Merge pull request #96 from stocnet/develop

Develop
stocnet · Sep 2, 2024 · 0fcddaf · 0fcddaf
2 parents e429a7b + abcaaa6
commit 0fcddaf
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.6.7
-Date: 2024-04-11 11:53:04 UTC
-SHA: 859b5bcfafb03bd44ce97a810673b5fd943d92ef
+Version: 1.6.8
+Date: 2024-04-11 15:22:41 UTC
+SHA: e429a7b18059ead79de506ae04d0f10fd47db4e4
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: goldfish
 Type: Package
 Title: Statistical Network Models for Dynamic Network Data
-Version: 1.6.8
-Date: 2024-04-11
+Version: 1.6.9
+Date: 2024-09-02
 Authors@R: c(person("James", "Hollway", role = c("aut", "dtc"), 
                     email = "[email protected]",
                     comment = c("IHEID", ORCID = "0000-0002-8361-9647")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# goldfish 1.6.9
+
+* Solve issue on `Makevars.in` file that produced a note when check as CRAN. 
+
 # goldfish 1.6.8
 
 * `checkEvents()` method addresses S3 generic/method consistency.

diff --git a/README.Rmd b/README.Rmd
@@ -24,7 +24,7 @@ library(goldfish)
 ![GitHub All Releases](https://img.shields.io/github/downloads/stocnet/goldfish/total)
 [![R-CMD-check](https://github.com/stocnet/goldfish/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/stocnet/goldfish/actions/workflows/R-CMD-check.yml)
 [![Codecov test coverage](https://codecov.io/gh/stocnet/goldfish/branch/main/graph/badge.svg)](https://app.codecov.io/gh/stocnet/goldfish?branch=main)
-[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/4563/badge)](https://bestpractices.coreinfrastructure.org/projects/4563)
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/4563/badge)](https://www.bestpractices.dev/projects/4563)
 <!-- badges: end -->
 
 <!-- [![CodeFactor](https://www.codefactor.io/repository/github/stocnet/goldfish/badge)](https://www.codefactor.io/repository/github/stocnet/goldfish) -->

diff --git a/README.md b/README.md
@@ -15,8 +15,8 @@ Releases](https://img.shields.io/github/downloads/stocnet/goldfish/total)
 [![R-CMD-check](https://github.com/stocnet/goldfish/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/stocnet/goldfish/actions/workflows/R-CMD-check.yml)
 [![Codecov test
 coverage](https://codecov.io/gh/stocnet/goldfish/branch/main/graph/badge.svg)](https://app.codecov.io/gh/stocnet/goldfish?branch=main)
-[![CII Best
-Practices](https://bestpractices.coreinfrastructure.org/projects/4563/badge)](https://bestpractices.coreinfrastructure.org/projects/4563)
+[![OpenSSF Best
+Practices](https://www.bestpractices.dev/projects/4563/badge)](https://www.bestpractices.dev/projects/4563)
 <!-- badges: end -->
 
 <!-- [![CodeFactor](https://www.codefactor.io/repository/github/stocnet/goldfish/badge)](https://www.codefactor.io/repository/github/stocnet/goldfish) -->

diff --git a/configure b/configure
@@ -2439,6 +2439,263 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
 
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+  if test -n "$CCC"; then
+    CXX=$CCC
+  else
+    if test -n "$ac_tool_prefix"; then
+  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CXX+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$CXX"; then
+  ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+    test -n "$CXX" && break
+  done
+fi
+if test -z "$CXX"; then
+  ac_ct_CXX=$CXX
+  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CXX+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$ac_ct_CXX"; then
+  ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_ac_ct_CXX="$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+  test -n "$ac_ct_CXX" && break
+done
+
+  if test "x$ac_ct_CXX" = x; then
+    CXX="g++"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+    CXX=$ac_ct_CXX
+  fi
+fi
+
+  fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+  { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+  ac_status=$?
+  if test -s conftest.err; then
+    sed '10a\
+... rest of stderr output deleted ...
+         10q' conftest.err >conftest.er1
+    cat conftest.er1 >&5
+  fi
+  rm -f conftest.er1 conftest.err
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if ${ac_cv_cxx_compiler_gnu+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+#ifndef __GNUC__
+       choke me
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  ac_compiler_gnu=yes
+else
+  ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+  GXX=yes
+else
+  GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if ${ac_cv_prog_cxx_g+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+   ac_cxx_werror_flag=yes
+   ac_cv_prog_cxx_g=no
+   CXXFLAGS="-g"
+   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  ac_cv_prog_cxx_g=yes
+else
+  CXXFLAGS=""
+      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+  ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+	 CXXFLAGS="-g"
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+   ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+  CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+  if test "$GXX" = yes; then
+    CXXFLAGS="-g -O2"
+  else
+    CXXFLAGS="-g"
+  fi
+else
+  if test "$GXX" = yes; then
+    CXXFLAGS="-O2"
+  else
+    CXXFLAGS=
+  fi
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
 
 # check openMP
 openmp_flag=""

diff --git a/configure.ac b/configure.ac
@@ -22,6 +22,7 @@ CXXFLAGS=$("${R_HOME}/bin/R" CMD config CXXFLAGS)
 ## We are using C++
 AC_LANG(C++)
 AC_REQUIRE_CPP
+AC_PROG_CXX
 
 # check openMP
 openmp_flag=""

diff --git a/src/Makevars.in b/src/Makevars.in
@@ -1,4 +1,5 @@
 ## -*- mode: makefile; -*-
 
+PKG_CPPFLAGS = -I../inst/include
 PKG_CXXFLAGS =  @OPENMP_FLAG@
-PKG_LIBS= @OPENMP_CFLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS= @OPENMP_FLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)