fixing test suite compiling

.travis.yml

@@ -50,7 +50,6 @@ before_install:
 - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
 - sudo apt-get install wget
 - sudo apt-get -qq update
-- mkdir test_data && cd test_data && wget --recursive -np -nc -nH --cut-dirs=4 --random-wait --wait 1 -e robots=off -A "test*" -A "small*" -A "motif*" -A "example*" https://data.broadinstitute.org/snowman/SeqLib/ && cd ..
 - if [ "${TRAVIS_BRANCH}" = "master" ]; then export BOOST_VERSION="${BOOST_VERSION_MIN}"; else export BOOST_VERSION="${BOOST_VERSION_MAX}"; fi
 - if [ -n "${BOOST_VERSION}" ]; then export BOOST_ROOT="${TRAVIS_BUILD_DIR}/../boost-trunk"; export CMAKE_MODULE_PATH="${BOOST_ROOT}"; fi
 - if [ "${TRAVIS_OS_NAME}" = "osx" -a "${CXX}" = "clang++" ]; then export CXX="$(which c++)"; export CC="$(which cc)"; fi

seq_test/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.16.3 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2020 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,
@@ -190,8 +190,8 @@ am__can_run_installinfo = \
     n|no|NO) false;; \
     *) (install-info --version) >/dev/null 2>&1;; \
   esac
-am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP) \
-	config.h.in
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
+	$(LISP)config.h.in
 # Read a list of newline-separated strings from the standard input,
 # and print each of them once, without duplicates.  Input order is
 # *not* preserved.
@@ -228,8 +228,6 @@ am__post_remove_distdir = $(am__remove_distdir)
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 DIST_TARGETS = dist-gzip
-# Exists only to be overridden by the user if desired.
-AM_DISTCHECK_DVI_TARGET = dvi
 distuninstallcheck_listfiles = find . -type f -print
 am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
   | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
@@ -321,6 +319,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -873,10 +872,6 @@ dist-xz: distdir
 	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
 	$(am__post_remove_distdir)
 
-dist-zstd: distdir
-	tardir=$(distdir) && $(am__tar) | zstd -c $${ZSTD_CLEVEL-$${ZSTD_OPT--19}} >$(distdir).tar.zst
-	$(am__post_remove_distdir)
-
 dist-tarZ: distdir
 	@echo WARNING: "Support for distribution archives compressed with" \
 		       "legacy program 'compress' is deprecated." >&2
@@ -919,8 +914,6 @@ distcheck: dist
 	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
-	*.tar.zst*) \
-	  zstd -dc $(distdir).tar.zst | $(am__untar) ;;\
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
@@ -936,7 +929,7 @@ distcheck: dist
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
 	    --srcdir=../.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) $(AM_DISTCHECK_DVI_TARGET) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
 	  && $(MAKE) $(AM_MAKEFLAGS) install \
 	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
@@ -1132,10 +1125,10 @@ uninstall-am: uninstall-binPROGRAMS
 	check-am clean clean-binPROGRAMS clean-cscope clean-generic \
 	cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
 	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
-	dist-zstd distcheck distclean distclean-compile \
-	distclean-generic distclean-hdr distclean-tags distcleancheck \
-	distdir distuninstallcheck dvi dvi-am html html-am info \
-	info-am install install-am install-binPROGRAMS install-data \
+	distcheck distclean distclean-compile distclean-generic \
+	distclean-hdr distclean-tags distcleancheck distdir \
+	distuninstallcheck 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 \

seq_test/configure

@@ -703,6 +703,7 @@ infodir
 docdir
 oldincludedir
 includedir
+runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -782,6 +783,7 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
+runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -1034,6 +1036,15 @@ do
   | -silent | --silent | --silen | --sile | --sil)
     silent=yes ;;
 
+  -runstatedir | --runstatedir | --runstatedi | --runstated \
+  | --runstate | --runstat | --runsta | --runst | --runs \
+  | --run | --ru | --r)
+    ac_prev=runstatedir ;;
+  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
+  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
+  | --run=* | --ru=* | --r=*)
+    runstatedir=$ac_optarg ;;
+
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1171,7 +1182,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir
+		libdir localedir mandir runstatedir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1324,6 +1335,7 @@ Fine tuning of the installation directories:
   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
+  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
   --libdir=DIR            object code libraries [EPREFIX/lib]
   --includedir=DIR        C header files [PREFIX/include]
   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
@@ -2346,7 +2358,12 @@ program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
 am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 if test x"${MISSING+set}" != xset; then
-  MISSING="\${SHELL} '$am_aux_dir/missing'"
+  case $am_aux_dir in
+  *\ * | *\	*)
+    MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+  *)
+    MISSING="\${SHELL} $am_aux_dir/missing" ;;
+  esac
 fi
 # Use eval to expand $SHELL
 if eval "$MISSING --is-lightweight"; then
@@ -4823,7 +4840,7 @@ if test "${with_boost+set}" = set; then :
 fi
 
 if test "$with_boost" -a -d "$with_boost"; then
-    boost_include="-I$with_boost"
+    boost_include="-I$with_boost/include"
     as_ac_File=`$as_echo "ac_cv_file_"$with_boost/stage/lib"" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for \"$with_boost/stage/lib\"" >&5
 $as_echo_n "checking for \"$with_boost/stage/lib\"... " >&6; }
@@ -6312,9 +6329,7 @@ $as_echo X/"$am_mf" |
     { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "Something went wrong bootstrapping makefile fragments
-    for automatic dependency tracking.  If GNU make was not used, consider
-    re-running the configure script with MAKE=\"gmake\" (or whatever is
-    necessary).  You can also try re-running configure with the
+    for automatic dependency tracking.  Try re-running configure with the
     '--disable-dependency-tracking' option to at least be able to build
     the package (albeit without support for automatic dependency tracking).
 See \`config.log' for more details" "$LINENO" 5; }

seq_test/configure.ac

@@ -23,12 +23,12 @@ AC_SEARCH_LIBS([clock_gettime], [rt], [AC_DEFINE([HAVE_CLOCK_GETTIME], [1], [clo
 AC_ARG_WITH(boost, AS_HELP_STRING([--with-boost=PATH],
 	[specify directory containing the boost library)]))
 if test "$with_boost" -a -d "$with_boost"; then
-    boost_include="-I$with_boost"
+    boost_include="-I$with_boost/include"
     AC_CHECK_FILE("$with_boost/stage/lib", STAGE_PATH=1, STAGE_PATH=0)
     if test ${STAGE_PATH} = 1; then
-        boost_lib="-L$with_boost/stage/lib"  
+        boost_lib="-L$with_boost/stage/lib"
     else
-        boost_lib="-L$with_boost/lib"        
+        boost_lib="-L$with_boost/lib"
     fi
     AC_SUBST(boost_lib)	
 fi

seq_test/seq_test.cpp

@@ -3,7 +3,7 @@
 #include<boost/test/unit_test.hpp>
 
 #include <climits>
-#include <boost/test/unit_test.hpp>
+#include <boost/test/included/unit_test.hpp>
 
 #include "SeqLib/BWAWrapper.h"
 #include "SeqLib/BamReader.h"