path: root/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad

--- 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@ncbi.nlm.nih.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 */
 
 /*