From cb7af5375a7fbfdfaeddf149fed723aa81e1827e Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Mon, 23 Jun 2014 22:38:29 +0200 Subject: dropped the duplicate part from the patch --- .../files/ncbi-tools++-12.0.0-configure.patch | 1660 -------------------- 1 file changed, 1660 deletions(-) (limited to 'sci-biology/ncbi-tools++') 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 0d4bd39d4..4c779910b 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 $CPPFLAGS" -+ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only -+ # in C++ mode. Set it for C code as well to ensure consistent -+ # header behavior, taking care to match the C standard version -+ # (as enforced by ). -+ case "$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 ], ncbi_cv_func_is_sorted, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( -- [[#include ]], -- [[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 "$ncbi_cv_func_is_sorted" = yes; then -- AC_DEFINE(HAVE_IS_SORTED, 1, -- [Define to 1 if supplies `std::is_sorted<>'.]) --fi -- -- - - AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, - AC_LINK_IFELSE([AC_LANG_PROGRAM([#include -@@ -3400,7 +3521,7 @@ - AC_CACHE_CHECK([whether the C compiler supports C99 restrict], - ncbi_cv_c_restrict, - [ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$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 $ODBC_PATH}], -+ ncbi_cv_lib_odbc, - [AC_LINK_IFELSE([AC_LANG_PROGRAM( - [[#include ]], - [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x"; -@@ -4542,7 +4673,7 @@ - AC_PATH_PROG(PERL, perl, [], [$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 $orig_LIBS" -+ [AC_LINK_IFELSE( -+ [AC_LANG_PROGRAM([[#include ]], -+ [[return boost::filesystem::portable_name("foo");]])], -+ [ncbi_cv_lib_boost_filesystem=yes], -+ [ncbi_cv_lib_boost_filesystem=no])]) -+ - BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${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 $orig_CPPFLAGS" - AC_LINK_IFELSE([AC_LANG_PROGRAM( - [[#include ]], -@@ -5416,7 +5583,11 @@ - else - with_included_sss=no - fi -+ if test "${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 ], - [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::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 ], - [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 -+ 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, $MONGODB_LIBDIR) -+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient, -+ [AC_LANG_PROGRAM([#include ], -+ [std::vector v; -+ mongo::DBClientReplicaSet client("foo", v); -+ client.connect();])], -+ [$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 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 does not define. */ -+/* Define to `unsigned int' if 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 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 header file. */ - /* #undef HAVE_MALLOC_H */ - -@@ -589,15 +589,15 @@ - /* Define to 1 if you have the 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 does not define. */ -+/* Define to `unsigned int' if 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 @@ -- cgit v1.2.3-65-gdbad