 2.[[0-9]][[0-9]]* )
--         NCBI_PACKAGE(wx2.8)
--         wxlibs=std,richtext,aui
-+      1.* | 2.[[0-7]].*)
-+         wxlibs=std
-          ;;
-       *)
--         wxlibs=std
-+         NCBI_PACKAGE(wx2.8)
-+         wxlibs=std,richtext,aui,propgrid
-          ;;
-    esac
-    # The "yes" may have been cached; get the actual settings again if needed
-@@ -5328,9 +5494,9 @@
-       WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
-    fi
-    NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs],
--      [$libsed; ])
-+      [$libsed; s/ -lm / /g;])
-    WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \
--      2>/dev/null | sed -e "$basesed"`
-+      2>/dev/null | sed -e "$basesed; s/ -lm / /g;"`
-    if test -n "$WXWIDGETS_STATIC_LIBS"; then
-       # Allow direct use of underlying libraries with strict linkers
-       WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`"
-@@ -5350,7 +5516,7 @@
- ## In-house Fast-CGI library
- if test "$with_fastcgi" != "no" ; then
-    case "$with_fastcgi" in
--      yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;;
-+      yes | "" ) ;;
-       */*      ) FASTCGI_PATH=$with_fastcgi              ;;
-       *        ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;;
-    esac
-@@ -5366,7 +5532,8 @@
-    NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS])
-    FASTCGI_OBJS="fcgibuf"
-    LIBS="$FASTCGI_LIBS $orig_LIBS"
--   AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi,
-+   AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}],
-+      ncbi_cv_lib_fcgi,
-       [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS"
-        AC_LINK_IFELSE([AC_LANG_PROGRAM(
-           [[#include <fcgiapp.h>]],
-@@ -5416,7 +5583,11 @@
-    else
-       with_included_sss=no
-    fi
-+   if test "${with_sss-yes}" = yes; then
-    NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"}
-+   else
-+      NCBI_SSS_PATH=$with_sss
-+   fi
-    NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"}
-    if test -z "$NCBI_SSS_LIBPATH" ; then
-       NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}"
-@@ -5424,7 +5595,8 @@
-          NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt"
-       fi
-    fi
--   AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH])
-+   AC_MSG_CHECKING(
-+      [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}])
-    if test "$with_included_sss" = "yes"; then
-       AC_MSG_RESULT([yes]) # duh
-    elif test ! -d "${NCBI_SSS_LIBPATH}"  -o  ! -d "${NCBI_SSS_INCLUDE}" ; then
-@@ -5510,7 +5682,6 @@
- 
- # SP
- if test "$with_sp" != "no" ; then
--   SP_PATH=${SP_PATH:="$NCBI/SP"}
-    if test -n "$SP_INCLUDE"; then
-       SP_GENERIC="$SP_INCLUDE/../generic"
-    else
-@@ -5520,7 +5691,7 @@
-    if test -z "$SP_LIBPATH" ; then
-       SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}"
-    fi
--   AC_MSG_CHECKING([for SP directories in $SP_PATH])
-+   AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}])
-    if test ! -d "${SP_LIBPATH}"  -o  ! -d "${SP_INCLUDE}" ; then
-       AC_MSG_RESULT([no])
-       NCBI_MISSING_PACKAGE(sp)
-@@ -5558,19 +5729,13 @@
- 
- 
- ## ORBacus CORBA
--if test "${with_orbacus:-yes}" = yes; then
--   if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then
--      : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT}
--   else
--      : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1}
--   fi
--elif test "$with_orbacus" != no; then
-+if test "$with_orbacus" != no; then
-+   if test "$with_orbacus" != yes; then
-     ORBACUS_PATH=$with_orbacus
- fi
- if test -d "$ORBACUS_PATH"; then
-    NCBI_FIX_DIR(ORBACUS_PATH)
- fi
--if test "$with_orbacus" != no; then
-    fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx}
-    if test -f ${fullpath}/inc/OB/Config.h ; then
-       : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"}
-@@ -5594,7 +5759,8 @@
-          LIBIMR=
-          ;;
-    esac
--   AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus,
-+   AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}],
-+      ncbi_cv_lib_orbacus,
-       [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS"
-        LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS"
-        AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5633,7 +5799,7 @@
- 
- if test "$with_icu" != "no" ; then
-    case "$with_icu" in
--      yes | "" ) : ${ICU_PATH=$NCBI/icu} ;;
-+      yes | "" ) ;;
-       *        ) ICU_PATH=$with_icu ;;
-    esac
-    if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \
-@@ -5648,7 +5814,8 @@
-    ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"}
-    ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"}
-    ICU_INCLUDE=
--   AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu,
-+   AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}],
-+      ncbi_cv_lib_icu,
-       [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config
-        if test -x "$ICU_CONFIG" ; then
-           ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath`
-@@ -5690,9 +5857,6 @@
- 
- 
- ### XML/XSL libraries
--if test -d "$NCBI/expat/include"; then
--   : ${EXPAT_PATH=$NCBI/expat}
--fi
- NCBI_CHECK_THIRD_PARTY_LIB(expat,
-  AC_LANG_PROGRAM([#include <expat.h>],
-     [XML_Parser parser = XML_ParserCreate("utf-8");]))
-@@ -5701,7 +5865,6 @@
- else
-    EXPAT_STATIC_LIBS=${EXPAT_LIBS}
- fi
--: ${SABLOT_PATH=$NCBI/Sablot}
- vpath="$SABLOT_PATH/${compiler_vpfx}build"
- test -d "$vpath"  &&  SABLOT_PATH=$vpath
- if test -d "$SABLOT_PATH"; then
-@@ -5718,7 +5881,6 @@
-    SABLOT_STATIC_LIBS=${SABLOT_LIBS}
- fi
- 
--: ${LIBXML_PATH=$NCBI/libxml}
- # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null`
- if test "$with_libxml" != "no"; then
-    case "$with_libxml" in
-@@ -5813,7 +5975,6 @@
-    LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS}
- fi
- 
--: ${XERCES_PATH=$NCBI/xerces}
- if test "$with_xerces" != no; then
-    if test "${with_xerces-yes}" != yes; then
-       XERCES_PATH=$with_xerces
-@@ -5838,7 +5999,7 @@
-          NCBI_FIX_DIR(XERCES_LIBPATH)
-       fi
-    fi
--   if test -d $XERCES_PATH; then
-+   if test -d "$XERCES_PATH"; then
-       in_path=" in $XERCES_PATH"
-       : ${XERCES_INCLUDE=-I$XERCES_PATH/include}
-       : ${XERCES_LIBPATH=$XERCES_PATH/lib}
-@@ -5875,7 +6036,6 @@
-    XERCES_STATIC_LIBS=
- fi
- 
--: ${XALAN_PATH=$NCBI/xalan}
- if test "$with_xalan" != no; then
-    if test "${with_xalan-yes}" != yes; then
-       XALAN_PATH=$with_xalan
-@@ -5900,7 +6060,7 @@
-          NCBI_FIX_DIR(XALAN_LIBPATH)
-       fi
-    fi
--   if test -d $XALAN_PATH; then
-+   if test -d "$XALAN_PATH"; then
-       in_path=" in $XALAN_PATH"
-       : ${XALAN_INCLUDE=-I$XALAN_PATH/include}
-       : ${XALAN_LIBPATH=$XALAN_PATH/lib}
-@@ -5937,7 +6097,6 @@
- 
- test -d SunWS_cache  &&  rm -r SunWS_cache
- 
--: ${ZORBA_PATH=$NCBI/zorba}
- if test "$with_zorba" != no; then
-    if test "${with_zorba-yes}" != yes; then
-       ZORBA_PATH=$with_zorba
-@@ -5967,7 +6126,7 @@
-       ZORBA_PATH=`$ZORBA_CONFIG --prefix`
-       : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`}
-    fi
--   if test -d $ZORBA_PATH; then
-+   if test -d "$ZORBA_PATH"; then
-       in_path=" in $ZORBA_PATH"
-       : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include}
-       : ${ZORBA_LIBPATH=$ZORBA_PATH/lib}
-@@ -6010,7 +6169,7 @@
- 
- ### SQLite
- case "$with_sqlite3" in
--   yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;;
-+   yes | '' ) ;;
-    *        ) SQLITE3_PATH=$with_sqlite3 ;;
- esac
- 
-@@ -6048,7 +6207,6 @@
- ### OEChem
- # somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
- # which depend on oechem....
--: ${OECHEM_PATH=$NCBI/oechem}
- NCBI_CHECK_THIRD_PARTY_LIB(oechem,
-  AC_LANG_PROGRAM([#include <oechem.h>],
-     [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]),
-@@ -6091,7 +6249,7 @@
- 
- ### muParser
- case "$with_muparser" in
--   yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;;
-+   yes | '' ) ;;
-    *        ) MUPARSER_PATH=$with_muparser ;;
- esac
- 
-@@ -6111,7 +6269,7 @@
- 
- ### hdf5
- case "$with_hdf5" in
--   yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;;
-+   yes | '' ) ;;
-    *        ) HDF5_PATH=$with_hdf5 ;;
- esac
- 
-@@ -6176,7 +6334,7 @@
-    GIF_LIBS=$UNGIF_LIBS
- fi
- 
--test -n "$x_libraries"  &&  : ${XPM_PATH=`dirname "$x_libraries"`}
-+case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac
- NCBI_CHECK_THIRD_PARTY_LIB(Xpm,
-  AC_LANG_PROGRAM([#include <X11/xpm.h>],
-     [XpmImage image; XpmInfo info;
-@@ -6241,7 +6399,7 @@
- fi
- 
- case "$with_ftgl" in
--   yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;;
-+   yes | '' ) ;;
-    *        ) FTGL_PATH=$with_ftgl ;;
- esac
- 
-@@ -6268,7 +6426,7 @@
- 
- # Mimetic
- case "$with_mimetic" in
--   yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;;
-+   yes | '' ) ;;
-    *        ) MIMETIC_PATH=$with_mimetic ;;
- esac
- if test -d "$MIMETIC_PATH"; then
-@@ -6293,6 +6451,88 @@
-        [mimetic::MimeEntity me;])])
- 
- 
-+# gSOAP++
-+case "$with_gsoap" in
-+   yes | '' ) ;;
-+   *        ) GSOAP_PATH=$with_gsoap ;;
-+esac
-+if test -d "$GSOAP_PATH"; then
-+   NCBI_FIX_DIR(GSOAP_PATH)
-+fi
-+for d in "$GSOAP_LIBDIR" \
-+         "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+         "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+         "$GSOAP_PATH/lib${bit64_sfx}" \
-+         "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+         "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+         "$GSOAP_PATH/lib"; do
-+   if test -d "$d"; then
-+      GSOAP_LIBDIR=$d
-+      NCBI_FIX_DIR(GSOAP_LIBDIR)
-+      break
-+   fi
-+done
-+NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR)
-+
-+: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin}
-+AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH)
-+AC_PATH_PROG(GSOAP_WSDL2H,   wsdl2h,   [], $GSOAP_BINDIR:$PATH)
-+
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++,
-+   [AC_LANG_PROGRAM([#include <stdsoap2.h>
-+        SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*)
-+        { return NULL; }
-+        SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { }
-+        SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; }
-+        SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; }
-+        SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { }
-+        SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; }
-+        SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }],
-+       [soap s;])],
-+   $OPENSSL_LIBS $Z_LIBS)
-+
-+case "$with_sqlite3" in
-+   yes | '' ) ;;
-+   *        ) SQLITE3_PATH=$with_sqlite3 ;;
-+esac
-+
-+
-+# MongoDB
-+if test -d "$MONGODB_PATH"; then
-+   NCBI_FIX_DIR(MONGODB_PATH)
-+fi
-+if test -d $MONGODB_PATH/lib${bit64_sfx}; then
-+   MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx}
-+else
-+   MONGODB_LIBDIR=$MONGODB_PATH/lib
-+fi
-+# need Boost rpath
-+NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR)
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
-+   [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>],
-+      [std::vector<mongo::HostAndPort> v;
-+       mongo::DBClientReplicaSet client("foo", v);
-+       client.connect();])],
-+   [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [],
-+   [$BOOST_INCLUDE])
-+# MongoDB's own library is normally static, but its supporting Boost
-+# libraries might not be by default.
-+if test -n "$MONGODB_LIBS"; then
-+   MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS"
-+else
-+   MONGODB_STATIC_LIBS=
-+fi
-+
- ### Restore original compiler/linker flags
- LIBS="$orig_LIBS"
- CPPFLAGS="$orig_CPPFLAGS"
-@@ -6499,16 +6739,6 @@
- fi
- 
- 
--## Sequence Read Archive SDK, which may be attached on either the
--## public or the internal side
--
--if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then
--   sra=sra
--else
--   sra=
--fi
--
--
- ## `internal' project cluster
- 
- if test "$with_internal" = "no"  \
-@@ -6781,6 +7011,7 @@
- AC_SUBST(C_LINK)
- AC_SUBST(TAIL_N)
- AC_SUBST(EGREP_Q)
-+AC_SUBST(LDD_R)
- 
- AC_SUBST(CFLAGS)
- AC_SUBST(FAST_CFLAGS)
-@@ -6829,7 +7060,6 @@
- AC_SUBST(algo)
- AC_SUBST(app)
- AC_SUBST(internal)
--AC_SUBST(sra)
- 
- AC_SUBST(check)
- AC_SUBST(CHECK_ARG)
-@@ -6865,6 +7095,7 @@
- 
- AC_SUBST(THREAD_LIBS)
- AC_SUBST(NCBIATOMIC_LIB)
-+AC_SUBST(OPENMP_FLAGS)
- AC_SUBST(NETWORK_LIBS)
- AC_SUBST(NETWORK_PURE_LIBS)
- AC_SUBST(RESOLVER_LIBS)
-@@ -6902,6 +7133,8 @@
- AC_SUBST(BOOST_INCLUDE)
- AC_SUBST(BOOST_LIBPATH)
- AC_SUBST(BOOST_TAG)
-+AC_SUBST(BOOST_FILESYSTEM_LIBS)
-+AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS)
- AC_SUBST(BOOST_REGEX_LIBS)
- AC_SUBST(BOOST_REGEX_STATIC_LIBS)
- AC_SUBST(BOOST_SYSTEM_LIBS)
-@@ -6968,6 +7201,8 @@
- AC_SUBST(SQLITE3_STATIC_LIBS)
- AC_SUBST(FREETYPE_INCLUDE)
- AC_SUBST(FREETYPE_LIBS)
-+AC_SUBST(GSOAP_PATH)
-+AC_SUBST(MONGODB_STATIC_LIBS)
- AC_SUBST(ncbi_xreader_pubseqos)
- AC_SUBST(ncbi_xreader_pubseqos2)
- AC_SUBST(UNLESS_PUBSEQOS)
-@@ -7194,7 +7429,9 @@
- 
- cat << EOCONF
- ===============================================================================
--NCBI C++ Toolkit documentation:  doc/index.html,  doc/config.html#ref_Running
-+NCBI C++ Toolkit documentation:
-+  Online:   http://www.ncbi.nlm.nih.gov/toolkit/doc/book/
-+  Local:    ./doc/public/index.html
- For the available configuration flags run:  ./configure --help
- 
- CFLAGS   = $CFLAGS
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori	2014-06-23 17:36:18.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4	2014-06-23 17:36:59.000000000 +0200
-@@ -1,126 +1,45 @@
--# Hacked up in various ways, since Autoconf's version doesn't quite
--# suit our (unusual) conventions.  (Originally from status.m4)
--m4_define([_AC_SRCPATHS],
--[#ac_builddir=. # Useless!
--ac_builddir=$builddir
--dnl Base source directories on path to *input* file.
--if test -n "$ac_file_in"; then
--   ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
-+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
-+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
-+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
-+m4_define([_AC_SRCDIRS],
-+[# Base source directories on path to *input* file.
-+if test -n "$ac_f"; then
-+   ac_dir_in=`AS_DIRNAME(["$ac_f"])`
- else
-    ac_dir_in=$1
- fi
- 
--if test $ac_dir_in != .; then
--  ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
--  # A "../" for each directory in $ac_dir_suffix.
--  ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
--else
--  ac_dir_suffix= ac_top_builddir=
--fi
-+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
- 
--case $srcdir in
--  .)  # No --srcdir option.  We are building in place.
--    ac_srcdir=.
--    if test -z "$ac_top_builddir"; then
--       ac_top_srcdir=.
--    else
--       ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
--    fi ;;
--  [[\\/]]* | ?:[[\\/]]* )  # Absolute path.
--    ac_srcdir=$srcdir/$ac_dir_suffix;
--    ac_top_srcdir=$srcdir ;;
--  *) # Relative path.
--    ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
--    ac_top_srcdir=$ac_top_builddir$srcdir ;;
--esac
--# Do not use `cd foo && pwd` to compute absolute paths, because
--# the directories may not exist.
--AS_SET_CATFILE([ac_abs_builddir],   [$builddir],        [$1])
--AS_SET_CATFILE([ac_abs_top_builddir],
--                                    [$ac_abs_builddir], [${ac_top_builddir}.])
- AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in],       [$real_srcdir])
--AS_SET_CATFILE([ac_abs_srcdir],     [$ac_abs_top_srcdir], [$ac_dir_suffix])
--])# _AC_SRCPATHS
--
-+ac_builddir=$builddir
-+])
- 
--# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
--# last resort due to issues with sourcing .bashrc.
--m4_define([_AS_LINENO_PREPARE],
--[_AS_LINENO_WORKS || {
--  # Find who we are.  Look in the path if we contain no path at all
--  # relative or not.
--  case $[0] in
--    *[[\\/]]* ) as_myself=$[0] ;;
--    *) _AS_PATH_WALK([],
--                   [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
--       ;;
--  esac
--  # We did not find ourselves, most probably we were run as `sh COMMAND'
--  # in which case we are not to be found in the path.
--  if test "x$as_myself" = x; then
--    as_myself=$[0]
--  fi
--  if test ! -f "$as_myself"; then
--    AS_ERROR([cannot find myself; rerun with an absolute path])
--  fi
--  case $CONFIG_SHELL in
--  '')
--    AS_UNSET(ZSH_VERSION)
--    for as_base in sh ksh sh5 bash; do
--      _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
--         [case $as_dir in
--         /*)
--           if ("$as_dir/$as_base" -c \
--                 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
--           then
--             AS_UNSET(BASH_ENV)
--             AS_UNSET(ENV)
--             CONFIG_SHELL=$as_dir/$as_base
--             export CONFIG_SHELL
--             exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
--           fi;;
--         esac
--       done]);;
--  esac
- 
--  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
--  # uniformly replaced by the line number.  The first 'sed' inserts a
--  # line-number line before each line; the second 'sed' does the real
--  # work.  The second script uses 'N' to pair each line-number line
--  # with the numbered line, and appends trailing '-' during
--  # substitution so that $LINENO is not a special case at line end.
--  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
--  # second 'sed' script.  Blame Lee E. McMahon for sed's syntax.  :-)
--  sed '=' <$as_myself |
--    sed '
--      N
--      s,$,-,
--      : loop
--      s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
--      t loop
--      s,-$,,
--      s,^[['$as_cr_digits']]*\n,,
--    ' >$as_me.lineno &&
--  chmod +x $as_me.lineno ||
--    AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
--
--  # Don't try to exec as it changes $[0], causing all sort of problems
--  # (the dirname of $[0] is not the place where we might find the
--  # original and so on.  Autoconf is especially sensible to this).
--  . ./$as_me.lineno
--  # Exit status is that of the last command.
--  exit
--}
--])# _AS_LINENO_PREPARE
-+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
-+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
-+# bash a last resort due to issues with sourcing .bashrc while entirely
-+# avoiding zsh, which passes itself off as ksh on some systems but runs
-+# parent shells' exit handlers from subshells, resulting in premature
-+# cleanup of temporary files (notably confdefs.h).
-+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
-+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
-+
-+m4_define([_AS_DETECT_BETTER_SHELL],
-+  [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
-+     [sh bash ksh sh5], [sh ksh sh5 bash])])
-+m4_define([_AS_RUN],
-+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
-+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
- 
- 
- # One more hack: suppress PACKAGE_*, as we don't use them and some
- # third-party libraries expose their corresponding settings, leading
- # to preprocessor warnings.
--m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
-+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
- m4_define([AC_DEFINE_UNQUOTED],
-    [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
--       [NCBI_ORIG_ACDU($@)])])
-+       [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
- 
- 
- AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +77,7 @@
-        AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
-     * )
-        echo "$1 [[y/N]]"
--       read answer
-+       read answer <& AS_ORIGINAL_STDIN_FD
-        case "$answer" in
-          [[Yy]]* )  AC_MSG_WARN([Proceeding at your own risk...]) ;;
-          *       )  AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori	2014-06-23 17:38:56.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in	2014-06-23 17:39:04.000000000 +0200
-@@ -98,6 +98,9 @@
- /* Define to 1 if you have the `getaddrinfo' function. */
- #undef HAVE_GETADDRINFO
- 
-+/* Define to 1 if you have the `getgrouplist' function. */
-+#undef HAVE_GETGROUPLIST
-+
- /* If you have the `gethostbyaddr_r' function, define to the number of
-    arguments it takes (normally 7 or 8). */
- #undef HAVE_GETHOSTBYADDR_R
-@@ -176,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
- 
-@@ -234,6 +234,9 @@
- /* Define to 1 if libgnutls is available. */
- #undef HAVE_LIBGNUTLS
- 
-+/* Define to 1 if libgsoapssl++ is available. */
-+#undef HAVE_LIBGSOAP
-+
- /* Define to 1 if libhdf5_cpp is available. */
- #undef HAVE_LIBHDF5
- 
-@@ -260,6 +263,9 @@
- /* Define to 1 if libmimetic is available. */
- #undef HAVE_LIBMIMETIC
- 
-+/* Define to 1 if libmongoclient is available. */
-+#undef HAVE_LIBMONGODB
-+
- /* Define to 1 if libmuparser is available. */
- #undef HAVE_LIBMUPARSER
- 
-@@ -382,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
- 
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
- 
-@@ -799,37 +802,37 @@
-    by a signal. */
- #undef SELECT_UPDATES_TIMEOUT
- 
--/* The size of a `char', as computed by sizeof. */
-+/* The size of `char', as computed by sizeof. */
- #undef SIZEOF_CHAR
- 
--/* The size of a `double', as computed by sizeof. */
-+/* The size of `double', as computed by sizeof. */
- #undef SIZEOF_DOUBLE
- 
--/* The size of a `float', as computed by sizeof. */
-+/* The size of `float', as computed by sizeof. */
- #undef SIZEOF_FLOAT
- 
--/* The size of a `int', as computed by sizeof. */
-+/* The size of `int', as computed by sizeof. */
- #undef SIZEOF_INT
- 
--/* The size of a `long', as computed by sizeof. */
-+/* The size of `long', as computed by sizeof. */
- #undef SIZEOF_LONG
- 
--/* The size of a `long double', as computed by sizeof. */
-+/* The size of `long double', as computed by sizeof. */
- #undef SIZEOF_LONG_DOUBLE
- 
--/* The size of a `long long', as computed by sizeof. */
-+/* The size of `long long', as computed by sizeof. */
- #undef SIZEOF_LONG_LONG
- 
--/* The size of a `short', as computed by sizeof. */
-+/* The size of `short', as computed by sizeof. */
- #undef SIZEOF_SHORT
- 
--/* The size of a `size_t', as computed by sizeof. */
-+/* The size of `size_t', as computed by sizeof. */
- #undef SIZEOF_SIZE_T
- 
--/* The size of a `void*', as computed by sizeof. */
-+/* The size of `void*', as computed by sizeof. */
- #undef SIZEOF_VOIDP
- 
--/* The size of a `__int64', as computed by sizeof. */
-+/* The size of `__int64', as computed by sizeof. */
- #undef SIZEOF___INT64
- 
- /* Define to 1 if the stack grows down. */
-@@ -870,5 +873,5 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- #undef const
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- #undef size_t
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori	2014-06-23 17:40:40.000000000 +0200
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h	2014-06-23 17:40:57.000000000 +0200
-@@ -1,4 +1,4 @@
--/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $
-+/* $Id$
-  * By Vlad Lebedev, NCBI (lebedev@××××××××××××.gov)
-  *
-  * Mac OS X - xCode Build
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
- 
-@@ -358,6 +355,9 @@
- /* Define to 1 if you have the `lutimes' function. */
- /* #undef HAVE_LUTIMES */
- 
-+/* Define to 1 if you have the `madvise' function. */
-+#define HAVE_MADVISE 1
-+
- /* Define to 1 if you have the <malloc.h> header file. */
- /* #undef HAVE_MALLOC_H */
- 
-@@ -589,15 +589,15 @@
- /* Define to 1 if you have the <windows.h> header file. */
- /* #undef HAVE_WINDOWS_H */
- 
-+/* Define to 1 if you have the `writev' function. */
-+#define HAVE_WRITEV 1
-+
- /* Define to 1 if the system has the type `wstring'. */
- #define HAVE_WSTRING 1
- 
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
- 
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- #  define ICONV_CONST
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
- 
- /*
 --- ncbi_cxx--12_0_0/src/build-system/configure.ori	2013-05-20 23:03:20.000000000 +0200
 +++ ncbi_cxx--12_0_0/src/build-system/configure	2014-06-23 22:22:50.000000000 +0200
 @@ -1,19 +1,13 @@