From: Olivier Sallou Date: Mon, 12 Mar 2012 17:11:08 +0000 (+0000) Subject: revert to UNRELEASE, need more fixes in patch X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~299 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=17c581fee936ed8a521252142588bede5bd4a657;p=ncbi-blast%2B.git revert to UNRELEASE, need more fixes in patch --- diff --git a/debian/changelog b/debian/changelog index 559d47fa..26ffa968 100644 --- a/debian/changelog +++ b/debian/changelog @@ -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) diff --git a/debian/patches/wrong_path_to_touch.patch b/debian/patches/wrong_path_to_touch.patch index 82d9f950..f418da73 100644 --- a/debian/patches/wrong_path_to_touch.patch +++ b/debian/patches/wrong_path_to_touch.patch @@ -34,6 +34,16 @@ Last-Updated: 12/03/2012 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 $?`"; then --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure @@ -318,7 +318,7 @@ @@ -45,162 +55,7 @@ Last-Updated: 12/03/2012 ac_subst_files='' # Initialize some variables set by options. -@@ -874,6 +874,7 @@ - =============================================================================== - =============== NCBI C++ Toolkit specific configuration flags ================= - --without-debug build non-debug versions of libs and apps -+ --with-max-debug, enable extra runtime checks (esp. of STL usage) - --with-symbols retain debugging symbols in non-debug mode - --without-optimization turn off optimization flags in non-debug mode - --with-profiling build profiled versions of libs and apps -@@ -893,6 +894,7 @@ - --with-relative-runpath=P specify an executable-relative DLL search path - --with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - --with-lfs enable large file support to the extent possible -+ --with-limited-linker don't attempt to build especially large projects - --with-extra-action= script to call after the configuration is complete - --with-autodep automatic generation of dependencies (GNU make) - --with-build-root=DIR specify a non-default build directory name -@@ -1846,6 +1848,12 @@ - - fi; - -+# Check whether --with-max-debug or --without-max-debug was given. -+if test "${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 , 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 @@ Last-Updated: 12/03/2012 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,@DISTCC@,$DISTCC,;t t s,@CCACHE@,$CCACHE,;t t s,@TAIL@,$TAIL,;t t @@ -418,22 +110,3 @@ Last-Updated: 12/03/2012 s,@EGREP@,$EGREP,;t t s,@VALGRIND_PATH@,$VALGRIND_PATH,;t t s,@CXXCPP@,$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