path: root/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch

--- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori       2014/05/05 12:38:59     62744
+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/05 13:59:33     62745
@@ -1,126 +1,44 @@
-# 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
-
-
-# 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
+ac_builddir=$builddir
+])
+
+
+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
+# bash a last resort due to issues with sourcing .bashrc while entirely
+# avoiding zsh, which passes itself off as ksh on some systems but runs
+# parent shells' exit handlers from subshells, resulting in premature
+# cleanup of temporary files (notably confdefs.h).
+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
+
+m4_define([_AS_DETECT_BETTER_SHELL],
+  [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
+     [sh bash ksh sh5], [sh ksh sh5 bash])])
+m4_define([_AS_RUN],
+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
+NCBI_ORIG___AS_RUN([test -z "${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 +76,7 @@
        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/configure.ac.ori     2014/05/05 12:38:59     62744
+++ ncbi_cxx--12_0_0/src/build-system/configure.ac     2014/05/05 13:59:33     62745
@@ -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
@@ -493,6 +493,10 @@
    [***** 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 \
@@ -564,7 +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)
       ;;
 
       * )
@@ -572,6 +576,8 @@
       ;;
    esac
 done
+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
+AC_DIVERT_POP
 
 
 if test "$with_gbench" = "yes" ; then
@@ -2176,7 +2182,7 @@
 fi
 
 AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
-AC_PATH_PROG(GREP, grep)
+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
--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori    2014/05/05 14:10:55     62749
+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h    2014/05/05 14:23:49     62750
@@ -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 */
 
 /*
--- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori      2014/05/05 14:10:55     62749
+++ ncbi_cxx--12_0_0/src/build-system/config.h.in      2014/05/05 14:23:49     62750
@@ -802,37 +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. */
@@ -873,5 +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/src/build-system/aclocal.m4.ori       2014/05/06 13:12:18     62759
+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/06 13:42:48     62760
@@ -11,6 +11,7 @@
 
 NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
 
+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
 ac_builddir=$builddir
 ])