From 270a49ad47934e29ca002da355d240211e112d55 Mon Sep 17 00:00:00 2001 From: walaj Date: Wed, 6 Jan 2021 20:18:03 -0800 Subject: [PATCH] fixing test suite compiling --- .travis.yml | 1 - seq_test/Makefile.in | 27 ++++++++++----------------- seq_test/configure | 27 +++++++++++++++++++++------ seq_test/configure.ac | 6 +++--- seq_test/seq_test.cpp | 2 +- 5 files changed, 35 insertions(+), 28 deletions(-) diff --git a/.travis.yml b/.travis.yml index e266a5c94..c9130f580 100644 --- a/.travis.yml +++ b/.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 diff --git a/seq_test/Makefile.in b/seq_test/Makefile.in index 3cdc05385..be5806f35 100644 --- a/seq_test/Makefile.in +++ b/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) $(AM_MAKEFLAGS) installcheck \ @@ -1132,10 +1125,10 @@ uninstall-am: uninstall-binPROGRAMS check-am clean clean-binPROGRAMS clean-cscope clean-generic \ cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \ dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \ - dist-zstd distcheck distclean distclean-compile \ - distclean-generic distclean-hdr distclean-tags distcleancheck \ - distdir distuninstallcheck dvi dvi-am html html-am info \ - info-am install install-am install-binPROGRAMS install-data \ + distcheck distclean distclean-compile distclean-generic \ + distclean-hdr distclean-tags distcleancheck distdir \ + distuninstallcheck dvi dvi-am html html-am info info-am \ + install install-am install-binPROGRAMS install-data \ install-data-am install-dvi install-dvi-am install-exec \ install-exec-am install-html install-html-am install-info \ install-info-am install-man install-pdf install-pdf-am \ diff --git a/seq_test/configure b/seq_test/configure index da5ee2825..1c10490cc 100755 --- a/seq_test/configure +++ b/seq_test/configure @@ -703,6 +703,7 @@ infodir docdir oldincludedir includedir +runstatedir localstatedir sharedstatedir sysconfdir @@ -782,6 +783,7 @@ datadir='${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; } diff --git a/seq_test/configure.ac b/seq_test/configure.ac index 704ba2e3b..751ec9441 100644 --- a/seq_test/configure.ac +++ b/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 diff --git a/seq_test/seq_test.cpp b/seq_test/seq_test.cpp index ab7392897..f0e0ddf9f 100644 --- a/seq_test/seq_test.cpp +++ b/seq_test/seq_test.cpp @@ -3,7 +3,7 @@ #include #include -#include +#include #include "SeqLib/BWAWrapper.h" #include "SeqLib/BamReader.h"