Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/Makefile.in
+++ b/Makefile.in
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@

-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
 #                                                                             #
 ###############################################################################
 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
  case $${target_option-} in \
      ?) ;; \
@@ -177,18 +187,6 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = .
-DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \
-	$(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(top_srcdir)/configure $(am__configure_deps) \
-	$(top_srcdir)/config/config.h.in $(srcdir)/control.in \
-	$(srcdir)/crac.spec.in COPYING config/compile \
-	config/config.guess config/config.sub config/depcomp \
-	config/install-sh config/missing config/texinfo.tex \
-	config/ltmain.sh $(top_srcdir)/config/compile \
-	$(top_srcdir)/config/config.guess \
-	$(top_srcdir)/config/config.sub \
-	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
-	$(top_srcdir)/config/missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -198,6 +196,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
+	$(am__configure_deps) $(am__DIST_COMMON)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
 configure.lineno config.status.lineno
 mkinstalldirs = $(install_sh) -d
@@ -238,7 +238,7 @@ am__recursive_targets = \
  $(RECURSIVE_CLEAN_TARGETS) \
  $(am__extra_recursive_targets)
 AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
-	cscope distdir dist dist-all distcheck
+	cscope distdir distdir-am dist dist-all distcheck
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
 # Read a list of newline-separated strings from the standard input,
 # and print each of them once, without duplicates.  Input order is
@@ -260,6 +260,16 @@ ETAGS = etags
 CTAGS = ctags
 CSCOPE = cscope
 DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/control.in \
+	$(srcdir)/crac.spec.in $(top_srcdir)/config/compile \
+	$(top_srcdir)/config/config.guess \
+	$(top_srcdir)/config/config.h.in \
+	$(top_srcdir)/config/config.sub \
+	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
+	$(top_srcdir)/config/missing AUTHORS COPYING ChangeLog INSTALL \
+	NEWS README config/compile config/config.guess \
+	config/config.sub config/depcomp config/install-sh \
+	config/ltmain.sh config/missing config/texinfo.tex
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -349,6 +359,7 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
@@ -419,6 +430,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -457,15 +469,14 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
 	    echo ' $(SHELL) ./config.status'; \
 	    $(SHELL) ./config.status;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \
 	esac;

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -611,7 +622,10 @@ distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files

-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	$(am__remove_distdir)
 	test -d "$(distdir)" || mkdir "$(distdir)"
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -676,7 +690,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)

 dist-bzip2: distdir
@@ -692,17 +706,17 @@ dist-xz: distdir
 	$(am__post_remove_distdir)

 dist-tarZ: distdir
-	@echo WARNING: "Support for shar distribution archives is" \
-	               "deprecated." >&2
+	@echo WARNING: "Support for distribution archives compressed with" \
+		       "legacy program 'compress' is deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
 	$(am__post_remove_distdir)

 dist-shar: distdir
-	@echo WARNING: "Support for distribution archives compressed with" \
-		       "legacy program 'compress' is deprecated." >&2
+	@echo WARNING: "Support for shar distribution archives is" \
+	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)

 dist-zip: distdir
@@ -720,7 +734,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -730,23 +744,23 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
-	mkdir $(distdir)/_build $(distdir)/_inst
+	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
 	chmod a-w $(distdir)
 	test -d $(distdir)/_build || exit 0; \
 	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
 	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build \
-	  && ../configure \
+	  && $(am__cd) $(distdir)/_build/sub \
+	  && ../../configure \
 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
-	    --srcdir=.. --prefix="$$dc_install_base" \
+	    --srcdir=../.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
@@ -927,6 +941,8 @@ uninstall-am:
 	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
 	uninstall-am

+.PRECIOUS: Makefile
+
 # dist-hook:
 # 	rm -rf `find $(distdir) -type d -name .svn`


--- a/aclocal.m4
+++ b/aclocal.m4
-# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.16.1 -*- Autoconf -*-

-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.

 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])

-# Copyright (C) 2002-2013 Free Software Foundation, Inc.
+# Copyright (C) 2002-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
 # generated from the m4 files accompanying Automake X.Y.
 # (This private macro should not be called outside this file.)
 AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.14'
+[am__api_version='1.16'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.14.1], [],
+m4_if([$1], [1.16.1], [],
      [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])

@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.14.1])dnl
+[AM_AUTOMAKE_VERSION([1.16.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
  [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])

 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -110,7 +110,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`

 # AM_CONDITIONAL                                            -*- Autoconf -*-

-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -141,7 +141,7 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])

-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -332,13 +332,12 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl

 # Generate code to set up dependency tracking.              -*- Autoconf -*-

-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.

-
 # _AM_OUTPUT_DEPENDENCY_COMMANDS
 # ------------------------------
 AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
@@ -346,49 +345,41 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
  # Older Autoconf quotes --file arguments for eval, but not when files
  # are listed without --file.  Let's play safe and only enable the eval
  # if we detect the quoting.
-  case $CONFIG_FILES in
-  *\'*) eval set x "$CONFIG_FILES" ;;
-  *)   set x $CONFIG_FILES ;;
-  esac
+  # TODO: see whether this extra hack can be removed once we start
+  # requiring Autoconf 2.70 or later.
+  AS_CASE([$CONFIG_FILES],
+          [*\'*], [eval set x "$CONFIG_FILES"],
+          [*], [set x $CONFIG_FILES])
  shift
-  for mf
+  # Used to flag and report bootstrapping failures.
+  am_rc=0
+  for am_mf
  do
    # Strip MF so we end up with the name of the file.
-    mf=`echo "$mf" | sed -e 's/:.*$//'`
-    # Check whether this is an Automake generated Makefile or not.
-    # We used to match only the files named 'Makefile.in', but
-    # some people rename them; so instead we look at the file content.
-    # Grep'ing the first line is not enough: some people post-process
-    # each Makefile.in and add a new line on top of each file to say so.
-    # Grep'ing the whole file is not good either: AIX grep has a line
+    am_mf=`AS_ECHO(["$am_mf"]) | sed -e 's/:.*$//'`
+    # Check whether this is an Automake generated Makefile which includes
+    # dependency-tracking related rules and includes.
+    # Grep'ing the whole file directly is not great: AIX grep has a line
    # limit of 2048, but all sed's we know have understand at least 4000.
-    if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
-      dirpart=`AS_DIRNAME("$mf")`
-    else
-      continue
-    fi
-    # Extract the definition of DEPDIR, am__include, and am__quote
-    # from the Makefile without running 'make'.
-    DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
-    test -z "$DEPDIR" && continue
-    am__include=`sed -n 's/^am__include = //p' < "$mf"`
-    test -z "$am__include" && continue
-    am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-    # Find all dependency output files, they are included files with
-    # $(DEPDIR) in their names.  We invoke sed twice because it is the
-    # simplest approach to changing $(DEPDIR) to its actual value in the
-    # expansion.
-    for file in `sed -n "
-      s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
-      # Make sure the directory exists.
-      test -f "$dirpart/$file" && continue
-      fdir=`AS_DIRNAME(["$file"])`
-      AS_MKDIR_P([$dirpart/$fdir])
-      # echo "creating $dirpart/$file"
-      echo '# dummy' > "$dirpart/$file"
-    done
+    sed -n 's,^am--depfiles:.*,X,p' "$am_mf" | grep X >/dev/null 2>&1 \
+      || continue
+    am_dirpart=`AS_DIRNAME(["$am_mf"])`
+    am_filepart=`AS_BASENAME(["$am_mf"])`
+    AM_RUN_LOG([cd "$am_dirpart" \
+      && sed -e '/# am--include-marker/d' "$am_filepart" \
+        | $MAKE -f - am--depfiles]) || am_rc=$?
  done
+  if test $am_rc -ne 0; then
+    AC_MSG_FAILURE([Something went wrong bootstrapping makefile fragments
+    for automatic dependency tracking.  Try re-running configure with the
+    '--disable-dependency-tracking' option to at least be able to build
+    the package (albeit without support for automatic dependency tracking).])
+  fi
+  AS_UNSET([am_dirpart])
+  AS_UNSET([am_filepart])
+  AS_UNSET([am_mf])
+  AS_UNSET([am_rc])
+  rm -f conftest-deps.mk
 }
 ])# _AM_OUTPUT_DEPENDENCY_COMMANDS

@@ -397,18 +388,17 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
 # -----------------------------
 # This macro should only be invoked once -- use via AC_REQUIRE.
 #
-# This code is only required when automatic dependency tracking
-# is enabled.  FIXME.  This creates each '.P' file that we will
-# need in order to bootstrap the dependency handling code.
+# This code is only required when automatic dependency tracking is enabled.
+# This creates each '.Po' and '.Plo' makefile fragment that we'll need in
+# order to bootstrap the dependency handling code.
 AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 [AC_CONFIG_COMMANDS([depfiles],
     [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
-     [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
-])
+     [AMDEP_TRUE="$AMDEP_TRUE" MAKE="${MAKE-make}"])])

 # Do all the work for Automake.                             -*- Autoconf -*-

-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -495,11 +485,11 @@ AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
 AC_REQUIRE([AC_PROG_MKDIR_P])dnl
 # For better backward compatibility.  To be removed once Automake 1.9.x
 # dies out for good.  For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
 AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target.  The system "awk" is bad on
-# some platforms.
+# We need awk for the "check" target (and possibly the TAP driver).  The
+# system "awk" is bad on some platforms.
 AC_REQUIRE([AC_PROG_AWK])dnl
 AC_REQUIRE([AC_PROG_MAKE_SET])dnl
 AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -563,7 +553,7 @@ END
 Aborting the configuration process, to ensure you take notice of the issue.

 You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
+that behaves properly: <https://www.gnu.org/software/coreutils/>.

 If you want to complete the configuration process using your problematic
 'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
@@ -573,6 +563,9 @@ END
    AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
  fi
 fi
+dnl The trailing newline in this macro's definition is deliberate, for
+dnl backward compatibility and to allow trailing 'dnl'-style comments
+dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
 ])

 dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not
@@ -602,7 +595,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -613,7 +606,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
 # Define $install_sh.
 AC_DEFUN([AM_PROG_INSTALL_SH],
 [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh}" != xset; then
+if test x"${install_sh+set}" != xset; then
  case $am_aux_dir in
  *\ * | *\	*)
    install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -623,7 +616,7 @@ if test x"${install_sh}" != xset; then
 fi
 AC_SUBST([install_sh])])

-# Copyright (C) 2003-2013 Free Software Foundation, Inc.
+# Copyright (C) 2003-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -644,7 +637,7 @@ AC_SUBST([am__leading_dot])])

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -652,49 +645,42 @@ AC_SUBST([am__leading_dot])])

 # AM_MAKE_INCLUDE()
 # -----------------
-# Check to see how make treats includes.
+# Check whether make has an 'include' directive that can support all
+# the idioms we need for our automatic dependency tracking code.
 AC_DEFUN([AM_MAKE_INCLUDE],
-[am_make=${MAKE-make}
-cat > confinc << 'END'
+[AC_MSG_CHECKING([whether ${MAKE-make} supports the include directive])
+cat > confinc.mk << 'END'
 am__doit:
-	@echo this is the am__doit target
+	@echo this is the am__doit target >confinc.out
 .PHONY: am__doit
 END
-# If we don't find an include directive, just comment out the code.
-AC_MSG_CHECKING([for style of include used by $am_make])
 am__include="#"
 am__quote=
-_am_result=none
-# First try GNU make style include.
-echo "include confinc" > confmf
-# Ignore all kinds of additional output from 'make'.
-case `$am_make -s -f confmf 2> /dev/null` in #(
-*the\ am__doit\ target*)
-  am__include=include
-  am__quote=
-  _am_result=GNU
-  ;;
-esac
-# Now try BSD make style include.
-if test "$am__include" = "#"; then
-   echo '.include "confinc"' > confmf
-   case `$am_make -s -f confmf 2> /dev/null` in #(
-   *the\ am__doit\ target*)
-     am__include=.include
-     am__quote="\""
-     _am_result=BSD
-     ;;
-   esac
-fi
-AC_SUBST([am__include])
-AC_SUBST([am__quote])
-AC_MSG_RESULT([$_am_result])
-rm -f confinc confmf
-])
+# BSD make does it like this.
+echo '.include "confinc.mk" # ignored' > confmf.BSD
+# Other make implementations (GNU, Solaris 10, AIX) do it like this.
+echo 'include confinc.mk # ignored' > confmf.GNU
+_am_result=no
+for s in GNU BSD; do
+  AM_RUN_LOG([${MAKE-make} -f confmf.$s && cat confinc.out])
+  AS_CASE([$?:`cat confinc.out 2>/dev/null`],
+      ['0:this is the am__doit target'],
+      [AS_CASE([$s],
+          [BSD], [am__include='.include' am__quote='"'],
+          [am__include='include' am__quote=''])])
+  if test "$am__include" != "#"; then
+    _am_result="yes ($s style)"
+    break
+  fi
+done
+rm -f confinc.* confmf.*
+AC_MSG_RESULT([${_am_result}])
+AC_SUBST([am__include])])
+AC_SUBST([am__quote])])

 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-

-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -733,7 +719,7 @@ fi

 # Helper functions for option handling.                     -*- Autoconf -*-

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -762,7 +748,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])

-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -809,7 +795,7 @@ AC_LANG_POP([C])])
 # For backward compatibility.
 AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -828,7 +814,7 @@ AC_DEFUN([AM_RUN_LOG],

 # Check to make sure that the build environment is sane.    -*- Autoconf -*-

-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -909,7 +895,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])

-# Copyright (C) 2009-2013 Free Software Foundation, Inc.
+# Copyright (C) 2009-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -969,7 +955,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])

-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -997,7 +983,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])

-# Copyright (C) 2006-2013 Free Software Foundation, Inc.
+# Copyright (C) 2006-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1016,7 +1002,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])

 # Check how to create a tarball.                            -*- Autoconf -*-

-# Copyright (C) 2004-2013 Free Software Foundation, Inc.
+# Copyright (C) 2004-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
@@ -56,7 +56,7 @@ dnl Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.64])
 m4_define([V_MAJOR], [2])
 m4_define([V_MINOR], [5])
-m4_define([V_MICRO], [0])
+m4_define([V_MICRO], [2])

 AC_INIT(
  [crac],
@@ -153,7 +153,8 @@ AC_PROG_LN_S
 AC_SUBST([VERSION])

 dnl Disable shared library construction by default (must appear before LT_INIT)
-AC_DISABLE_SHARED
+AC_ENABLE_SHARED
+AC_DISABLE_STATIC

 LT_INIT
 LT_PATH_LD
@@ -307,7 +308,7 @@ AM_CONDITIONAL([INCLUDED_PROGRESSBAR], [test "x$with_included_ProgressBar" == "x
 AC_CHECK_LIB([z], [gzread], ,
             [AC_MSG_ERROR([zlib not found, see http://www.zlib.net])])

-AC_CHECK_LIB([hts], [hts_open], ,
+AC_CHECK_LIB([hts], [hts_hopen], ,
             [AC_MSG_ERROR([htslib not found, see http://www.htslib.org/])])

 GK_OK=1
@@ -359,7 +360,8 @@ AS_IF([test "x$enable_shared" == "xyes" ],
      [AS_VAR_APPEND([ac_configure_args], [" --enable-shared"])],
      [AS_VAR_APPEND([ac_configure_args], [" --disable-shared"])])
 AS_IF([test "x$enable_static" == "xyes" ],
-      [AS_VAR_APPEND([ac_configure_args], [" --enable-static"])],
+      [LDFLAGS="$LDFLAGS -all-static"
+       AS_VAR_APPEND([ac_configure_args], [" --enable-static"])],
      [AS_VAR_APPEND([ac_configure_args], [" --disable-static"])])

 dnl Forward FLAGS to libGkArrays/libProgressBar configure scripts if needed

--- a/debian/changelog
+++ b/debian/changelog
-crac (2.5.0+dfsg-4) UNRELEASED; urgency=medium
+crac (2.5.2+dfsg-1) unstable; urgency=medium

  [ Andreas Tille ]
  * Correct sequence of autopkgtest as in build time test
@@ -6,7 +6,12 @@ crac (2.5.0+dfsg-4) UNRELEASED; urgency=medium
  [ Jelmer Vernooĳ ]
  * Use secure copyright file specification URI.

- -- Andreas Tille <tille@debian.org>  Thu, 13 Sep 2018 14:22:19 +0200
+  [ Andreas Tille ]
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Fri, 19 Jul 2019 20:00:52 +0200

 crac (2.5.0+dfsg-3) unstable; urgency=low


--- a/debian/compat
+++ b/debian/compat
-11
+12
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
               zlib1g-dev,
               libhts-dev,
               libjellyfish-2.0-dev,
@@ -11,7 +11,7 @@ Build-Depends: debhelper (>= 11~),
               libgkarrays-dev,
               pkg-config,
               rsync
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/crac
 Vcs-Git: https://salsa.debian.org/med-team/crac.git
 Homepage: http://crac.gforge.inria.fr/

--- a/debian/patches/fix_includes.patch
+++ b/debian/patches/fix_includes.patch
-Author: Andreas Tille <tille@debian.org>
-Last-update: Sat, 10 Sep 2016 23:41:37 +0200
-Description: Add missing include
-
--- a/src/Support.cpp
-+++ b/src/Support.cpp
-@@ -53,6 +53,7 @@
- #include <utility>
- #include <vector>
- #include <algorithm>
-+#include <math.h>
- #include "Support.h"
- #include "BreakList.h"
- #include "utils.h"
--- a/debian/patches/reproducible_build.patch
+++ b/debian/patches/reproducible_build.patch
@@ -2,9 +2,9 @@ Description: Make the build reproducible
 Author: Chris Lamb <lamby@debian.org>
 Last-Update: 2017-04-01

--- crac-2.5.0+dfsg.orig/configure.ac
-+++ crac-2.5.0+dfsg/configure.ac
-@@ -159,6 +159,10 @@ LT_INIT
+--- a/configure.ac
+++ b/configure.ac
+@@ -160,6 +160,10 @@ LT_INIT
 LT_PATH_LD
 
 ISODATE=`date +%Y-%m-%d`

--- a/debian/patches/series
+++ b/debian/patches/series
 use_debian_packaged_libgzstream.patch
 use_debian_packaged_libjellyfish.patch
-fix_includes.patch
 skip_failed_test_bug-14958.patch
 use_debian_packages_libgtarrays.patch
 reproducible_build.patch
--- a/debian/patches/use_debian_packaged_libgzstream.patch
+++ b/debian/patches/use_debian_packaged_libgzstream.patch
@@ -4,7 +4,7 @@ Description: Use Debian packaged libgzstream

 --- a/configure.ac
 +++ b/configure.ac
-@@ -374,7 +374,6 @@ AC_CONFIG_FILES([\
+@@ -376,7 +376,6 @@ AC_CONFIG_FILES([\
   control crac.spec                             \
   Makefile src/Makefile scripts/Makefile        \
   src/libReadsInfo/Makefile src/libSSA/Makefile \
@@ -14,7 +14,7 @@ Description: Use Debian packaged libgzstream
   man/Makefile man/crac.1                       \
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -105,7 +105,7 @@ CRAC_LINKS = crac-index
+@@ -107,7 +107,7 @@ CRAC_LINKS = crac-index
 all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
 
 
@@ -23,7 +23,7 @@ Description: Use Debian packaged libgzstream
 if INCLUDED_GKARRAYS
   SUBDIRS += libGkArrays
 endif
-@@ -131,7 +131,7 @@ crac_SOURCES =                    \
+@@ -133,7 +133,7 @@ crac_SOURCES =                    \
   locateServer.cpp locateServer.h \
   utils.cpp utils.h \
   Bitset.cpp Bitset.h
@@ -32,7 +32,7 @@ Description: Use Debian packaged libgzstream
 
 #crac_index_SOURCES = @abs_srcdir@/libSSA/cracIndex.cpp
 #crac_index_LDADD = @abs_builddir@/libSSA/libSSA.a
-@@ -143,8 +143,8 @@ crac-emt: @abs_builddir@/libSSA/crac-emt
+@@ -145,8 +145,8 @@ crac-emt: @abs_builddir@/libSSA/crac-emt
 	$(LN_S) -f $^ $@
 
 

--- a/debian/patches/use_debian_packaged_libjellyfish.patch
+++ b/debian/patches/use_debian_packaged_libjellyfish.patch
@@ -4,7 +4,7 @@ Description: Use Debian packaged libjellyfish-2.0

 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -109,9 +109,6 @@ SUBDIRS = libReadsInfo libSSA libReadsRe
+@@ -111,9 +111,6 @@ SUBDIRS = libReadsInfo libSSA libReadsRe
 if INCLUDED_GKARRAYS
   SUBDIRS += libGkArrays
 endif
@@ -14,7 +14,7 @@ Description: Use Debian packaged libjellyfish-2.0
 
 crac_SOURCES =                    \
   basic.h const.h types.h         \
-@@ -147,8 +144,8 @@ AM_LDFLAGS = -lm -lpthread -lhts -lSSA -
+@@ -149,8 +146,8 @@ AM_LDFLAGS = -lm -lpthread -lhts -lSSA -
 AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@ -I@abs_srcdir@/libSSA -I@abs_srcdir@/libSSA/karkkainen_bw
 
 if INCLUDED_JELLYFISH

--- a/debian/patches/use_debian_packages_libgtarrays.patch
+++ b/debian/patches/use_debian_packages_libgtarrays.patch
@@ -4,7 +4,7 @@ Description: Use Debian packaged libgtkarrays

 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -106,9 +106,6 @@ all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
+@@ -108,9 +108,6 @@ all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
 
 
 SUBDIRS = libReadsInfo libSSA libReadsReader
@@ -14,7 +14,7 @@ Description: Use Debian packaged libgtkarrays
 
 crac_SOURCES =                    \
   basic.h const.h types.h         \
-@@ -150,11 +147,11 @@ if INCLUDED_JELLYFISH
+@@ -152,11 +149,11 @@ if INCLUDED_JELLYFISH
 endif
 
 if INCLUDED_GKARRAYS

--- a/man/Makefile.in
+++ b/man/Makefile.in
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@

-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -113,7 +113,17 @@
 #                                                                             #
 ###############################################################################
 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
  case $${target_option-} in \
      ?) ;; \
@@ -177,8 +187,6 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = man
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(srcdir)/crac.1.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -188,6 +196,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config/config.h
 CONFIG_CLEAN_FILES = crac.1
@@ -243,6 +252,7 @@ am__installdirs = "$(DESTDIR)$(man1dir)"
 NROFF = nroff
 MANS = $(man_MANS)
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/crac.1.in
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = @ACLOCAL@
 ALLOCA = @ALLOCA@
@@ -291,6 +301,7 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
@@ -361,6 +372,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -396,14 +408,13 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu man/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu man/Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
 	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
 	esac;

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -472,7 +483,10 @@ ctags CTAGS:
 cscope cscopelist:


-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \
@@ -626,6 +640,8 @@ uninstall-man: uninstall-man1
 	ps ps-am tags-am uninstall uninstall-am uninstall-man \
 	uninstall-man1

+.PRECIOUS: Makefile
+

 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.

--- a/scripts/Makefile.in
+++ b/scripts/Makefile.in
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@

-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -100,7 +100,17 @@
 ###############################################################################

 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
  case $${target_option-} in \
      ?) ;; \
@@ -164,8 +174,6 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = scripts
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(srcdir)/crac-client.in $(dist_bin_SCRIPTS)
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -175,6 +183,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(dist_bin_SCRIPTS) \
+	$(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config/config.h
 CONFIG_CLEAN_FILES = crac-client
@@ -228,6 +238,7 @@ am__can_run_installinfo = \
    *) (install-info --version) >/dev/null 2>&1;; \
  esac
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/crac-client.in
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = @ACLOCAL@
 ALLOCA = @ALLOCA@
@@ -276,6 +287,7 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
@@ -346,6 +358,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -375,14 +388,13 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu scripts/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu scripts/Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
 	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
 	esac;

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -443,7 +455,10 @@ ctags CTAGS:
 cscope cscopelist:


-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \
@@ -595,6 +610,8 @@ uninstall-am: uninstall-dist_binSCRIPTS
 	mostlyclean-libtool pdf pdf-am ps ps-am tags-am uninstall \
 	uninstall-am uninstall-dist_binSCRIPTS

+.PRECIOUS: Makefile
+

 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.

--- a/scripts/crac-client
+++ b/scripts/crac-client
@@ -113,7 +113,7 @@ do
 done

 if [ $QUIET -eq 0 ]; then
-   echo "This is the client of crac v. 2.5.0";
+   echo "This is the client of crac v. 2.5.2";
 fi

 [ -p $PIPE ] || PIPE=${PIPE/`dirname $0`/$PWD}

--- a/src/Bitset.h
+++ b/src/Bitset.h
@@ -53,6 +53,7 @@

 #include <cstdlib> // for uint
 #include <vector> // std::vector
+#include "types.h"

 class Bitset {
  public:

--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -98,6 +98,8 @@
 ###############################################################################


+AUTOMAKE_OPTIONS = subdir-objects
+
 bin_PROGRAMS=crac

 CRAC_LINKS = crac-index

--- a/src/Makefile.in
+++ b/src/Makefile.in
-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@

-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -114,7 +114,17 @@
 ###############################################################################

 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
  case $${target_option-} in \
      ?) ;; \
@@ -189,8 +199,6 @@ bin_PROGRAMS = crac$(EXEEXT)
 @HAVE_LIBGKARRAYS_TRUE@am__append_9 = -lGkArrays
 @HAVE_LIBJELLYFISH_TRUE@am__append_10 = -ljellyfish-2.0
 subdir = src
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(top_srcdir)/config/depcomp
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/config/m4/ltoptions.m4 \
@@ -200,6 +208,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/m4/libtool.m4 \
 	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config/config.h
 CONFIG_CLEAN_FILES =
@@ -237,7 +246,14 @@ am__v_at_0 = @
 am__v_at_1 = 
 DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/config
 depcomp = $(SHELL) $(top_srcdir)/config/depcomp
-am__depfiles_maybe = depfiles
+am__maybe_remake_depfiles = depfiles
+am__depfiles_remade = ./$(DEPDIR)/Bitset.Po ./$(DEPDIR)/BreakList.Po \
+	./$(DEPDIR)/CandidatBreak.Po ./$(DEPDIR)/Classifier.Po \
+	./$(DEPDIR)/GkReadIndex.Po ./$(DEPDIR)/JellyReadIndex.Po \
+	./$(DEPDIR)/Parameters.Po ./$(DEPDIR)/Support.Po \
+	./$(DEPDIR)/SupportBreak.Po ./$(DEPDIR)/classifyTags.Po \
+	./$(DEPDIR)/crac.Po ./$(DEPDIR)/locateServer.Po \
+	./$(DEPDIR)/utils.Po
 am__mv = mv -f
 CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
 	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
@@ -297,7 +313,7 @@ am__recursive_targets = \
  $(RECURSIVE_CLEAN_TARGETS) \
  $(am__extra_recursive_targets)
 AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
-	distdir
+	distdir distdir-am
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
 # Read a list of newline-separated strings from the standard input,
 # and print each of them once, without duplicates.  Input order is
@@ -319,6 +335,7 @@ ETAGS = etags
 CTAGS = ctags
 DIST_SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader \
 	libGkArrays libJellyfish-2.0
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/depcomp
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 am__relativize = \
  dir0=`pwd`; \
@@ -392,6 +409,7 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
@@ -462,6 +480,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -471,6 +490,7 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = subdir-objects
 CRAC_LINKS = crac-index
 SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader \
 	$(am__append_1) $(am__append_2)
@@ -525,14 +545,13 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu src/Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
 	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
 	esac;

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -603,37 +622,46 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Bitset.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/BreakList.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/CandidatBreak.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Classifier.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GkReadIndex.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/JellyReadIndex.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Parameters.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Support.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/SupportBreak.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/classifyTags.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/crac.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/locateServer.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Bitset.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/BreakList.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/CandidatBreak.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Classifier.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GkReadIndex.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/JellyReadIndex.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Parameters.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Support.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/SupportBreak.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/classifyTags.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/crac.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/locateServer.Po@am__quote@ # am--include-marker
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@ # am--include-marker
+
+$(am__depfiles_remade):
+	@$(MKDIR_P) $(@D)
+	@echo '# dummy' >$@-t && $(am__mv) $@-t $@
+
+am--depfiles: $(am__depfiles_remade)

 .cpp.o:
-@am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.o$$||'`;\
+@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
+@am__fastdepCXX_TRUE@	$(am__mv) $$depbase.Tpo $$depbase.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ $<

 .cpp.obj:
-@am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-@am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.obj$$||'`;\
+@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ `$(CYGPATH_W) '$<'` &&\
+@am__fastdepCXX_TRUE@	$(am__mv) $$depbase.Tpo $$depbase.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`

 .cpp.lo:
-@am__fastdepCXX_TRUE@	$(AM_V_CXX)$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+@am__fastdepCXX_TRUE@	$(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.lo$$||'`;\
+@am__fastdepCXX_TRUE@	$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
+@am__fastdepCXX_TRUE@	$(am__mv) $$depbase.Tpo $$depbase.Plo
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX@am__nodep@)$(LTCXXCOMPILE) -c -o $@ $<
@@ -743,7 +771,10 @@ cscopelist-am: $(am__tagged_files)
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags

-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \
@@ -845,7 +876,19 @@ clean: clean-recursive
 clean-am: clean-binPROGRAMS clean-generic clean-libtool mostlyclean-am

 distclean: distclean-recursive
-	-rm -rf ./$(DEPDIR)
+		-rm -f ./$(DEPDIR)/Bitset.Po
+	-rm -f ./$(DEPDIR)/BreakList.Po
+	-rm -f ./$(DEPDIR)/CandidatBreak.Po
+	-rm -f ./$(DEPDIR)/Classifier.Po
+	-rm -f ./$(DEPDIR)/GkReadIndex.Po
+	-rm -f ./$(DEPDIR)/JellyReadIndex.Po
+	-rm -f ./$(DEPDIR)/Parameters.Po
+	-rm -f ./$(DEPDIR)/Support.Po
+	-rm -f ./$(DEPDIR)/SupportBreak.Po
+	-rm -f ./$(DEPDIR)/classifyTags.Po
+	-rm -f ./$(DEPDIR)/crac.Po
+	-rm -f ./$(DEPDIR)/locateServer.Po
+	-rm -f ./$(DEPDIR)/utils.Po
 	-rm -f Makefile
 distclean-am: clean-am distclean-compile distclean-generic \
 	distclean-tags
@@ -891,7 +934,19 @@ install-ps-am:
 installcheck-am:

 maintainer-clean: maintainer-clean-recursive
-	-rm -rf ./$(DEPDIR)
+		-rm -f ./$(DEPDIR)/Bitset.Po
+	-rm -f ./$(DEPDIR)/BreakList.Po
+	-rm -f ./$(DEPDIR)/CandidatBreak.Po
+	-rm -f ./$(DEPDIR)/Classifier.Po
+	-rm -f ./$(DEPDIR)/GkReadIndex.Po
+	-rm -f ./$(DEPDIR)/JellyReadIndex.Po
+	-rm -f ./$(DEPDIR)/Parameters.Po
+	-rm -f ./$(DEPDIR)/Support.Po
+	-rm -f ./$(DEPDIR)/SupportBreak.Po
+	-rm -f ./$(DEPDIR)/classifyTags.Po
+	-rm -f ./$(DEPDIR)/crac.Po
+	-rm -f ./$(DEPDIR)/locateServer.Po
+	-rm -f ./$(DEPDIR)/utils.Po
 	-rm -f Makefile
 maintainer-clean-am: distclean-am maintainer-clean-generic

@@ -913,19 +968,22 @@ uninstall-am: uninstall-binPROGRAMS
 .MAKE: $(am__recursive_targets) install-am install-strip

 .PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am all-local \
-	check check-am clean clean-binPROGRAMS clean-generic \
-	clean-libtool cscopelist-am ctags ctags-am distclean \
-	distclean-compile distclean-generic distclean-libtool \
-	distclean-tags distdir dvi dvi-am html html-am info info-am \
-	install install-am install-binPROGRAMS install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-html install-html-am install-info \
-	install-info-am install-man install-pdf install-pdf-am \
-	install-ps install-ps-am install-strip installcheck \
-	installcheck-am installdirs installdirs-am maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-compile \
-	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
-	tags tags-am uninstall uninstall-am uninstall-binPROGRAMS
+	am--depfiles check check-am clean clean-binPROGRAMS \
+	clean-generic clean-libtool cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic \
+	distclean-libtool distclean-tags distdir dvi dvi-am html \
+	html-am info info-am install install-am install-binPROGRAMS \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+	pdf pdf-am ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile


 all-local: $(bin_PROGRAMS) $(CRAC_LINKS)

--- a/src/Support.cpp
+++ b/src/Support.cpp
@@ -53,6 +53,7 @@
 #include <utility>
 #include <vector>
 #include <algorithm>
+#include <cmath>
 #include "Support.h"
 #include "BreakList.h"
 #include "utils.h"