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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2014-06-23 18:10:25 +0200 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2014-06-23 18:10:25 +0200 |
commit | 8d30af0e3afd031e00f5d69fce3683233a23b487 (patch) | |
tree | e4e43900544e9f84d0aedcaa5ceedf10920f0cd4 /sci-biology | |
parent | multiple move to EAPI=5 and regression fixes (diff) | |
download | sci-8d30af0e3afd031e00f5d69fce3683233a23b487.tar.gz sci-8d30af0e3afd031e00f5d69fce3683233a23b487.tar.bz2 sci-8d30af0e3afd031e00f5d69fce3683233a23b487.zip |
add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed)
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch | 1660 | ||||
-rw-r--r-- | sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 10 |
2 files changed, 1667 insertions, 3 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch new file mode 100644 index 000000000..80b23e987 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch @@ -0,0 +1,1660 @@ +--- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200 ++++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200 +@@ -1,5 +1,5 @@ + ############################################################################# +-# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $ ++# $Id$ + # Derived from configure.in version 1.173. + # ========================================================================== + # +@@ -38,7 +38,7 @@ + # + ############################################################################# + +-AC_PREREQ(2.59) ++AC_PREREQ(2.60) + + dnl Early setup, most crucially for locking. The diversion magic lets + dnl this occur before AC_INIT, which already interferes with other +@@ -71,7 +71,7 @@ + python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat, + sablot, libxml, libxslt, libexslt, xerces, xalan, zorba, + oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm, +- magic, curl], ++ magic, curl, gsoap, mongodb], + [if test "${[with_]X-no}" != "no"; then + AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw]) + else +@@ -143,6 +143,8 @@ + [ --with-bin-release build executables suitable for public release]) + AC_ARG_WITH(mt, + [ --with-mt compile in a MultiThread-safe manner]) ++AC_ARG_WITH(openmp, ++ [ --with-openmp enable OpenMP extensions for all projects]) + AC_ARG_WITH(64, + [ --with-64 compile to 64-bit code]) + AC_ARG_WITH(universal, +@@ -220,11 +222,15 @@ + + ## NCBI packages + AC_ARG_WITH(ncbi-c, ++ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR]) ++AC_ARG_WITH(ncbi-c2, + [ --without-ncbi-c do not use NCBI C Toolkit]) + AC_ARG_WITH(sss, ++ [ --with-sss=DIR use NCBI SSS installation in DIR]) ++AC_ARG_WITH(sss2, + [ --without-sss do not use NCBI SSS libraries]) + AC_ARG_WITH(sssutils, +- [ --without-sssutils do not use NCBI SSS UTIL library]) ++ [ --without-utils do not use NCBI SSS UTIL library]) + AC_ARG_WITH(sssdb, + [ --without-sssdb do not use NCBI SSS DB library]) + AC_ARG_WITH(included-sss, +@@ -439,6 +445,14 @@ + [ --with-mimetic=DIR use libmimetic installation in DIR]) + AC_ARG_WITH(mimetic2, + [ --without-mimetic do not use libmimetic]) ++AC_ARG_WITH(gsoap, ++ [ --with-gsoap=DIR use gSOAP++ installation in DIR]) ++AC_ARG_WITH(gsoap2, ++ [ --without-gsoap do not use gSOAP++]) ++AC_ARG_WITH(mongodb, ++ [ --with-mongodb=DIR use MongoDB installation in DIR]) ++AC_ARG_WITH(mongodb2, ++ [ --without-mongodb do not use MongoDB]) + AC_ARG_WITH(3psw, + [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.]) + AC_ARG_WITH(3psw2, +@@ -479,24 +493,28 @@ + [***** See also HTML documentation in ./doc/index.html *****]) + + ++AC_DIVERT_PUSH(PARSE_ARGS) ++dnl As of Autoconf 2.60, this needs to run too early for config.log, ++dnl to which AC_MSG_ERROR normally copies its output, to be available. ++m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD]) + #### Check the passed arguments against the list of available ones + x_with_list="\ + debug max-debug symbols optimization profiling tcheck dll static static-exe \ + plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \ +-lfs limited-linker \ ++lfs limited-linker openmp \ + autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \ + deactivation makefile-auto-update projects flat-makefile configure-dialog \ + check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ +-ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ ++ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ + bdb python perl jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt libexslt xerces xalan zorba \ + oechem sge muparser hdf5 \ +-gif jpeg tiff png xpm magic curl mimetic 3psw \ ++gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench x" ++serial objects dbapi app ctools gui algo internal gbench" + + changequote(, )dnl + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` +@@ -522,7 +540,6 @@ + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ +- | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) + ;; +@@ -533,12 +550,11 @@ + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ +- | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [[A-Z]*=*] \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ +- | --with-pcre=* \ ++ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \ + | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \ +- | --with-krb5=* | --with-curl=* \ ++ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \ + | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \ + | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \ + | --with-sqlite3=* | --with-expat=* | --with-sablot=* \ +@@ -552,7 +568,7 @@ + | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \ + | --x-includes=* | --x-libraries=* | --with-3psw=* \ + | --target=* | --with-runpath=* | --with-relative-runpath=* \ +- | --no-create | --no-recursion) ++ | --help | --no-create | --no-recursion) + ;; + + * ) +@@ -560,6 +576,8 @@ + ;; + esac + done ++m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD]) ++AC_DIVERT_POP + + + if test "$with_gbench" = "yes" ; then +@@ -604,6 +622,13 @@ + : ${with_optimization=no} + fi + ++if test "$with_openmp" = yes; then ++ if test "$with_mt" = no; then ++ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp]) ++ fi ++ : ${with_mt=yes} ++fi ++ + #### Check for special options + if test "$with_extra_action" = "yes" ; then + AC_MSG_ERROR([--with-extra-action must have a value after =]) +@@ -649,15 +674,10 @@ + *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; + esac + fi +-if test -n "$with_projects"; then +- case "$with_projects" in +- /* ) abs_projects=$with_projects ;; +- yes) abs_projects=$srcdir/projects ;; +- * ) abs_projects=$srcdir/$with_projects ;; +- esac +- test -r "$abs_projects" || \ +- AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) +-fi ++# Generally save any originally specified flags. ++USER_CFLAGS=$CFLAGS ++USER_CXXFLAGS=$CXXFLAGS ++USER_LDFLAGS=$LDFLAGS + + #### Always define this + AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) +@@ -675,6 +695,23 @@ + #### Make some provisions for traditional operation + AC_PROG_INSTALL + ++#### Point ICC at a suitable GCC version ASAP. ++case "/$CXX" in ++ */icpc ) ++ if test -d /usr/local/gcc; then ++ case "`$CXX -dumpversion`:$host_cpu" in ++ *:i?86) v=4.4.5 ;; ++ ?.* | 1[[01]].* ) v=4.0.1 ;; ++ *) v=4.4.2 ;; ++ esac ++ gcc=/usr/local/gcc/$v/bin/gcc ++ if test -x $gcc; then ++ CC="$CC -gcc-name=$gcc" ++ CXX="$CXX -gcc-name=$gcc" ++ fi ++ fi ++ ;; ++esac + + #### C and C++ compilers + AC_LANG(C++) +@@ -987,6 +1024,30 @@ + ;; + * ) NCBIATOMIC_LIB=xncbi ;; + esac ++ case "$compiler" in ++ GCC ) ++ if $CC -v | grep clang >/dev/null; then ++ : ++ # Will allegedly support -openmp at some point, but as of 3.4, ++ # just parses it as specifying an output filename: -o penmp. ++ else ++ case "$compiler_version" in ++ [[123]]?? | 4[[01]]? ) ;; ++ * ) : ${OPENMP_FLAGS=-fopenmp} ;; ++ esac ++ fi ++ ;; ++ ICC ) ++ : ${OPENMP_FLAGS=-openmp} ++ ;; ++ WorkShop* ) ++ : ${OPENMP_FLAGS=-xopenmp=parallel} ++ ;; ++ esac ++ if test "$with_openmp" = yes; then ++ MT_FLAG="$MT_FLAG $OPENMP_FLAGS" ++ OPENMP_FLAGS= ++ fi + mt_sfx="MT" + NCBI_FEATURE(MT) + else +@@ -994,6 +1055,7 @@ + MT_FLAG= + THREAD_LIBS= + NCBIATOMIC_LIB= ++ OPENMP_FLAGS= + mt_sfx="" + fi + MT_SFX="${mt_sfx}" +@@ -1006,6 +1068,9 @@ + APP_LDFLAGS= + DLL_LDFLAGS= + ++### Should go before any test compiler runs ++AC_GNU_SOURCE ++ + case "$host_os:$compiler" in + darwin*:GCC ) + AC_CACHE_CHECK([whether $CC supports -Wl,-rpath], +@@ -1047,6 +1112,47 @@ + ;; + esac + ++case "$compiler:$compiler_version" in ++ GCC:4[[0-6]]? | ICC:1[[01]]?? ) ++ ncbi_cv_prog_cxx_11=no ++ ncbi_cv_prog_c_99=no ++ ;; ++ ICC:* ) ++ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline' ++ ;; ++esac ++ ++AC_CACHE_CHECK([how to enable C++ '11 features in $CXX], ++ ncbi_cv_prog_cxx_11, ++ [orig_CXX=$CXX ++ ncbi_cv_prog_cxx_11=no ++ for x in -std=gnu++11 -std=gnu++0x; do ++ CXX="$orig_CXX $x" ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])], ++ [ncbi_cv_prog_cxx_11=$x]) ++ test "x$ncbi_cv_prog_cxx_11" = "xno" || break ++ done ++ CXX=$orig_CXX]) ++test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11" ++ ++AC_LANG_PUSH(C) ++AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC], ++ ncbi_cv_prog_c_99, ++ [orig_CC=$CC ++ ncbi_cv_prog_c_99=no ++ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \ ++ "-std=gnu1x -fgnu89-inline" \ ++ "-std=gnu99 -fgnu89-inline" \ ++ "-std=gnu9x -fgnu89-inline"; do ++ CC="$orig_CC $x" ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])], ++ [ncbi_cv_prog_c_99=$x]) ++ test "x$ncbi_cv_prog_c_99" = "xno" || break ++ done ++ CC=$orig_CC]) ++AC_LANG_POP(C) ++test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99" ++ + #### Provide default environment setup for known platforms/compilers + DEPFLAGS="-M" + DEPFLAGS_POST="" # Needed for VisualAge +@@ -1059,7 +1165,15 @@ + ;; + + solaris*:GCC ) +- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS" ++ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only ++ # in C++ mode. Set it for C code as well to ensure consistent ++ # header behavior, taking care to match the C standard version ++ # (as enforced by <sys/feature_tests.h>). ++ case "$ncbi_cv_prog_c_99" in ++ no) CC="$CC -D_XOPEN_SOURCE=500" ;; ++ *) CC="$CC -D_XOPEN_SOURCE=600" ;; ++ esac ++ + STRIP="@:" + ;; + +@@ -1202,11 +1316,19 @@ + LDFLAGS="-flat_namespace $LDFLAGS" + + if test "$with_ncbi_public" = yes; then ++ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ++ case "$host_os" in ++ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older + TARGET='-mmacosx-version-min=10.5' +- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk' ++ sdks="/Developer/SDKs/MacOSX10.6.sdk" + if test "$with_64:${with_universal-no}" != "yes:no"; then + sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks" + fi ++ ;; ++ * ) ++ TARGET='-mmacosx-version-min=10.7' ++ ;; ++ esac + for sdk in $sdks; do + if test -d "$sdk"; then + TARGET="-isysroot $sdk $TARGET" +@@ -1487,8 +1609,8 @@ + ;; + GCC:* ) + DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing" +- case "$host_os" in +- freebsd* ) ;; ++ case "$host_os:$host_cpu:$compiler_version" in ++ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;; + * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;; + esac + if test "$with_profiling" != "yes"; then +@@ -1587,13 +1709,9 @@ + solaris* ) + CONF_f_runpath="-R" + ;; +- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) ++ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) + CONF_f_runpath="-Wl,-rpath," + ;; +- linux*:ICC ) +- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop +- CONF_f_runpath="-Xlinker -rpath -Xlinker " +- ;; + irix*:* | linux*:KCC | *:Compaq ) + CONF_f_runpath="-rpath " + ;; +@@ -1697,8 +1815,11 @@ + LINK="$LINK -Kc++" + ;; + ICC:1???:* ) +- APP_LDFLAGS="-static-intel $APP_LDFLAGS" +- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS" ++ # Suppress "warning #10237: -lcilkrts linked in dynamically, static ++ # library not available" which is not a problem in practice due to ++ # as-needed linkage. ++ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS" ++ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS" + # Redundant for apps, but necessary for plugins to be adequately + # self-contained, at least on 32-bit Linux. + LIBS="$LIBS -lstdc++" +@@ -1817,18 +1938,6 @@ + + #### Intel compiler:: common flags and definitions + if test "$compiler" = "ICC" ; then +- if test -d /usr/local/gcc; then +- case "$compiler_version:$HOST_CPU" in +- *:i?86) v=4.4.5 ;; +- ???:* | 1[[01]]??:* ) v=4.0.1 ;; +- *) v=4.4.2 ;; +- esac +- gcc=/usr/local/gcc/$v/bin/gcc +- if test -x $gcc; then +- CC="$CC -gcc-name=$gcc" +- CXX="$CXX -gcc-name=$gcc" +- fi +- fi + if test -n "$icc_license" ; then + icc_CC="$CC" + icc_CXX="$CXX" +@@ -2073,6 +2182,7 @@ + fi + + AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) ++dnl AC_PATH_PROG(GREP, grep) + AC_PROG_EGREP + AC_MSG_CHECKING([how to run $EGREP quietly]) + if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then +@@ -2086,6 +2196,16 @@ + + AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind) + ++AC_PATH_PROG(LDD, ldd) ++if test -n "$LDD"; then ++ AC_MSG_CHECKING([whether $LDD accepts -r]) ++ if $LDD -r /bin/ls >/dev/null 2>&1; then ++ AC_MSG_RESULT(yes) ++ LDD_R="$LDD -r" ++ else ++ AC_MSG_RESULT(no) ++ fi ++fi + + #### Check if "${build_root}" is defined; provide a default one + if test -n "${with_build_root}" ; then +@@ -2170,9 +2290,6 @@ + fi + + +-### Should go before any test compiler runs +-AC_GNU_SOURCE +- + #### Determine whether this is implicitly a 64-bit platform + AC_TYPE_SIZE_T + if test "${with_universal-no}" = "no"; then +@@ -2342,7 +2459,7 @@ + fi + ;; + *:ICC ) +- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)" ++ runpath="$runpath -Wl,-rpath-link,\$(libdir)" + ;; + esac + elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then +@@ -2658,15 +2775,30 @@ + dbgrx1="$wsrx-g[^cx$wschars]*$wsrx" + dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx" + optrx="$wsrx-x*O[0-9s]*$wsrx" ++ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` ++ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` ++ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` + if test "$with_symbols" = "no" ; then +- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` +- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` +- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` ++ CFLAGS=$NDEB_CFLAGS ++ CXXFLAGS=$NDEB_CXXFLAGS ++ LDFLAGS=$NDEB_LDFLAGS + else + echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g" + echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g" + echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g" + STRIP="@:" ++ case "$compiler:$compiler_version" in ++ GCC:4[89]? | GCC:[5-9]? | GCC:???? ) ++ # GCC 4.8 defaults to DWARF 4, which Totalview for one ++ # can't handle; roll back to version 3 by default. ++ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ ++ CFLAGS="$NDEB_CFLAGS -gdwarf-3" ++ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ ++ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3" ++ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ ++ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3" ++ ;; ++ esac + fi + + NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"` +@@ -3024,9 +3156,9 @@ + ### Check for other standard library functions + + AC_FUNC_VPRINTF +-AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \ +- getpass getpassphrase getpwuid getrusage gettimeofday \ +- getuid memrchr readpassphrase readv usleep \ ++AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \ ++ getpagesize getpass getpassphrase getpwuid getrusage \ ++ gettimeofday getuid memrchr readpassphrase readv usleep \ + asprintf vasprintf vsnprintf select statfs statvfs \ + strcasecmp strlcat strlcpy strdup strndup strtok_r \ + sysmp timegm utimes lutimes writev) +@@ -3253,17 +3385,6 @@ + fi + + +-AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted, +- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( +- [[#include <algorithm>]], +- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])], +- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])]) +-if test "$ncbi_cv_func_is_sorted" = yes; then +- AC_DEFINE(HAVE_IS_SORTED, 1, +- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.]) +-fi +- +- + + AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, + AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h> +@@ -3400,7 +3521,7 @@ + AC_CACHE_CHECK([whether the C compiler supports C99 restrict], + ncbi_cv_c_restrict, + [ncbi_cv_c_restrict=no +- for restrict in restrict __restrict__ __restrict; do ++ for restrict in __restrict__ __restrict restrict; do + test "$ncbi_cv_c_restrict" = "no" || break + AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], + [ncbi_cv_c_restrict=$restrict], []) +@@ -3420,7 +3541,7 @@ + AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict], + ncbi_cv_cxx_restrict, + [ncbi_cv_cxx_restrict=no +- for restrict in restrict __restrict__ __restrict; do ++ for restrict in __restrict__ __restrict restrict; do + test "$ncbi_cv_cxx_restrict" = "no" || break + AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], + [ncbi_cv_cxx_restrict=$restrict], []) +@@ -3525,14 +3646,6 @@ + unaligned addresses.]) + fi + +-AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr, +- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])], +- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])]) +-if test "$ncbi_cv_cxx_nullptr" = yes; then +- AC_DEFINE(HAVE_NULLPTR, 1, +- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.]) +-fi +- + ### Check for the availability of other packages + ### -------------------------------------------- + +@@ -3630,7 +3743,16 @@ + dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop) + AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)]) + LIBS=$orig_LIBS ++# Temporarily drop OpenMP flags for this test, as some toolchains count ++# its support library's indirect use of librt when building applications ++# but not when building shared libraries with --no-undefined. ++orig_CXXFLAGS=$CXXFLAGS ++orig_LDFLAGS=$LDFLAGS ++CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'` ++LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'` + NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime) ++CXXFLAGS=$orig_CXXFLAGS ++LDFLAGS=$orig_LDFLAGS + NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle) + # Add to (orig_)LIBS if present for the sake of corelib and the + # following call to AC_CHECK_FUNCS. +@@ -3734,7 +3856,6 @@ + NCBI_PACKAGE(LocalBZ2) + fi + +-: ${LZO_PATH=$NCBI/lzo2} + if test -d "$LZO_PATH"; then + NCBI_FIX_DIR(LZO_PATH) + fi +@@ -3767,7 +3888,7 @@ + ## SSL/TLS libraries + case "$with_gcrypt" in + no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;; +- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;; ++ yes | '' ) ;; + * ) GCRYPT_PATH=$with_gcrypt ;; + esac + if test -d "$GCRYPT_PATH"; then +@@ -3802,13 +3923,16 @@ + + case "$with_gnutls" in + no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;; +- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;; ++ yes | '' ) ;; + * ) GNUTLS_PATH=$with_gnutls ;; + esac + if test -d "$GNUTLS_PATH"; then + NCBI_FIX_DIR(GNUTLS_PATH) ++ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin ++else ++ gnutls_config_path=$PATH + fi +-AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin:$PATH]) ++AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path]) + + if test "x$with_gnutls" != xno; then + if test -x "$LIBGNUTLS_CONFIG"; then +@@ -3817,7 +3941,7 @@ + test "x$p" = "x/usr" || GNUTLS_PATH=$p + fi + else +- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls" ++ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static" + $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no + fi + case "$LIBGNUTLS_CONFIG" in +@@ -3846,6 +3970,10 @@ + $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS) + if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then + NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib]) ++ # Conservatively build against gcrypt if available even when gnutls ++ # uses nettle instead, because gcrypt needs explicit initialization ++ # to be thread-safe, but gnutls's headers don't indicate which ++ # underlying crypto library it's actually using. + case "$GNUTLS_INCLUDE" in + *$GCRYPT_INCLUDE* ) ;; + * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;; +@@ -4108,7 +4236,8 @@ + SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS" + SYBASE_DLLS="$SYBASE_DLLLIST" + +- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase, ++ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}], ++ ncbi_cv_lib_sybase, + [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS" + LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS" + AC_LINK_IFELSE([AC_LANG_PROGRAM( +@@ -4216,7 +4345,8 @@ + AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH]) + else + FTDS_LIBS="$FTDS_CTLIBS" +- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds, ++ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}], ++ ncbi_cv_lib_freetds, + [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS" + LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS" + AC_LINK_IFELSE([AC_LANG_PROGRAM( +@@ -4281,7 +4411,7 @@ + # Kill off single quotes, due to later requoting + : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`} + NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r}, +- [s/'//g; ]) ++ [s/'//g; $no_usr_lib]) + AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql, + [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS" + LIBS="$MYSQL_LIBS $orig_LIBS" +@@ -4310,7 +4440,6 @@ + if test "$with_bdb" != "no" ; then + case "$with_bdb" in + yes | "" ) +- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"} + ;; + */*) + BERKELEYDB_PATH=$with_bdb +@@ -4351,7 +4480,8 @@ + else + BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS} + fi +- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH], ++ AC_CACHE_CHECK( ++ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}], + ncbi_cv_lib_berkeley_db, + [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS" + LIBS="$BERKELEYDB_LIBS $orig_LIBS" +@@ -4450,7 +4580,8 @@ + NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst]) + CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS" + LIBS="$ODBC_LIBS $orig_LIBS" +- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc, ++ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}], ++ ncbi_cv_lib_odbc, + [AC_LINK_IFELSE([AC_LANG_PROGRAM( + [[#include <sql.h>]], + [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x"; +@@ -4542,7 +4673,7 @@ + AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH]) + if test -x "$PERL"; then + PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'` +- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'` ++ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'` + PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS" + PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'` + NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS]) +@@ -4603,9 +4734,7 @@ + + ## Boost + if test "$with_boost" != "no"; then +- if test "${with_boost-yes}" = yes; then +- : ${BOOST_PATH=$NCBI/boost} +- else ++ if test "${with_boost-yes}" != yes; then + BOOST_PATH=$with_boost + fi + if test -d "$BOOST_PATH"; then +@@ -4644,17 +4773,22 @@ + if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then + BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version} + fi +- case "$ncbi_compiler" in +- MIPSPRO) ++ case "$compiler:$ncbi_compiler_ver" in ++ MIPSpro*) + BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers" + ;; +- WORKSHOP) ++ WorkShop*) + # Boost.Test's macros yield a *lot* of spurious "should not initialize + # a non-const reference with a temporary" warnings, to the point of + # overwhelming the compiler in some cases; turn them off altogether + # when using Boost at all. + BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp" + ;; ++ GCC*:4[[7-9]]* | GCC*:5*) ++ # Some portions of Boost also have a lot of "unused" typedefs ++ # from concept checking. ++ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs" ++ ;; + esac + case "$ncbi_cv_lib_boost_version" in + 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;; +@@ -4666,7 +4800,7 @@ + fi + with_boost=no + ;; +- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;; ++ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;; + '' ) with_boost=no ;; + * ) + AC_MSG_WARN( +@@ -4751,7 +4885,9 @@ + BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS + fi + +- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex, ++ in_path=${BOOST_PATH:+ in $BOOST_PATH} ++ ++ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex, + CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" + LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS" + [AC_LINK_IFELSE( +@@ -4759,7 +4895,7 @@ + [[throw boost::regex_error(boost::regex_constants::error_stack);]])], + [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])]) + +- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit, ++ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit, + CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" + LIBS="$RT_LIBS $orig_LIBS" + [AC_LINK_IFELSE( +@@ -4774,7 +4910,7 @@ + BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS + fi + +- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system, ++ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system, + CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" + LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS" + [AC_LINK_IFELSE( +@@ -4785,6 +4921,24 @@ + BOOST_SYSTEM_LIBS= + BOOST_SYSTEM_STATIC_LIBS=])]) + ++ boost_fs_lib=-lboost_filesystem${BOOST_TAG} ++ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then ++ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static ++ else ++ boost_fs_static_lib=$boost_fs_lib ++ fi ++ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS" ++ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS" ++ ++ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem, ++ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" ++ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS" ++ [AC_LINK_IFELSE( ++ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]], ++ [[return boost::filesystem::portable_name("foo");]])], ++ [ncbi_cv_lib_boost_filesystem=yes], ++ [ncbi_cv_lib_boost_filesystem=no])]) ++ + BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG} + if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then + BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static +@@ -4813,7 +4967,7 @@ + BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS + BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS + +- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test, ++ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test, + CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" + LIBS="$RT_LIBS $orig_LIBS" + found= +@@ -4853,7 +5007,7 @@ + BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS + fi + +- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread, ++ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread, + CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" + LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS" + [AC_LINK_IFELSE( +@@ -4864,12 +5018,25 @@ + BOOST_INCLUDE= + BOOST_LIBPATH= + BOOST_TAG= ++ ncbi_cv_lib_boost_filesystem=no + ncbi_cv_lib_boost_regex=no + ncbi_cv_lib_boost_spirit=no ++ ncbi_cv_lib_boost_system=no + ncbi_cv_lib_boost_test=no + ncbi_cv_lib_boost_thread=no + fi + ++if test "$ncbi_cv_lib_boost_filesystem" != "no"; then ++ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1, ++ dnl [Define to 1 if the `Boost.Filesystem' library is available.]) ++ NCBI_PACKAGE(Boost.Filesystem) ++else ++ boost_fs_lib= ++ boost_fs_static_lib= ++ BOOST_FILESYSTEM_LIBS= ++ BOOST_FILESYSTEM_STATIC_LIBS= ++fi ++ + if test "$ncbi_cv_lib_boost_regex" != "no"; then + AC_DEFINE(HAVE_BOOST_REGEX, 1, + [Define to 1 if the `Boost.Regex' library is available.]) +@@ -4927,7 +5094,10 @@ + + ## NCBI C Toolkit + if test "$with_ncbi_c" != "no" ; then +- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"} ++ if test "${with_ncbi_c-yes}" != yes; then ++ NCBI_C_PATH=$with_ncbi_c ++ fi ++ : ${NCBI_C_PATH="$NCBI"} + if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then + NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc + fi +@@ -4949,7 +5119,8 @@ + NCBI_C_ncbi="-lncbi" + fi + NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH" +- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools, ++ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}], ++ ncbi_cv_lib_ctools, + [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS" + LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS" + AC_LINK_IFELSE([AC_LANG_PROGRAM( +@@ -5000,11 +5171,7 @@ + + ## OpenGL + if test "$with_opengl" != "no"; then +- if test "${with_opengl-yes}" = yes; then +- if test -d $NCBI/MesaGL; then +- : ${OPENGL_PATH=$NCBI/MesaGL} +- fi +- else ++ if test "${with_opengl-yes}" != yes; then + OPENGL_PATH=$with_opengl + fi + if test -d "$OPENGL_PATH"; then +@@ -5101,7 +5268,6 @@ + else + OSMESA_STATIC_LIBS=$OSMESA_LIBS + fi +- : ${GLUT_PATH=$NCBI/glut} + if test "$with_glut" != "no"; then + if test "${with_glut-yes}" != "yes"; then + GLUT_PATH=$with_glut +@@ -5121,7 +5287,6 @@ + NCBI_MISSING_PACKAGE(glut) + fi + fi +- : ${GLEW_PATH=$NCBI/glew} + if test "$with_glew" != "no"; then + if test "${with_glew-yes}" != "yes"; then + GLEW_PATH=$with_glew +@@ -5214,7 +5379,7 @@ + : ${with_wxwidgets_ucs=no} + if test "$with_wxwidgets" != "no" ; then + case "$with_wxwidgets" in +- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;; ++ yes | "" ) ;; + * ) WXWIDGETS_PATH=$with_wxwidgets ;; + esac + if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ +@@ -5283,12 +5448,13 @@ + libsed=$basesed + ;; + esac +- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH], ++ AC_CACHE_CHECK( ++ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}], + ncbi_cv_lib_wxwidgets, + [if test -x "$wxconf" ; then + WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`" + NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs], +- [$libsed; ]) ++ [$libsed; s/ -lm / /g;]) + + CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS" + LIBS="$WXWIDGETS_LIBS $orig_LIBS" +@@ -5315,12 +5481,12 @@ + else + NCBI_PACKAGE(wxWidgets) + case "`"$wxconf" $wxcfflags --version`" in +- 2.[[89]].* | 2.[[0-9]][[0-9]]* ) +- NCBI_PACKAGE(wx2.8) +- wxlibs=std,richtext,aui ++ 1.* | 2.[[0-7]].*) ++ wxlibs=std + ;; + *) +- wxlibs=std ++ NCBI_PACKAGE(wx2.8) ++ wxlibs=std,richtext,aui,propgrid + ;; + esac + # The "yes" may have been cached; get the actual settings again if needed +@@ -5328,9 +5494,9 @@ + WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`" + fi + NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs], +- [$libsed; ]) ++ [$libsed; s/ -lm / /g;]) + WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \ +- 2>/dev/null | sed -e "$basesed"` ++ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"` + if test -n "$WXWIDGETS_STATIC_LIBS"; then + # Allow direct use of underlying libraries with strict linkers + WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`" +@@ -5350,7 +5516,7 @@ + ## In-house Fast-CGI library + if test "$with_fastcgi" != "no" ; then + case "$with_fastcgi" in +- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;; ++ yes | "" ) ;; + */* ) FASTCGI_PATH=$with_fastcgi ;; + * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;; + esac +@@ -5366,7 +5532,8 @@ + NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS]) + FASTCGI_OBJS="fcgibuf" + LIBS="$FASTCGI_LIBS $orig_LIBS" +- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi, ++ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}], ++ ncbi_cv_lib_fcgi, + [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS" + AC_LINK_IFELSE([AC_LANG_PROGRAM( + [[#include <fcgiapp.h>]], +@@ -5416,7 +5583,11 @@ + else + with_included_sss=no + fi ++ if test "${with_sss-yes}" = yes; then + NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"} ++ else ++ NCBI_SSS_PATH=$with_sss ++ fi + NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"} + if test -z "$NCBI_SSS_LIBPATH" ; then + NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}" +@@ -5424,7 +5595,8 @@ + NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt" + fi + fi +- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH]) ++ AC_MSG_CHECKING( ++ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}]) + if test "$with_included_sss" = "yes"; then + AC_MSG_RESULT([yes]) # duh + elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then +@@ -5510,7 +5682,6 @@ + + # SP + if test "$with_sp" != "no" ; then +- SP_PATH=${SP_PATH:="$NCBI/SP"} + if test -n "$SP_INCLUDE"; then + SP_GENERIC="$SP_INCLUDE/../generic" + else +@@ -5520,7 +5691,7 @@ + if test -z "$SP_LIBPATH" ; then + SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}" + fi +- AC_MSG_CHECKING([for SP directories in $SP_PATH]) ++ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}]) + if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then + AC_MSG_RESULT([no]) + NCBI_MISSING_PACKAGE(sp) +@@ -5558,19 +5729,13 @@ + + + ## ORBacus CORBA +-if test "${with_orbacus:-yes}" = yes; then +- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then +- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT} +- else +- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1} +- fi +-elif test "$with_orbacus" != no; then ++if test "$with_orbacus" != no; then ++ if test "$with_orbacus" != yes; then + ORBACUS_PATH=$with_orbacus + fi + if test -d "$ORBACUS_PATH"; then + NCBI_FIX_DIR(ORBACUS_PATH) + fi +-if test "$with_orbacus" != no; then + fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx} + if test -f ${fullpath}/inc/OB/Config.h ; then + : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"} +@@ -5594,7 +5759,8 @@ + LIBIMR= + ;; + esac +- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus, ++ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}], ++ ncbi_cv_lib_orbacus, + [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS" + LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS" + AC_LINK_IFELSE([AC_LANG_PROGRAM( +@@ -5633,7 +5799,7 @@ + + if test "$with_icu" != "no" ; then + case "$with_icu" in +- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;; ++ yes | "" ) ;; + * ) ICU_PATH=$with_icu ;; + esac + if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \ +@@ -5648,7 +5814,8 @@ + ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"} + ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"} + ICU_INCLUDE= +- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu, ++ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}], ++ ncbi_cv_lib_icu, + [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config + if test -x "$ICU_CONFIG" ; then + ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath` +@@ -5690,9 +5857,6 @@ + + + ### XML/XSL libraries +-if test -d "$NCBI/expat/include"; then +- : ${EXPAT_PATH=$NCBI/expat} +-fi + NCBI_CHECK_THIRD_PARTY_LIB(expat, + AC_LANG_PROGRAM([#include <expat.h>], + [XML_Parser parser = XML_ParserCreate("utf-8");])) +@@ -5701,7 +5865,6 @@ + else + EXPAT_STATIC_LIBS=${EXPAT_LIBS} + fi +-: ${SABLOT_PATH=$NCBI/Sablot} + vpath="$SABLOT_PATH/${compiler_vpfx}build" + test -d "$vpath" && SABLOT_PATH=$vpath + if test -d "$SABLOT_PATH"; then +@@ -5718,7 +5881,6 @@ + SABLOT_STATIC_LIBS=${SABLOT_LIBS} + fi + +-: ${LIBXML_PATH=$NCBI/libxml} + # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null` + if test "$with_libxml" != "no"; then + case "$with_libxml" in +@@ -5813,7 +5975,6 @@ + LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS} + fi + +-: ${XERCES_PATH=$NCBI/xerces} + if test "$with_xerces" != no; then + if test "${with_xerces-yes}" != yes; then + XERCES_PATH=$with_xerces +@@ -5838,7 +5999,7 @@ + NCBI_FIX_DIR(XERCES_LIBPATH) + fi + fi +- if test -d $XERCES_PATH; then ++ if test -d "$XERCES_PATH"; then + in_path=" in $XERCES_PATH" + : ${XERCES_INCLUDE=-I$XERCES_PATH/include} + : ${XERCES_LIBPATH=$XERCES_PATH/lib} +@@ -5875,7 +6036,6 @@ + XERCES_STATIC_LIBS= + fi + +-: ${XALAN_PATH=$NCBI/xalan} + if test "$with_xalan" != no; then + if test "${with_xalan-yes}" != yes; then + XALAN_PATH=$with_xalan +@@ -5900,7 +6060,7 @@ + NCBI_FIX_DIR(XALAN_LIBPATH) + fi + fi +- if test -d $XALAN_PATH; then ++ if test -d "$XALAN_PATH"; then + in_path=" in $XALAN_PATH" + : ${XALAN_INCLUDE=-I$XALAN_PATH/include} + : ${XALAN_LIBPATH=$XALAN_PATH/lib} +@@ -5937,7 +6097,6 @@ + + test -d SunWS_cache && rm -r SunWS_cache + +-: ${ZORBA_PATH=$NCBI/zorba} + if test "$with_zorba" != no; then + if test "${with_zorba-yes}" != yes; then + ZORBA_PATH=$with_zorba +@@ -5967,7 +6126,7 @@ + ZORBA_PATH=`$ZORBA_CONFIG --prefix` + : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`} + fi +- if test -d $ZORBA_PATH; then ++ if test -d "$ZORBA_PATH"; then + in_path=" in $ZORBA_PATH" + : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include} + : ${ZORBA_LIBPATH=$ZORBA_PATH/lib} +@@ -6010,7 +6169,7 @@ + + ### SQLite + case "$with_sqlite3" in +- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;; ++ yes | '' ) ;; + * ) SQLITE3_PATH=$with_sqlite3 ;; + esac + +@@ -6048,7 +6207,6 @@ + ### OEChem + # somewhat kludgish, as we now wanto to add in oeiupac and oedepict, + # which depend on oechem.... +-: ${OECHEM_PATH=$NCBI/oechem} + NCBI_CHECK_THIRD_PARTY_LIB(oechem, + AC_LANG_PROGRAM([#include <oechem.h>], + [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]), +@@ -6091,7 +6249,7 @@ + + ### muParser + case "$with_muparser" in +- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;; ++ yes | '' ) ;; + * ) MUPARSER_PATH=$with_muparser ;; + esac + +@@ -6111,7 +6269,7 @@ + + ### hdf5 + case "$with_hdf5" in +- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;; ++ yes | '' ) ;; + * ) HDF5_PATH=$with_hdf5 ;; + esac + +@@ -6176,7 +6334,7 @@ + GIF_LIBS=$UNGIF_LIBS + fi + +-test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`} ++case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac + NCBI_CHECK_THIRD_PARTY_LIB(Xpm, + AC_LANG_PROGRAM([#include <X11/xpm.h>], + [XpmImage image; XpmInfo info; +@@ -6241,7 +6399,7 @@ + fi + + case "$with_ftgl" in +- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;; ++ yes | '' ) ;; + * ) FTGL_PATH=$with_ftgl ;; + esac + +@@ -6268,7 +6426,7 @@ + + # Mimetic + case "$with_mimetic" in +- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;; ++ yes | '' ) ;; + * ) MIMETIC_PATH=$with_mimetic ;; + esac + if test -d "$MIMETIC_PATH"; then +@@ -6293,6 +6451,88 @@ + [mimetic::MimeEntity me;])]) + + ++# gSOAP++ ++case "$with_gsoap" in ++ yes | '' ) ;; ++ * ) GSOAP_PATH=$with_gsoap ;; ++esac ++if test -d "$GSOAP_PATH"; then ++ NCBI_FIX_DIR(GSOAP_PATH) ++fi ++for d in "$GSOAP_LIBDIR" \ ++ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ ++ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ ++ "$GSOAP_PATH/lib${bit64_sfx}" \ ++ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \ ++ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \ ++ "$GSOAP_PATH/lib"; do ++ if test -d "$d"; then ++ GSOAP_LIBDIR=$d ++ NCBI_FIX_DIR(GSOAP_LIBDIR) ++ break ++ fi ++done ++NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR) ++ ++: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin} ++AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH) ++AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH) ++ ++NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++, ++ [AC_LANG_PROGRAM([#include <stdsoap2.h> ++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*) ++ { return NULL; } ++ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { } ++ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; } ++ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; } ++ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { } ++ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; } ++ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }], ++ [soap s;])], ++ $OPENSSL_LIBS $Z_LIBS) ++ ++case "$with_sqlite3" in ++ yes | '' ) ;; ++ * ) SQLITE3_PATH=$with_sqlite3 ;; ++esac ++ ++ ++# MongoDB ++if test -d "$MONGODB_PATH"; then ++ NCBI_FIX_DIR(MONGODB_PATH) ++fi ++if test -d $MONGODB_PATH/lib${bit64_sfx}; then ++ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx} ++else ++ MONGODB_LIBDIR=$MONGODB_PATH/lib ++fi ++# need Boost rpath ++NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR) ++NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient, ++ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>], ++ [std::vector<mongo::HostAndPort> v; ++ mongo::DBClientReplicaSet client("foo", v); ++ client.connect();])], ++ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [], ++ [$BOOST_INCLUDE]) ++# MongoDB's own library is normally static, but its supporting Boost ++# libraries might not be by default. ++if test -n "$MONGODB_LIBS"; then ++ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS" ++else ++ MONGODB_STATIC_LIBS= ++fi ++ + ### Restore original compiler/linker flags + LIBS="$orig_LIBS" + CPPFLAGS="$orig_CPPFLAGS" +@@ -6499,16 +6739,6 @@ + fi + + +-## Sequence Read Archive SDK, which may be attached on either the +-## public or the internal side +- +-if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then +- sra=sra +-else +- sra= +-fi +- +- + ## `internal' project cluster + + if test "$with_internal" = "no" \ +@@ -6781,6 +7011,7 @@ + AC_SUBST(C_LINK) + AC_SUBST(TAIL_N) + AC_SUBST(EGREP_Q) ++AC_SUBST(LDD_R) + + AC_SUBST(CFLAGS) + AC_SUBST(FAST_CFLAGS) +@@ -6829,7 +7060,6 @@ + AC_SUBST(algo) + AC_SUBST(app) + AC_SUBST(internal) +-AC_SUBST(sra) + + AC_SUBST(check) + AC_SUBST(CHECK_ARG) +@@ -6865,6 +7095,7 @@ + + AC_SUBST(THREAD_LIBS) + AC_SUBST(NCBIATOMIC_LIB) ++AC_SUBST(OPENMP_FLAGS) + AC_SUBST(NETWORK_LIBS) + AC_SUBST(NETWORK_PURE_LIBS) + AC_SUBST(RESOLVER_LIBS) +@@ -6902,6 +7133,8 @@ + AC_SUBST(BOOST_INCLUDE) + AC_SUBST(BOOST_LIBPATH) + AC_SUBST(BOOST_TAG) ++AC_SUBST(BOOST_FILESYSTEM_LIBS) ++AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS) + AC_SUBST(BOOST_REGEX_LIBS) + AC_SUBST(BOOST_REGEX_STATIC_LIBS) + AC_SUBST(BOOST_SYSTEM_LIBS) +@@ -6968,6 +7201,8 @@ + AC_SUBST(SQLITE3_STATIC_LIBS) + AC_SUBST(FREETYPE_INCLUDE) + AC_SUBST(FREETYPE_LIBS) ++AC_SUBST(GSOAP_PATH) ++AC_SUBST(MONGODB_STATIC_LIBS) + AC_SUBST(ncbi_xreader_pubseqos) + AC_SUBST(ncbi_xreader_pubseqos2) + AC_SUBST(UNLESS_PUBSEQOS) +@@ -7194,7 +7429,9 @@ + + cat << EOCONF + =============================================================================== +-NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running ++NCBI C++ Toolkit documentation: ++ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ ++ Local: ./doc/public/index.html + For the available configuration flags run: ./configure --help + + CFLAGS = $CFLAGS +--- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200 ++++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200 +@@ -1,126 +1,45 @@ +-# Hacked up in various ways, since Autoconf's version doesn't quite +-# suit our (unusual) conventions. (Originally from status.m4) +-m4_define([_AC_SRCPATHS], +-[#ac_builddir=. # Useless! +-ac_builddir=$builddir +-dnl Base source directories on path to *input* file. +-if test -n "$ac_file_in"; then +- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])` ++# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS) ++# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly. ++m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS]) ++m4_define([_AC_SRCDIRS], ++[# Base source directories on path to *input* file. ++if test -n "$ac_f"; then ++ ac_dir_in=`AS_DIRNAME(["$ac_f"])` + else + ac_dir_in=$1 + fi + +-if test $ac_dir_in != .; then +- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'` +- # A "../" for each directory in $ac_dir_suffix. +- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'` +-else +- ac_dir_suffix= ac_top_builddir= +-fi ++NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) + +-case $srcdir in +- .) # No --srcdir option. We are building in place. +- ac_srcdir=. +- if test -z "$ac_top_builddir"; then +- ac_top_srcdir=. +- else +- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` +- fi ;; +- [[\\/]]* | ?:[[\\/]]* ) # Absolute path. +- ac_srcdir=$srcdir/$ac_dir_suffix; +- ac_top_srcdir=$srcdir ;; +- *) # Relative path. +- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix +- ac_top_srcdir=$ac_top_builddir$srcdir ;; +-esac +-# Do not use `cd foo && pwd` to compute absolute paths, because +-# the directories may not exist. +-AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1]) +-AS_SET_CATFILE([ac_abs_top_builddir], +- [$ac_abs_builddir], [${ac_top_builddir}.]) + AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) +-AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix]) +-])# _AC_SRCPATHS +- ++ac_builddir=$builddir ++]) + +-# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a +-# last resort due to issues with sourcing .bashrc. +-m4_define([_AS_LINENO_PREPARE], +-[_AS_LINENO_WORKS || { +- # Find who we are. Look in the path if we contain no path at all +- # relative or not. +- case $[0] in +- *[[\\/]]* ) as_myself=$[0] ;; +- *) _AS_PATH_WALK([], +- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break]) +- ;; +- esac +- # We did not find ourselves, most probably we were run as `sh COMMAND' +- # in which case we are not to be found in the path. +- if test "x$as_myself" = x; then +- as_myself=$[0] +- fi +- if test ! -f "$as_myself"; then +- AS_ERROR([cannot find myself; rerun with an absolute path]) +- fi +- case $CONFIG_SHELL in +- '') +- AS_UNSET(ZSH_VERSION) +- for as_base in sh ksh sh5 bash; do +- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH], +- [case $as_dir in +- /*) +- if ("$as_dir/$as_base" -c \ +- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null +- then +- AS_UNSET(BASH_ENV) +- AS_UNSET(ENV) +- CONFIG_SHELL=$as_dir/$as_base +- export CONFIG_SHELL +- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"} +- fi;; +- esac +- done]);; +- esac + +- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO +- # uniformly replaced by the line number. The first 'sed' inserts a +- # line-number line before each line; the second 'sed' does the real +- # work. The second script uses 'N' to pair each line-number line +- # with the numbered line, and appends trailing '-' during +- # substitution so that $LINENO is not a special case at line end. +- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the +- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) +- sed '=' <$as_myself | +- sed ' +- N +- s,$,-, +- : loop +- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3, +- t loop +- s,-$,, +- s,^[['$as_cr_digits']]*\n,, +- ' >$as_me.lineno && +- chmod +x $as_me.lineno || +- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell]) +- +- # Don't try to exec as it changes $[0], causing all sort of problems +- # (the dirname of $[0] is not the place where we might find the +- # original and so on. Autoconf is especially sensible to this). +- . ./$as_me.lineno +- # Exit status is that of the last command. +- exit +-} +-])# _AS_LINENO_PREPARE ++# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both ++# historically part of _AS_LINENO_PREPARE) also need tweaking, to make ++# bash a last resort due to issues with sourcing .bashrc while entirely ++# avoiding zsh, which passes itself off as ksh on some systems but runs ++# parent shells' exit handlers from subshells, resulting in premature ++# cleanup of temporary files (notably confdefs.h). ++m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL]) ++m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN]) ++ ++m4_define([_AS_DETECT_BETTER_SHELL], ++ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]), ++ [sh bash ksh sh5], [sh ksh sh5 bash])]) ++m4_define([_AS_RUN], ++[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl ++NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])]) + + + # One more hack: suppress PACKAGE_*, as we don't use them and some + # third-party libraries expose their corresponding settings, leading + # to preprocessor warnings. +-m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED])) ++m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED]) + m4_define([AC_DEFINE_UNQUOTED], + [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [], +- [NCBI_ORIG_ACDU($@)])]) ++ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])]) + + + AC_DEFUN(NCBI_FIX_DIR, +@@ -158,7 +77,7 @@ + AC_MSG_WARN([Proceeding without questions per --without-caution]) ;; + * ) + echo "$1 [[y/N]]" +- read answer ++ read answer <& AS_ORIGINAL_STDIN_FD + case "$answer" in + [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;; + * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;; +--- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200 ++++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200 +@@ -98,6 +98,9 @@ + /* Define to 1 if you have the `getaddrinfo' function. */ + #undef HAVE_GETADDRINFO + ++/* Define to 1 if you have the `getgrouplist' function. */ ++#undef HAVE_GETGROUPLIST ++ + /* If you have the `gethostbyaddr_r' function, define to the number of + arguments it takes (normally 7 or 8). */ + #undef HAVE_GETHOSTBYADDR_R +@@ -176,9 +179,6 @@ + /* Define to 1 if you have `ios(_base)::register_callback'. */ + #undef HAVE_IOS_REGISTER_CALLBACK + +-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ +-#undef HAVE_IS_SORTED +- + /* Define to 1 if you have the `lchown' function. */ + #undef HAVE_LCHOWN + +@@ -234,6 +234,9 @@ + /* Define to 1 if libgnutls is available. */ + #undef HAVE_LIBGNUTLS + ++/* Define to 1 if libgsoapssl++ is available. */ ++#undef HAVE_LIBGSOAP ++ + /* Define to 1 if libhdf5_cpp is available. */ + #undef HAVE_LIBHDF5 + +@@ -260,6 +263,9 @@ + /* Define to 1 if libmimetic is available. */ + #undef HAVE_LIBMIMETIC + ++/* Define to 1 if libmongoclient is available. */ ++#undef HAVE_LIBMONGODB ++ + /* Define to 1 if libmuparser is available. */ + #undef HAVE_LIBMUPARSER + +@@ -382,9 +388,6 @@ + /* Define to 1 if `min'/`max' templates are not implemented. */ + #undef HAVE_NO_MINMAX_TEMPLATE + +-/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */ +-#undef HAVE_NULLPTR +- + /* Define to 1 if ODBC libraries are available. */ + #undef HAVE_ODBC + +@@ -799,37 +802,37 @@ + by a signal. */ + #undef SELECT_UPDATES_TIMEOUT + +-/* The size of a `char', as computed by sizeof. */ ++/* The size of `char', as computed by sizeof. */ + #undef SIZEOF_CHAR + +-/* The size of a `double', as computed by sizeof. */ ++/* The size of `double', as computed by sizeof. */ + #undef SIZEOF_DOUBLE + +-/* The size of a `float', as computed by sizeof. */ ++/* The size of `float', as computed by sizeof. */ + #undef SIZEOF_FLOAT + +-/* The size of a `int', as computed by sizeof. */ ++/* The size of `int', as computed by sizeof. */ + #undef SIZEOF_INT + +-/* The size of a `long', as computed by sizeof. */ ++/* The size of `long', as computed by sizeof. */ + #undef SIZEOF_LONG + +-/* The size of a `long double', as computed by sizeof. */ ++/* The size of `long double', as computed by sizeof. */ + #undef SIZEOF_LONG_DOUBLE + +-/* The size of a `long long', as computed by sizeof. */ ++/* The size of `long long', as computed by sizeof. */ + #undef SIZEOF_LONG_LONG + +-/* The size of a `short', as computed by sizeof. */ ++/* The size of `short', as computed by sizeof. */ + #undef SIZEOF_SHORT + +-/* The size of a `size_t', as computed by sizeof. */ ++/* The size of `size_t', as computed by sizeof. */ + #undef SIZEOF_SIZE_T + +-/* The size of a `void*', as computed by sizeof. */ ++/* The size of `void*', as computed by sizeof. */ + #undef SIZEOF_VOIDP + +-/* The size of a `__int64', as computed by sizeof. */ ++/* The size of `__int64', as computed by sizeof. */ + #undef SIZEOF___INT64 + + /* Define to 1 if the stack grows down. */ +@@ -870,5 +873,5 @@ + /* Define to empty if `const' does not conform to ANSI C. */ + #undef const + +-/* Define to `unsigned' if <sys/types.h> does not define. */ ++/* Define to `unsigned int' if <sys/types.h> does not define. */ + #undef size_t +--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200 ++++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200 +@@ -1,4 +1,4 @@ +-/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $ ++/* $Id$ + * By Vlad Lebedev, NCBI (lebedev@ncbi.nlm.nih.gov) + * + * Mac OS X - xCode Build +@@ -258,9 +258,6 @@ + /* Define to 1 if you have `ios(_base)::register_callback'. */ + #define HAVE_IOS_REGISTER_CALLBACK 1 + +-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ +-/* #undef HAVE_IS_SORTED */ +- + /* Define to 1 if you have the `lchown' function. */ + /* #undef HAVE_LCHOWN */ + +@@ -358,6 +355,9 @@ + /* Define to 1 if you have the `lutimes' function. */ + /* #undef HAVE_LUTIMES */ + ++/* Define to 1 if you have the `madvise' function. */ ++#define HAVE_MADVISE 1 ++ + /* Define to 1 if you have the <malloc.h> header file. */ + /* #undef HAVE_MALLOC_H */ + +@@ -589,15 +589,15 @@ + /* Define to 1 if you have the <windows.h> header file. */ + /* #undef HAVE_WINDOWS_H */ + ++/* Define to 1 if you have the `writev' function. */ ++#define HAVE_WRITEV 1 ++ + /* Define to 1 if the system has the type `wstring'. */ + #define HAVE_WSTRING 1 + + /* Define to 1 if wxWidgets is available. */ + /* #undef HAVE_WXWIDGETS */ + +-/* Define to 1 if nullptr keyword is available. */ +-/* #undef HAVE_NULLPTR */ +- + /* Define as const if the declaration of iconv() needs const. */ + #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */ + # define ICONV_CONST +@@ -694,7 +694,7 @@ + /* Define to empty if `const' does not conform to ANSI C. */ + /* #undef const */ + +-/* Define to `unsigned' if <sys/types.h> does not define. */ ++/* Define to `unsigned int' if <sys/types.h> does not define. */ + /* #undef size_t */ + + /* diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 3b19a9391..64e8c234e 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -26,12 +26,14 @@ IUSE=" debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python + glut hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" +# removed IUSE=gnutls due to Gentoo bug #421777 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" KEYWORDS="" # sys-libs/db should be compiled with USE=cxx +# dropped 'gnutls? ( net-libs/gnutls[lzo] )' from DEPEND due to Gentoo bug #421777 DEPEND=" berkdb? ( sys-libs/db:4.3[cxx] ) ftds? ( dev-db/freetds ) @@ -40,7 +42,6 @@ DEPEND=" sqlite? ( dev-db/sqlite ) sqlite3? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql ) - gnutls? ( net-libs/gnutls[lzo] ) ssl? ( dev-libs/openssl ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) @@ -112,6 +113,7 @@ src_prepare() { "${FILESDIR}"/${P}-fix-creaders-linking.patch "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch + "${FILESDIR}"/${P}-support-autoconf-2.60.patch ) epatch ${PATCHES[@]} @@ -120,8 +122,10 @@ src_prepare() { cd src/build-system || die # eautoreconf eautoconf + # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support } +# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site src_configure() { local myconf=() #--without-optimization turn off optimization flags in non-debug mode @@ -214,7 +218,7 @@ src_configure() { $(use_with pch) $(use_with lzo lzo "${EPREFIX}/usr") $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") +# $(use_with gnutls gnutls "${EPREFIX}/usr") $(use_with ssl openssl "${EPREFIX}/usr") $(use_with ftds ftds "${EPREFIX}/usr") $(use_with mysql mysql "${EPREFIX}/usr") |