[med-svn] r9984 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Mon Mar 12 17:11:08 UTC 2012
Author: osallou
Date: 2012-03-12 17:11:08 +0000 (Mon, 12 Mar 2012)
New Revision: 9984
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch
Log:
revert to UNRELEASE, need more fixes in patch
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-03-12 16:05:37 UTC (rev 9983)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-03-12 17:11:08 UTC (rev 9984)
@@ -1,4 +1,4 @@
-ncbi-blast+ (2.2.26-2) unstable; urgency=low
+ncbi-blast+ (2.2.26-2) UNRELEASED; urgency=low
* debian/patches/wrong_path_to_touch.patch :Fix upstream FTBFS on the Hurd
hardcodes wrong path to touch (Closes: #663244)
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch 2012-03-12 16:05:37 UTC (rev 9983)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch 2012-03-12 17:11:08 UTC (rev 9984)
@@ -34,6 +34,16 @@
2011-10-05: new @FEATURES@ variable for the unit test framework.
+
+2012-02-27: new @TOUCH@ variable to avoid hard-coded paths.
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1965,6 +1965,7 @@
+ AC_MSG_RESULT(no)
+ fi
+
++AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
+ AC_PROG_EGREP
+ AC_MSG_CHECKING([how to run $EGREP quietly])
+ if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
@@ -318,7 +318,7 @@
@@ -45,162 +55,7 @@
ac_subst_files=''
# Initialize some variables set by options.
-@@ -874,6 +874,7 @@
- ===============================================================================
- =============== NCBI C++ Toolkit specific configuration flags =================
- --without-debug build non-debug versions of libs and apps
-+ --with-max-debug, enable extra runtime checks (esp. of STL usage)
- --with-symbols retain debugging symbols in non-debug mode
- --without-optimization turn off optimization flags in non-debug mode
- --with-profiling build profiled versions of libs and apps
-@@ -893,6 +894,7 @@
- --with-relative-runpath=P specify an executable-relative DLL search path
- --with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
- --with-lfs enable large file support to the extent possible
-+ --with-limited-linker don't attempt to build especially large projects
- --with-extra-action= script to call after the configuration is complete
- --with-autodep automatic generation of dependencies (GNU make)
- --with-build-root=DIR specify a non-default build directory name
-@@ -1846,6 +1848,12 @@
-
- fi;
-
-+# Check whether --with-max-debug or --without-max-debug was given.
-+if test "${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 $abs_dir /etc/ld.so.conf.d/* || found=true
-+ found=true
- break
- ;;
- esac
-@@ -6615,6 +6642,46 @@
+@@ -6615,6 +6615,46 @@
echo "${ECHO_T}no" >&6
fi
@@ -247,170 +102,7 @@
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 @@
+@@ -33848,6 +33888,7 @@
s, at DISTCC@,$DISTCC,;t t
s, at CCACHE@,$CCACHE,;t t
s, at TAIL@,$TAIL,;t t
@@ -418,22 +110,3 @@
s, at EGREP@,$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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