update for new CRAN submission

.gitlab-ci.yml

@@ -63,3 +63,18 @@ release-package:
   only:
     - tags
 
+release-Mac:
+  tags:
+    - "Mac"  
+    - "R"
+  script:
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    - "R CMD build . --resave-data"
+    - "R CMD INSTALL --binary $(ls -rt landsepi_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt landsepi_*.tgz | tail -1)"
+  only:
+    - tags
+
+

DESCRIPTION

@@ -2,8 +2,8 @@ Package: landsepi
 Type: Package
 Encoding: UTF-8
 Title: Landscape Epidemiology and Evolution
-Version: 0.0.4
-Date: 2018-04-10
+Version: 0.0.5
+Date: 2018-04-25
 Authors@R: c(person("Loup", "Rimbaud", role = "aut", email = "loup.rimbaud@csiro.au"),
         person("Julien", "Papaix", role = "aut", email = "julien.papaix@inra.fr"),
         person("Jean-Francois", "Rey", role = "cre", email = "jean-francois.rey@inra.fr"))
@@ -17,7 +17,7 @@ Description: A spatio-temporal stochastic model to assess resistance deployment
     pathogen, and a SEIR (Susceptible-Exposed-Infectious-Removed) architecture to simulate 
     plant response to disease.
     Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, 
-    Peter H Thrall (2018) <doi:10.1101/260836>.
+    Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
 License: GPL (>= 2) | file LICENSE
 LazyData: true
 BuildVignettes: true

R/RcppExports.R

@@ -55,6 +55,6 @@
 #' @references Rimbaud L., Papaïx J., Rey J.-F., Barrett L. G. and Thrall P. H. (2018). Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. \emph{PLoS Computational Biology} 14(4):e1006067.
 #' @export
 modelLandsEPI <- function(times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP) {
-    invisible(.Call('landsepi_modelLandsEPI', PACKAGE = 'landsepi', times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP))
+    invisible(.Call('_landsepi_modelLandsEPI', PACKAGE = 'landsepi', times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP))
 }
 

R/landsepi.R

@@ -36,8 +36,8 @@
 #' @details \tabular{ll}{
 #'          Package: \tab lansepi\cr
 #'          Type: \tab Package\cr
-#'          Version: \tab 0.0.4\cr
-#'          Date: \tab 2018-04-10\cr
+#'          Version: \tab 0.0.5\cr
+#'          Date: \tab 2018-04-24\cr
 #'          License: \tab GPL (>=2)\cr
 #'          }
 #'

README.md

@@ -6,7 +6,7 @@ output:
 # R package landsepi
 Landscape Epidemiology and Evolution  
 
-<!--[![pipeline status](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/badges/master/pipeline.svg)](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/commits/master)  -->
+[![pipeline status](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/badges/master/pipeline.svg)](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/commits/master)
 
 ## Description
 A spatio-temporal stochastic model to assess resistance deployment strategies against plant pathogens.
@@ -65,8 +65,7 @@ R packages dependencies :
 
 To install :  
 ```r
-install.packages(c("Rcpp","sp","rgdal","Matrix","MASS","rgeos","maptools"
-,"fields","splancs","sf"))
+install.packages(c("Rcpp","sp","rgdal","Matrix","MASS","rgeos","maptools","fields","splancs","sf"))
 ```
 
 ### Install landsepi
@@ -87,7 +86,7 @@ Open R :
 ```r
 library(Rcpp)
 library(roxygen2)
-Rcpp::compileAttribute(pkg=".")
+Rcpp::compileAttributes(pkg=".")
 roxygen2::roxygenize('.', roclets=c('rd', 'namespace'))
 ```
 

inst/CITATION

@@ -22,8 +22,7 @@ bibentry(
   year = 2018,
   volume = 14,
   issue = 4,
-  pages = e1006067,
   doi = "10.1371/journal.pcbi.1006067",
-  journal = "PLoS Computational Biology")
+  journal = "PLOS Computational Biology")
 )
 

man/landsepi-package.Rd

@@ -17,8 +17,8 @@ architecture to simulate plant response to disease.
 \tabular{ll}{
          Package: \tab lansepi\cr
          Type: \tab Package\cr
-         Version: \tab 0.0.4\cr
-         Date: \tab 2018-04-10\cr
+         Version: \tab 0.0.5\cr
+         Date: \tab 2018-04-24\cr
          License: \tab GPL (>=2)\cr
          }
 

src/RcppExports.cpp

@@ -7,7 +7,7 @@ using namespace Rcpp;
 
 // modelLandsEPI
 void modelLandsEPI(Rcpp::List times, Rcpp::List landscape, Rcpp::List dispersal, Rcpp::List inits, int val_seed, Rcpp::List hostP, Rcpp::List epiP, Rcpp::List evolP);
-RcppExport SEXP landsepi_modelLandsEPI(SEXP timesSEXP, SEXP landscapeSEXP, SEXP dispersalSEXP, SEXP initsSEXP, SEXP val_seedSEXP, SEXP hostPSEXP, SEXP epiPSEXP, SEXP evolPSEXP) {
+RcppExport SEXP _landsepi_modelLandsEPI(SEXP timesSEXP, SEXP landscapeSEXP, SEXP dispersalSEXP, SEXP initsSEXP, SEXP val_seedSEXP, SEXP hostPSEXP, SEXP epiPSEXP, SEXP evolPSEXP) {
 BEGIN_RCPP
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< Rcpp::List >::type times(timesSEXP);
@@ -22,3 +22,13 @@ BEGIN_RCPP
     return R_NilValue;
 END_RCPP
 }
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_landsepi_modelLandsEPI", (DL_FUNC) &_landsepi_modelLandsEPI, 8},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_landsepi(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}