Address CRAN WARN checks in DEVEL (#24)

* Re-render documentation and compilation attributes * Update README badges & install text * Bump requirements * Remove specific CXX request
tmsalab · Nov 29, 2023 · 5df1c2b · 5df1c2b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,16 +28,16 @@ URL: https://tmsalab.github.io/simcdm, https://github.com/tmsalab/simcdm
 BugReports: https://github.com/tmsalab/simcdm/issues
 License: GPL (>= 2)
 Depends:
-    R (>= 3.5.0)
-Imports: Rcpp  (>= 1.0.0)
+    R (>= 4.1.0)
+Imports: Rcpp  (>= 1.0.11)
 LinkingTo: Rcpp,
-    RcppArmadillo (>= 0.9.200)
+    RcppArmadillo (>= 0.12.6.6.0)
 Suggests: 
     testthat,
     covr,
     knitr,
     rmarkdown
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -334,5 +334,5 @@ sim_subject_attributes <- function(N, K, probs = NULL) {
 
 # Register entry points for exported C++ functions
 methods::setLoadAction(function(ns) {
-    .Call('_simcdm_RcppExport_registerCCallable', PACKAGE = 'simcdm')
+    .Call(`_simcdm_RcppExport_registerCCallable`)
 })
diff --git a/README.Rmd b/README.Rmd
@@ -18,24 +18,24 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/tmsalab/simcdm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tmsalab/simcdm/actions/workflows/R-CMD-check.yaml)
 [![Package-License](http://img.shields.io/badge/license-GPL%20(%3E=2)-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
 [![CRAN Version Badge](http://www.r-pkg.org/badges/version/simcdm)](https://cran.r-project.org/package=simcdm)
-[![CRAN Status](https://cranchecks.info/badges/worst/simcdm)](https://cran.r-project.org/web/checks/check_results_simcdm.html)
+[![CRAN Status](https://badges.cranchecks.info/worst/simcdm.svg)](https://cran.r-project.org/web/checks/check_results_simcdm.html)
 [![RStudio CRAN Mirror's Monthly Downloads](http://cranlogs.r-pkg.org/badges/simcdm?color=brightgreen)](http://www.r-pkg.org/pkg/simcdm)
 [![RStudio CRAN Mirror's Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/simcdm?color=brightgreen)](http://www.r-pkg.org/pkg/simcdm)
-[![Coverage test coverage](https://codecov.io/gh/tmsalab/simcdm/branch/master/graph/badge.svg)](https://codecov.io/github/tmsalab/simcdm?branch=master)
+[![Coverage test coverage](https://codecov.io/gh/tmsalab/simcdm/branch/main/graph/badge.svg)](https://codecov.io/github/tmsalab/simcdm?branch=main)
 <!-- badges: end -->
 
 The goal of `simcdm` is to provide flexible ways to simulate data under
 cognitive diagnostic models.
 
 ## Installation
 
-You can install simcdm from GitHub with:
+You can install `simcdm` from GitHub with:
 
 ```{r}
 #| label: gh-installation
 #| eval: false
-# install.packages("devtools")
-devtools::install_github("tmsalab/simcdm")
+# install.packages("remotes")
+remotes::install_github("tmsalab/simcdm")
 ```
 
 ## Usage
@@ -59,8 +59,9 @@ There are four distinct sets of functions within the package:
 
 Functions that use random numbers to simulate values are named with the prefix of
 `sim_*()`. This is done to allow for functions to be quickly identified and used
-through autocomplete inside of the [RStudio IDE](https://www.rstudio.com). At
-a later time, the `attribute_*()` will likely be moved to a different package.
+through autocomplete inside of the [RStudio IDE](https://www.rstudio.com) or 
+[VS Code](https://code.visualstudio.com/). At a later time, the `attribute_*()`
+will likely be moved to a different package.
 
 For more details, please see the [package vignettes](vignettes/):
 

diff --git a/README.md b/README.md
@@ -10,25 +10,25 @@
 [![CRAN Version
 Badge](http://www.r-pkg.org/badges/version/simcdm)](https://cran.r-project.org/package=simcdm)
 [![CRAN
-Status](https://cranchecks.info/badges/worst/simcdm)](https://cran.r-project.org/web/checks/check_results_simcdm.html)
+Status](https://badges.cranchecks.info/worst/simcdm.svg)](https://cran.r-project.org/web/checks/check_results_simcdm.html)
 [![RStudio CRAN Mirror’s Monthly
 Downloads](http://cranlogs.r-pkg.org/badges/simcdm?color=brightgreen)](http://www.r-pkg.org/pkg/simcdm)
 [![RStudio CRAN Mirror’s Total
 Downloads](http://cranlogs.r-pkg.org/badges/grand-total/simcdm?color=brightgreen)](http://www.r-pkg.org/pkg/simcdm)
 [![Coverage test
-coverage](https://codecov.io/gh/tmsalab/simcdm/branch/master/graph/badge.svg)](https://codecov.io/github/tmsalab/simcdm?branch=master)
+coverage](https://codecov.io/gh/tmsalab/simcdm/branch/main/graph/badge.svg)](https://codecov.io/github/tmsalab/simcdm?branch=main)
 <!-- badges: end -->
 
 The goal of `simcdm` is to provide flexible ways to simulate data under
 cognitive diagnostic models.
 
 ## Installation
 
-You can install simcdm from GitHub with:
+You can install `simcdm` from GitHub with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("tmsalab/simcdm")
+# install.packages("remotes")
+remotes::install_github("tmsalab/simcdm")
 ```
 
 ## Usage
@@ -53,8 +53,9 @@ There are four distinct sets of functions within the package:
 Functions that use random numbers to simulate values are named with the
 prefix of `sim_*()`. This is done to allow for functions to be quickly
 identified and used through autocomplete inside of the [RStudio
-IDE](https://www.rstudio.com). At a later time, the `attribute_*()` will
-likely be moved to a different package.
+IDE](https://www.rstudio.com) or [VS
+Code](https://code.visualstudio.com/). At a later time, the
+`attribute_*()` will likely be moved to a different package.
 
 For more details, please see the [package vignettes](vignettes/):
 

diff --git a/man/attribute_bijection.Rd b/man/attribute_bijection.Rd
diff --git a/man/attribute_classes.Rd b/man/attribute_classes.Rd
diff --git a/man/attribute_inv_bijection.Rd b/man/attribute_inv_bijection.Rd
diff --git a/man/sim_dina_attributes.Rd b/man/sim_dina_attributes.Rd
diff --git a/man/sim_dina_class.Rd b/man/sim_dina_class.Rd
diff --git a/man/sim_dina_items.Rd b/man/sim_dina_items.Rd
diff --git a/man/sim_eta_matrix.Rd b/man/sim_eta_matrix.Rd
diff --git a/man/sim_q_matrix.Rd b/man/sim_q_matrix.Rd
diff --git a/man/sim_subject_attributes.Rd b/man/sim_subject_attributes.Rd
diff --git a/man/simcdm-package.Rd b/man/simcdm-package.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -1,6 +1,3 @@
-# Enable C++11
-CXX_STD = CXX11
-
 # Enable the header file and OpenMP
 PKG_CXXFLAGS = -I../inst/include $(SHLIB_OPENMP_CXXFLAGS) 
 

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,6 +1,3 @@
-# Enable C++11
-CXX_STD = CXX11
-
 # Enable the header file and OpenMP
 PKG_CXXFLAGS = -I../inst/include $(SHLIB_OPENMP_CXXFLAGS) 
 

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -9,6 +9,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // sim_dina_class
 arma::mat sim_dina_class(unsigned int N, unsigned int J, const arma::vec& CLASS, const arma::mat& ETA, const arma::vec& gs, const arma::vec& ss);
 static SEXP _simcdm_sim_dina_class_try(SEXP NSEXP, SEXP JSEXP, SEXP CLASSSEXP, SEXP ETASEXP, SEXP gsSEXP, SEXP ssSEXP) {
@@ -43,7 +48,7 @@ RcppExport SEXP _simcdm_sim_dina_class(SEXP NSEXP, SEXP JSEXP, SEXP CLASSSEXP, S
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -78,7 +83,7 @@ RcppExport SEXP _simcdm_sim_dina_attributes(SEXP alphasSEXP, SEXP QSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -115,7 +120,7 @@ RcppExport SEXP _simcdm_sim_dina_items(SEXP alphasSEXP, SEXP QSEXP, SEXP ssSEXP,
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -152,7 +157,7 @@ RcppExport SEXP _simcdm_sim_rrum_main(SEXP QSEXP, SEXP rstarSEXP, SEXP pistarSEX
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -189,7 +194,7 @@ RcppExport SEXP _simcdm_sim_rrum_items(SEXP QSEXP, SEXP rstarSEXP, SEXP pistarSE
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -223,7 +228,7 @@ RcppExport SEXP _simcdm_attribute_bijection(SEXP KSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -258,7 +263,7 @@ RcppExport SEXP _simcdm_attribute_inv_bijection(SEXP KSEXP, SEXP CLSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -293,7 +298,7 @@ RcppExport SEXP _simcdm_sim_q_matrix(SEXP JSEXP, SEXP KSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -329,7 +334,7 @@ RcppExport SEXP _simcdm_sim_eta_matrix(SEXP KSEXP, SEXP JSEXP, SEXP QSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -363,7 +368,7 @@ RcppExport SEXP _simcdm_attribute_classes(SEXP KSEXP) {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;
@@ -399,7 +404,7 @@ RcppExport SEXP _simcdm_sim_subject_attributes(SEXP NSEXP, SEXP KSEXP, SEXP prob
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;