[med-svn] r9983 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Mon Mar 12 16:05:37 UTC 2012
Author: osallou
Date: 2012-03-12 16:05:37 +0000 (Mon, 12 Mar 2012)
New Revision: 9983
Added:
trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/patches/series
Log:
fix upstream bug for Hurd build
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-03-10 20:33:37 UTC (rev 9982)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-03-12 16:05:37 UTC (rev 9983)
@@ -1,3 +1,10 @@
+ncbi-blast+ (2.2.26-2) unstable; urgency=low
+
+ * debian/patches/wrong_path_to_touch.patch :Fix upstream FTBFS on the Hurd
+ hardcodes wrong path to touch (Closes: #663244)
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 07 Mar 2012 17:29:23 +0100
+
ncbi-blast+ (2.2.26-1) unstable; urgency=low
[ Olivier Sallou ]
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2012-03-10 20:33:37 UTC (rev 9982)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series 2012-03-12 16:05:37 UTC (rev 9983)
@@ -2,3 +2,4 @@
legacy_rename_rpsblast
fix_lib_deps
no_multiarch_rpath
+wrong_path_to_touch.patch
Added: trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch 2012-03-12 16:05:37 UTC (rev 9983)
@@ -0,0 +1,439 @@
+Subject: upstream bug using hard path for touch
+Description: upstream makes use of a hard path that
+does not match on hurd systems. Patch comes from upstream
+ and will be included in next release
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 12/03/2012
+--- a/c++/src/build-system/Makefile.meta.in
++++ b/c++/src/build-system/Makefile.meta.in
+@@ -28,7 +28,7 @@
+
+ @make_shell@
+ RM = /bin/rm
+-TOUCH = /usr/bin/touch
++TOUCH = @TOUCH@
+ MKDIR = /bin/mkdir
+
+ signature = @signature@
+--- a/c++/src/build-system/Makefile.mk.in
++++ b/c++/src/build-system/Makefile.mk.in
+@@ -54,7 +54,7 @@
+ RMDIR = /bin/rm -rf
+ COPY = /bin/cp -p
+ BINCOPY = @BINCOPY@
+-TOUCH = /usr/bin/touch
++TOUCH = @TOUCH@
+ MKDIR = /bin/mkdir
+ BINTOUCH = $(TOUCH)
+ LN_S = @LN_S@
+--- a/c++/src/build-system/NEWS
++++ b/c++/src/build-system/NEWS
+@@ -8,3 +8,5 @@
+ 2011-05-17: new @ncbi_java@ variable for --with-jni builds.
+
+ 2011-10-05: new @FEATURES@ variable for the unit test framework.
++
++2012-02-27: new @TOUCH@ variable to avoid hard-coded paths.
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -318,7 +318,7 @@
+ # include <unistd.h>
+ #endif"
+
+-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
++ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL TOUCH EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
+ ac_subst_files=''
+
+ # Initialize some variables set by options.
+@@ -874,6 +874,7 @@
+ ===============================================================================
+ =============== NCBI C++ Toolkit specific configuration flags =================
+ --without-debug build non-debug versions of libs and apps
++ --with-max-debug, enable extra runtime checks (esp. of STL usage)
+ --with-symbols retain debugging symbols in non-debug mode
+ --without-optimization turn off optimization flags in non-debug mode
+ --with-profiling build profiled versions of libs and apps
+@@ -893,6 +894,7 @@
+ --with-relative-runpath=P specify an executable-relative DLL search path
+ --with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
+ --with-lfs enable large file support to the extent possible
++ --with-limited-linker don't attempt to build especially large projects
+ --with-extra-action= script to call after the configuration is complete
+ --with-autodep automatic generation of dependencies (GNU make)
+ --with-build-root=DIR specify a non-default build directory name
+@@ -1846,6 +1848,12 @@
+
+ fi;
+
++# Check whether --with-max-debug or --without-max-debug was given.
++if test "${with_max_debug+set}" = set; then
++ withval="$with_max_debug"
++
++fi;
++
+ # Check whether --with-symbols or --without-symbols was given.
+ if test "${with_symbols+set}" = set; then
+ withval="$with_symbols"
+@@ -1960,6 +1968,12 @@
+
+ fi;
+
++# Check whether --with-limited-linker or --without-limited-linker was given.
++if test "${with_limited_linker+set}" = set; then
++ withval="$with_limited_linker"
++
++fi;
++
+ ## Scripts, make features, and directory naming
+
+ # Check whether --with-extra-action or --without-extra-action was given.
+@@ -2812,8 +2826,9 @@
+
+ #### Check the passed arguments against the list of available ones
+ x_with_list="\
+-debug symbols optimization profiling tcheck dll static static-exe bundles \
+-plugin-auto-load bin-release mt 64 universal exe runpath hard-runpath lfs \
++debug max-debug symbols optimization profiling tcheck dll static static-exe \
++plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
++lfs limited-linker \
+ autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
+ deactivation makefile-auto-update projects flat-makefile configure-dialog \
+ check ncbi-public strip pch caution ccache distcc \
+@@ -2985,6 +3000,11 @@
+ if test "$with_debug" = no; then
+ : ${with_symbols=no}
+ : ${with_optimization=yes}
++ if test "$with_max_debug" = yes; then
++ { { echo "$as_me:$LINENO: error: incompatible options: --without-debug but --with-max-debug" >&5
++echo "$as_me: error: incompatible options: --without-debug but --with-max-debug" >&2;}
++ { (exit 1); exit 1; }; }
++ fi
+ else
+ : ${with_symbols=yes}
+ : ${with_optimization=no}
+@@ -4962,6 +4982,9 @@
+ echo "$as_me:$LINENO: result: $ncbi_cv_prog_cc_wl_rpath" >&5
+ echo "${ECHO_T}$ncbi_cv_prog_cc_wl_rpath" >&6
+ ;;
++ cygwin*:GCC )
++ LDFLAGS="-Wl,--export-all-symbols $LDFLAGS"
++ ;;
+ *:GCC | *:ICC )
+ echo "$as_me:$LINENO: checking whether $CC supports -Wl,-E" >&5
+ echo $ECHO_N "checking whether $CC supports -Wl,-E... $ECHO_C" >&6
+@@ -5217,6 +5240,10 @@
+ ;;
+
+ darwin*:GCC)
++ case `uname -m` in
++ *64 ) : ${with_64=yes} ;;
++ * ) : ${with_64=no} ;;
++ esac
+ # Per <http://fink.sourceforge.net/doc/porting/shared.php>, it was
+ # historically necessary to build plugins as Mach-O bundles rather than
+ # dynamic libraries. That's not such a big deal on modern Mac OS X
+@@ -5229,14 +5256,16 @@
+ fi
+ if $CXX -v 2>&1 | grep -q Apple; then
+ CFLAGS="-fpascal-strings $CFLAGS"
+- CXXFLAGS="-fno-permissive -fpascal-strings $CXXFLAGS"
++ CXXFLAGS="-fpascal-strings $CXXFLAGS"
++ $CXX -v 2>&1 | grep -q clang || CXXFLAGS="-fno-permissive $CXXFLAGS"
+ # -flat_namespace is necessary for proper handling of shared libraries
+ # that don't themselves link against all their dependencies.
+ LDFLAGS="-flat_namespace $LDFLAGS"
+
+ if test "$with_ncbi_public" = yes; then
+ TARGET='-mmacosx-version-min=10.5'
+- if test -d /Developer/SDKs/MacOSX10.5.sdk; then
++ if test "$with_64:${with_universal-no}" != "yes:no" \
++ -a -d /Developer/SDKs/MacOSX10.5.sdk; then
+ TARGET="-isysroot /Developer/SDKs/MacOSX10.5.sdk $TARGET"
+ fi
+ CC="$CC $TARGET"
+@@ -5271,11 +5300,6 @@
+
+ OBJCXX_CXXFLAGS='-x objective-c++'
+ OBJCXX_LIBS='-lobjc'
+-
+- case `uname -m` in
+- *64 ) : ${with_64=yes} ;;
+- * ) : ${with_64=no} ;;
+- esac
+ ;;
+ esac
+
+@@ -5579,6 +5603,9 @@
+ CPPFLAGS="$LFSFLAGS $CPPFLAGS"
+ fi
+
++tabchar=' '
++wschars=" $tabchar"
++wsrx="[$wschars]"
+
+ #### Flags to enable (potentially unsafe) extra optimization.
+ if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then
+@@ -5601,7 +5628,7 @@
+ ;;
+ WorkShop5[89]* | WorkShop510 )
+ # Limit optimization to -xO2 (-O now maps to -xO3) due to compiler bugs.
+- subst='s/[ ]-x*O[1-9]*//g'
++ subst="s/$wsrx-x*O[1-9]*//g"
+ CFLAGS="` echo \" $CFLAGS\" | sed -e \"$subst\"` -xO2"
+ CXXFLAGS="`echo \" $CXXFLAGS\" | sed -e \"$subst\"` -xO2"
+ LDFLAGS="` echo \" $LDFLAGS\" | sed -e \"$subst\"` -xO2"
+@@ -5688,7 +5715,7 @@
+ solaris* )
+ CONF_f_runpath="-R"
+ ;;
+- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
++ linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
+ CONF_f_runpath="-Wl,-rpath,"
+ ;;
+ linux*:ICC )
+@@ -5751,7 +5778,7 @@
+ break
+ ;;
+ /* )
+- fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true
++ found=true
+ break
+ ;;
+ esac
+@@ -6615,6 +6642,46 @@
+ echo "${ECHO_T}no" >&6
+ fi
+
++# Extract the first word of "touch", so it can be a program name with args.
++set dummy touch; ac_word=$2
++echo "$as_me:$LINENO: checking for $ac_word" >&5
++echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
++if test "${ac_cv_path_TOUCH+set}" = set; then
++ echo $ECHO_N "(cached) $ECHO_C" >&6
++else
++ case $TOUCH in
++ [\\/]* | ?:[\\/]*)
++ ac_cv_path_TOUCH="$TOUCH" # Let the user override the test with a path.
++ ;;
++ *)
++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
++as_dummy="/bin:/usr/bin:$PATH"
++for as_dir in $as_dummy
++do
++ IFS=$as_save_IFS
++ test -z "$as_dir" && as_dir=.
++ for ac_exec_ext in '' $ac_executable_extensions; do
++ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
++ ac_cv_path_TOUCH="$as_dir/$ac_word$ac_exec_ext"
++ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
++ break 2
++ fi
++done
++done
++
++ ;;
++esac
++fi
++TOUCH=$ac_cv_path_TOUCH
++
++if test -n "$TOUCH"; then
++ echo "$as_me:$LINENO: result: $TOUCH" >&5
++echo "${ECHO_T}$TOUCH" >&6
++else
++ echo "$as_me:$LINENO: result: no" >&5
++echo "${ECHO_T}no" >&6
++fi
++
+ echo "$as_me:$LINENO: checking for egrep" >&5
+ echo $ECHO_N "checking for egrep... $ECHO_C" >&6
+ if test "${ac_cv_prog_egrep+set}" = set; then
+@@ -8028,13 +8095,13 @@
+ _ACEOF
+
+ fi
+- if $CXX -v 2>&1 | grep -q Apple; then
++ if $CXX -v 2>&1 | egrep -q 'Apple|clang'; then
+ LINK_DLL="$LINK $ARCH_CFLAGS -dynamiclib -install_name ${pure_runpath%%:*}/\$(XDLL) -o"
+ LINK_LOADABLE="$LINK $ARCH_CFLAGS -bundle -o"
+ ALLOW_UNDEF='-undefined suppress'
+ FORBID_UNDEF='-undefined error'
+ else
+- LINK_DLL="$CC $ARCH_CFLAGS -nostartfiles -Wl,-dynamic -install_name ${pure_runpath%%:*}/\$(XDLL) -o"
++ LINK_DLL="$CC $ARCH_CFLAGS -nostartfiles -Wl,-dynamic -Wl,-dylib -Wl,-install_name,${pure_runpath%%:*}/\$(XDLL) -o"
+ LINK_LOADABLE="$CC $ARCH_CFLAGS -nostartfiles -Wl,-dynamic -Wl,-bundle -Wl,-read_only_relocs,warning -lbundle1.o -o"
+ ALLOW_UNDEF='-Wl,-undefined,suppress'
+ FORBID_UNDEF='-Wl,-undefined,error'
+@@ -8696,7 +8763,7 @@
+ fi
+
+
+-#### Manage the debug-vs.-optimization flags ("--with(out)-debug",
++#### Manage the debug-vs.-optimization flags ("--with(out)-(max-)debug",
+ #### "--with(out)-symbols", "--with(out)-optimization")
+ if test "$compiler" != "MSVC" ; then
+ if test "$with_debug" = "no" -o "$with_tcheck" != "no"; then
+@@ -8705,23 +8772,42 @@
+ CPPFLAGS="-D_DEBUG $CPPFLAGS"
+ fi
+
++ if test "$with_max_debug" = "yes"; then
++ case "$compiler" in
++ GCC )
++ CPPFLAGS="-D_GLIBCXX_DEBUG $CPPFLAGS"
++ CFLAGS="-fstack-check $CFLAGS"
++ CXXFLAGS="-fstack-check $CXXFLAGS"
++ ;;
++ ICC )
++ CPPFLAGS="-D_GLIBCXX_DEBUG $CPPFLAGS"
++ CFLAGS="-debug all -fstack-security-check -ftrapuv $CFLAGS"
++ CXXFLAGS="-debug all -fstack-security-check -ftrapuv $CXXFLAGS"
++ ;;
++ WorkShop* )
++ CFLAGS="-xcheck=%all $CFLAGS"
++ CXXFLAGS="-xcheck=%all $CXXFLAGS"
++ ;;
++ esac
++ WithFeatures="$WithFeatures${WithFeaturesSep}MaxDebug"; WithFeaturesSep=" "
++ fi
++ dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
++ dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
++ optrx="$wsrx-x*O[0-9s]*$wsrx"
+ if test "$with_symbols" = "no" ; then
+- CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-g[0-9]*//g'`
+- CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-g[0-9]*//g'`
+- LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-g[0-9]*//g'`
++ 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"`
+ else
+- if echo " $CFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ; then
+- CFLAGS="$CFLAGS -g" ; fi
+- if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ; then
+- CXXFLAGS="$CXXFLAGS -g" ; fi
+- if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ;
+- then LDFLAGS="$LDFLAGS -g" ; fi
++ 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="@:"
+ fi
+
+- NOPT_CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
+- NOPT_CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
+- NOPT_LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
++ NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"`
++ NOPT_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$optrx/ /g"`
++ NOPT_LDFLAGS=` echo " $LDFLAGS " | sed "s/$optrx/ /g"`
+ if test "${with_tcheck-no}" != "no"; then
+ # Suppress warnings when building with ICC.
+ NOPT_CFLAGS="$NOPT_CFLAGS -O0"
+@@ -8736,11 +8822,11 @@
+ FAST_CXXFLAGS="$CXXFLAGS"
+ FAST_LDFLAGS="$LDFLAGS"
+ else
+- if echo " $CFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
++ if echo " $CFLAGS " | grep -v "$optrx" >/dev/null ; then
+ CFLAGS="$CFLAGS -O" ; fi
+- if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
++ if echo " $CXXFLAGS " | grep -v "$optrx" >/dev/null ; then
+ CXXFLAGS="$CXXFLAGS -O" ; fi
+- if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
++ if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then
+ LDFLAGS="$LDFLAGS -O" ; fi
+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
+@@ -17916,8 +18002,8 @@
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+ else
+ ncbi_cv_c_forceinline=no
+- for fi in forceinline __forceinline__ __forceinline __always_inline \
+- "inline __attribute__((always_inline))" inline __inline__; do
++ for fi in __always_inline "inline __attribute__((always_inline))" \
++ forceinline __forceinline__ __forceinline inline __inline__; do
+ test "$ncbi_cv_c_forceinline" = "no" || break
+ cat >conftest.$ac_ext <<_ACEOF
+ /* confdefs.h. */
+@@ -22719,7 +22805,8 @@
+
+ _ACEOF
+ eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" \
+- 2>&5 | grep '^ncbi_cv_' | tr -d ' ' > conftest.sh
++ 2>&5 | grep '^ncbi_cv_' \
++ | tr -d "$wschars" > conftest.sh
+ . ./conftest.sh
+ rm -f contest*
+
+@@ -24277,7 +24364,8 @@
+
+ _ACEOF
+ eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" \
+- 2>&5 | grep '^ncbi_cv_' | tr -d ' ' > conftest.sh
++ 2>&5 | grep '^ncbi_cv_' \
++ | tr -d "$wschars" > conftest.sh
+ . ./conftest.sh
+ rm -f contest*
+
+@@ -24324,7 +24412,7 @@
+ case "$with_boost_tag" in
+ yes | "" )
+ case "$host_os:$ncbi_compiler" in
+- darwin*:GCC) BOOST_TAG="" ;;
++ darwin*:GCC) BOOST_TAG="-xgcc" ;;
+ *:GCC) BOOST_TAG="-gcc" ;;
+ *:KCC) BOOST_TAG="-kcc" ;;
+ linux*:ICC) BOOST_TAG="-il" ;;
+@@ -24335,8 +24423,8 @@
+ *:MSVC) BOOST_TAG="-vc" ;;
+ esac
+ case "$BOOST_TAG" in
+- -gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
+- * ) boost_comp_vers='' ;;
++ -*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
++ * ) boost_comp_vers='' ;;
+ esac
+ test "$with_mt" = "yes" && BOOST_MT=-mt
+ test "$with_debug" = "yes" && BOOST_D=-d
+@@ -32758,11 +32846,15 @@
+ ;;
+ esac
+
++if test "${with_limited_linker}" = "yes"; then
++ WithFeatures="$WithFeatures${WithFeaturesSep}LimitedLinker"; WithFeaturesSep=" "
++fi
++
+ FEATURES="$WithFeatures $WithPackages $WithProjects"
+
+ ### Compute Without{Features,Packages,Projects}. Takes quadratic time,
+ ### but that's life.
+-for x in GCC KCC ICC VisualAge CompaqCompiler WorkShop MIPSpro MSVC MT DLL DLL_BUILD MSWin unix WinMain AIX BSD Cygwin CygwinMT Darwin XCODE IRIX Linux OSF Solaris MacOS in-house-resources PubSeqOS JDK Ncbi-JNI check Valgrind; do
++for x in GCC KCC ICC VisualAge CompaqCompiler WorkShop MIPSpro MSVC MT DLL DLL_BUILD MaxDebug MSWin unix WinMain AIX BSD Cygwin CygwinMT Darwin XCODE IRIX Linux OSF Solaris MacOS in-house-resources PubSeqOS JDK Ncbi-JNI check Valgrind LimitedLinker; do
+ case " $WithFeatures " in
+ *" $x "*) ;;
+ *) WithoutFeatures="$WithoutFeatures$WithoutFeaturesSep$x"
+@@ -33848,6 +33940,7 @@
+ s, at DISTCC@,$DISTCC,;t t
+ s, at CCACHE@,$CCACHE,;t t
+ s, at TAIL@,$TAIL,;t t
++s, at TOUCH@,$TOUCH,;t t
+ s, at EGREP@,$EGREP,;t t
+ s, at VALGRIND_PATH@,$VALGRIND_PATH,;t t
+ s, at CXXCPP@,$CXXCPP,;t t
+@@ -34875,7 +34968,7 @@
+ -s "$real_srcdir" $cfm_flags && test -f "$builddir/Makefile.flat"; then
+ build_flat="Alternatively, cd $builddir && make -f Makefile.flat"
+ elif test -f "$builddir/Flat.configuration_log"; then
+- grep 'already defined' "$builddir/Flat.configuration_log"
++ $EGREP 'Error:|already defined' "$builddir/Flat.configuration_log"
+ { { echo "$as_me:$LINENO: error: flat makefile generation failed." >&5
+ echo "$as_me: error: flat makefile generation failed." >&2;}
+ { (exit 1); exit 1; }; }
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1965,6 +1965,7 @@
+ AC_MSG_RESULT(no)
+ fi
+
++AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
+ AC_PROG_EGREP
+ AC_MSG_CHECKING([how to run $EGREP quietly])
+ if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
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