matching gcov version with gcc in travis coveralls

.travis.scripts/coveralls.sh

@@ -10,6 +10,12 @@ then
     fi
     cd seq_test
 
+    ## download the latest matched gcov
+    sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/gcov-4.9 90
+    sudo ln -sf /usr/bin/gcov-4.9 /usr/bin/gcov
+    GCOV_VERSION=`gcov --version`
+    echo "GCOV version $GCOV_VERSION"
+
     ## download the test data
     mkdir test_data
     cd test_data
@@ -20,7 +26,8 @@ then
     echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
     ./configure --with-boost=${BOOST_ROOT}
     make CXXFLAGS='-DHAVE_C11=1 -std=c++11' CXX=$COMPILER
-    ./seq_test
+    ./seq_test 1> stdout.log 2> stderr.log
+    tail -n stderr.log 
 
     EXCL="-e src/non_api -e seq_test/seq_test.cpp -e htslib -e bwa -e fermi-lite -e config.h -e seq_test/config.h -e seq_test/config.h -e src/jsoncpp.cpp -e src/json -e src/SeqLib/ssw.h -e src/SeqLib/ssw_cpp.h -e src/ssw.c -e src/ssw_cpp.cpp"
     cpp-coveralls -r ../ -t ${COVERALLS_TOKEN} ${EXCL} ##--dryrun

config.status

@@ -363,11 +363,11 @@ Copyright (C) 2008 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
-ac_pwd='/Users/jwala/GIT/freebayes/SeqLib'
+ac_pwd='/xchip/gistic/Jeremiah/GIT/SeqLib'
 srcdir='.'
 INSTALL='/usr/bin/install -c'
-MKDIR_P='./install-sh -c -d'
-AWK='awk'
+MKDIR_P='/bin/mkdir -p'
+AWK='gawk'
 test -n "$AWK" || AWK=awk
 # The default lists apply if the user does not specify any file.
 ac_need_defaults=:
@@ -538,8 +538,8 @@ S["am__EXEEXT_TRUE"]="#"
 S["LTLIBOBJS"]=""
 S["LIBOBJS"]=""
 S["AM_CXXFLAGS"]="-g  -Wno-unknown-pragmas"
-S["EGREP"]="/usr/bin/grep -E"
-S["GREP"]="/usr/bin/grep"
+S["EGREP"]="/bin/grep -E"
+S["GREP"]="/bin/grep"
 S["CXXCPP"]="g++ -E"
 S["RANLIB"]="ranlib"
 S["am__fastdepCC_FALSE"]="#"
@@ -569,20 +569,20 @@ S["MAINTAINER_MODE_FALSE"]=""
 S["MAINTAINER_MODE_TRUE"]="#"
 S["am__untar"]="${AMTAR} xf -"
 S["am__tar"]="${AMTAR} chof - \"$$tardir\""
-S["AMTAR"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run tar"
+S["AMTAR"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run tar"
 S["am__leading_dot"]="."
 S["SET_MAKE"]=""
-S["AWK"]="awk"
-S["mkdir_p"]="$(top_builddir)/./install-sh -c -d"
-S["MKDIR_P"]="./install-sh -c -d"
+S["AWK"]="gawk"
+S["mkdir_p"]="/bin/mkdir -p"
+S["MKDIR_P"]="/bin/mkdir -p"
 S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
 S["STRIP"]=""
-S["install_sh"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/install-sh"
-S["MAKEINFO"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run makeinfo"
-S["AUTOHEADER"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run autoheader"
-S["AUTOMAKE"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run automake-1.11"
-S["AUTOCONF"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run autoconf"
-S["ACLOCAL"]="${SHELL} /Users/jwala/GIT/freebayes/SeqLib/missing --run aclocal-1.11"
+S["install_sh"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/install-sh"
+S["MAKEINFO"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run makeinfo"
+S["AUTOHEADER"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run autoheader"
+S["AUTOMAKE"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run automake-1.11"
+S["AUTOCONF"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run autoconf"
+S["ACLOCAL"]="${SHELL} /xchip/gistic/Jeremiah/GIT/SeqLib/missing --run aclocal-1.11"
 S["VERSION"]="1.0"
 S["PACKAGE"]="seqkit"
 S["CYGPATH_W"]="echo"
@@ -593,10 +593,10 @@ S["INSTALL_PROGRAM"]="${INSTALL}"
 S["target_alias"]=""
 S["host_alias"]=""
 S["build_alias"]=""
-S["LIBS"]="-lz  -pthread"
+S["LIBS"]="-lrt -lz  -pthread"
 S["ECHO_T"]=""
-S["ECHO_N"]=""
-S["ECHO_C"]="\\c"
+S["ECHO_N"]="-n"
+S["ECHO_C"]=""
 S["DEFS"]="-DHAVE_CONFIG_H"
 S["mandir"]="${datarootdir}/man"
 S["localedir"]="${datarootdir}/locale"
@@ -687,6 +687,7 @@ D["HAVE_STRINGS_H"]=" 1"
 D["HAVE_INTTYPES_H"]=" 1"
 D["HAVE_STDINT_H"]=" 1"
 D["HAVE_UNISTD_H"]=" 1"
+D["HAVE_CLOCK_GETTIME"]=" 1"
   for (key in D) D_is_set[key] = 1
   FS = ""
 }

seq_test/seq_test.cpp

@@ -96,7 +96,6 @@ BOOST_AUTO_TEST_CASE ( bfc ) {
   v.clear();
   b.FilterUnique();
   b.GetSequences(v);
-  std::cerr << " FILTERED NOW SIZE " << v.size() << std::endl;
 
   // do everything at once
   b.TrainAndCorrect(brv2);