update Mac OSX compilation and packaging

add Mac OS runner CI

.gitlab-ci.yml

@@ -14,6 +14,15 @@ package-devel:
     - "R CMD build . --resave-data"
     - "R CMD check --as-cran $(ls -rt landsepi_* |tail -1)"
 
+package-Mac-base:
+  tags:
+    - "Mac"  
+    - "R"
+  script:
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    - "R CMD build . --resave-data"
+    - "R CMD check --as-cran $(ls -rt landsepi_* |tail -1)"
+
 package-windows:
   tags:
     - "win10"

DESCRIPTION

@@ -2,7 +2,7 @@ Package: landsepi
 Type: Package
 Encoding: UTF-8
 Title: Landscape Epidemiology and Evolution
-Version: 0.0.2
+Version: 0.0.3
 Date: 2018-03-19
 Authors@R: c(person("Loup", "Rimbaud", role = "aut", email = "loup.rimbaud@csiro.au"),
         person("Julien", "Papaix", role = "aut", email = "julien.papaix@inra.fr"),
@@ -23,7 +23,7 @@ LazyData: true
 BuildVignettes: true
 NeedsCompilation: yes
 Biarch: true
-SystemRequirements: C++11, gsl, gdal >= 1.7.0
+SystemRequirements: C++11, gsl, gdal >= 1.11.0
 Depends:
     methods,
     utils,

R/landsepi.R

@@ -36,7 +36,7 @@
 #' @details \tabular{ll}{
 #'          Package: \tab lansepi\cr
 #'          Type: \tab Package\cr
-#'          Version: \tab 0.0.2\cr
+#'          Version: \tab 0.0.3\cr
 #'          Date: \tab 2018-03-19\cr
 #'          License: \tab GPL (>=2)\cr
 #'          }

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for landsepi 0.0.2.
+# Generated by GNU Autoconf 2.69 for landsepi 0.0.3.
 #
 # Report bugs to <jean-francois.rey@inra.fr>.
 #
@@ -579,13 +579,15 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='landsepi'
 PACKAGE_TARNAME='landsepi'
-PACKAGE_VERSION='0.0.2'
-PACKAGE_STRING='landsepi 0.0.2'
+PACKAGE_VERSION='0.0.3'
+PACKAGE_STRING='landsepi 0.0.3'
 PACKAGE_BUGREPORT='jean-francois.rey@inra.fr'
 PACKAGE_URL=''
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+CXX1XFLAGS
+CXX11
 OBJEXT
 EXEEXT
 ac_ct_CXX
@@ -1198,7 +1200,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures landsepi 0.0.2 to adapt to many kinds of systems.
+\`configure' configures landsepi 0.0.3 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1260,7 +1262,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of landsepi 0.0.2:";;
+     short | recursive ) echo "Configuration of landsepi 0.0.3:";;
    esac
   cat <<\_ACEOF
 
@@ -1345,7 +1347,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-landsepi configure 0.0.2
+landsepi configure 0.0.3
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1446,7 +1448,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by landsepi $as_me 0.0.2, which was
+It was created by landsepi $as_me 0.0.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -1804,9 +1806,11 @@ fi
 $as_echo "$as_me: ${R_HOME}" >&6;}
 CXX1X=`"${R_HOME}/bin/R" CMD config CXX1X`
 CXX1XSTD=`"${R_HOME}/bin/R" CMD config CXX1XSTD`
-CXX="${CXX1X} ${CXX1XSTD}"
+#CXX="${CXX1X} ${CXX1XSTD}"
+CXX=`"${R_HOME}/bin/R" CMD config CXX`
 CPP=`"${R_HOME}/bin/R" CMD config CPP`
-CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
+CXX1XFLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
 CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
@@ -2543,7 +2547,7 @@ $as_echo "yes" >&6; }
   CXXFLAGS="${CXXFLAGS} ${GDAL_CFLAGS}"
 fi
 
-LDFLAGS="${LDFLAGS} ${GDAL_LIBS}"
+LDFLAGS="${LDFLAGS} ${GDAL_LIBS} ${GDAL_DEP_LIBS}"
 
 CXXFLAGS="${CXXFLAGS}"
 
@@ -2553,6 +2557,8 @@ CXXFLAGS="${CXXFLAGS}"
 
 
 
+
+
 ac_config_files="$ac_config_files src/Makevars"
 
 
@@ -3098,7 +3104,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by landsepi $as_me 0.0.2, which was
+This file was extended by landsepi $as_me 0.0.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3151,7 +3157,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-landsepi config.status 0.0.2
+landsepi config.status 0.0.3
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -11,7 +11,7 @@ dnl -----------------------------------------------
 dnl Package name and version number (user defined)
 dnl -----------------------------------------------
 define([THE_PACKAGE_NAME],    [landsepi])
-define([THE_PACKAGE_VERSION], [0.0.2])
+define([THE_PACKAGE_VERSION], [0.0.3])
 define([THE_PACKAGE_MAINTAINER],  [jean-francois.rey@inra.fr])
 
 dnl --------------------------------
@@ -31,9 +31,11 @@ fi
 AC_MSG_NOTICE([${R_HOME}])
 CXX1X=`"${R_HOME}/bin/R" CMD config CXX1X`
 CXX1XSTD=`"${R_HOME}/bin/R" CMD config CXX1XSTD`
-CXX="${CXX1X} ${CXX1XSTD}"
+#CXX="${CXX1X} ${CXX1XSTD}"
+CXX=`"${R_HOME}/bin/R" CMD config CXX`
 CPP=`"${R_HOME}/bin/R" CMD config CPP`
-CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
+CXX1XFLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
 CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
@@ -108,7 +110,7 @@ else
   CXXFLAGS="${CXXFLAGS} ${GDAL_CFLAGS}"
 fi
 
-LDFLAGS="${LDFLAGS} ${GDAL_LIBS}"
+LDFLAGS="${LDFLAGS} ${GDAL_LIBS} ${GDAL_DEP_LIBS}"
 
 CXXFLAGS="${CXXFLAGS}"
 
@@ -117,7 +119,9 @@ dnl Generates Makefile's, configuration files and scripts
 dnl -----------------------------------------------
 # R mode
 AC_SUBST(CXX)
+AC_SUBST(CXX11)
 AC_SUBST(CXXFLAGS)
+AC_SUBST(CXX1XFLAGS)
 AC_SUBST(CPPFLAGS)
 AC_SUBST(LDFLAGS)
 

src/Makevars.in

 PKG_CXX = @CXX@
+PKG_CXX11 = @CXX11@
 PKG_CPPFLAGS = @CPPFLAGS@ 
 PKG_CXXFLAGS = @CXXFLAGS@
+PKG_CXX1XFLAGS = @CXX1XFLAGS@
 PKG_LIBS = @LDFLAGS@ 
 PKG_CFLAGS = @CXXFLAGS@
+CXX_STD=@CXX11@