Remove suppressions from polyk, supress OpenMP warning messages on st…

…artup, add gitattributes and fix cran-check action

.gitattributes

@@ -0,0 +1 @@
+configure.ac text eol=lf

.github/workflows/cran-check.yml

@@ -64,27 +64,16 @@ jobs:
       - name: Build and Check ToxicR
         if: runner.os != 'Windows'
         run: |
-          R CMD build .
-          file config.log
-          cat config.log
           r_output=$(R CMD build .)
-          echo "$r_output"
-          package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p") 
-          echo "$package_name"
+          package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p")
           R CMD check --as-cran --no-manual $package_name
         shell: bash
         working-directory: "."
       - name: Build and Check ToxicR
         if: runner.os == 'Windows'
         run: |
           r_output=$(R CMD build .)
-          echo "$r_output"
           package_name=$(echo "$r_output" | sed -n "s/.*building '\([^']*\.tar\.gz\)'.*/\1/p")
-          echo "$package_name"
           R CMD check --as-cran --no-manual $package_name
-          file ToxicR.Rcheck/00install.log
-          file ToxicR/ToxicR.Rcheck/00install.log
-          cat ToxicR.Rcheck/00install.log
-          cat ToxicR.Rcheck/00check.log
         shell: bash
         working-directory: "."

.gitignore

@@ -1,8 +1,10 @@
 *.o
 *.so
+*.Rproj
 .Rproj.user
 .Rhistory
 .vscode/*
 .RData
 *.tar.gz
-*.dll
+*.dll
+install.sh

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changes
-## Version 23.10.1.2.3 
-## The following cumulative fixes are in version 23.10.1.2.3
+## Version 23.10.1.2.4 
+## The following cumulative fixes are in version 23.10.1.2.4
 - Add the ability to set a seed for nlopt and GSL to allow for consistent results
 - Set additional checks and guards for openMP
 ## New Features 

DESCRIPTION

@@ -77,7 +77,7 @@ Imports: Rcpp (>= 1.0.0), ggplot2 (>= 3.3.2), shiny (>= 1.5.0), coda
         (>= 0.19-4), scales (>= 1.1.1), forcats, ggridges (>= 0.5.3),
         doBy (>= 4.6.11), multcomp (>= 1.4), dplyr (>= 1.0.7), remotes
 LinkingTo: Rcpp, RcppEigen, RcppGSL
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
 Suggests: plotly (>= 4.9.2.1), rmarkdown, actuar (>= 3.2-0),ggpubr (>=

R/RcppExports.R

@@ -42,6 +42,6 @@
 }
 
 .set_threads <- function(num_threads) {
-    invisible(.Call(`_ToxicR_set_threads`, num_threads))
+    .Call(`_ToxicR_set_threads`, num_threads)
 }
 

R/opening_messages.R

@@ -17,15 +17,16 @@
 # CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE
 # OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 .onAttach <- function(libname, pkgname) {
-  msg <- "
+  version <- as.character(utils::packageVersion("ToxicR"))
+  msg <- paste0("
 
   _______               _____
  |__   __|      \U1F913     |  __ \\
     | | _____  ___  ___| |__) |
     | |/ _ \\ \\/ / |/ __|  _  /
     | | (_) >  <| | (__| | \\ \\
     |_|\\___/_/\\_\\_|\\___|_|  \\_\\
-                           24.1.1.2.4
+                           ",version,"
     ___
     | |
     / \\                   ____()()
@@ -39,7 +40,7 @@ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIG
 HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE
 OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-"
+")
 
   # notify the option to update? (5 possible cases)
   # 1. error in getting the current package version -> yes
@@ -50,7 +51,7 @@ OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
   # in short, notify the option to update unless the version numbers match
   # get version of the currently installed package
   current_pkg_version <- tryCatch(
-    as.character(utils::packageVersion("ToxicR")),
+    version,
     error = function(e) "unknown")
   # github url
   github_url <- paste0(
@@ -81,7 +82,7 @@ OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
       compare_version_result == 0) {
     startup_message <- paste0(
       "Package attached: ToxicR v", current_pkg_version,
-      " (same as the most recent version available through GitHub).")
+      " (the most recent version available through GitHub).")
   } else if (
     # skip update for case 4
     current_pkg_version != "unknown" &
@@ -103,7 +104,13 @@ OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
   }
   packageStartupMessage(msg)
   packageStartupMessage(startup_message)
-  .set_threads(2);
-  open_mp_message <- "OpenMP threads set to 2.\n"
+  status <- .set_threads(2)
+  if (status == 1) {
+    open_mp_message <- "OpenMP threads set to 2.\n"
+  } else if (status == 0) {
+    open_mp_message <- "OpenMP will not be used for parallelization.\n"
+  } else {
+    open_mp_message <- "OpenMP is not supported on this architecture.\n"
+  }
   packageStartupMessage(open_mp_message)
 }

src/RcppExports.cpp

@@ -167,13 +167,14 @@ BEGIN_RCPP
 END_RCPP
 }
 // set_threads
-void set_threads(int num_threads);
+int set_threads(int num_threads);
 RcppExport SEXP _ToxicR_set_threads(SEXP num_threadsSEXP) {
 BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< int >::type num_threads(num_threadsSEXP);
-    set_threads(num_threads);
-    return R_NilValue;
+    rcpp_result_gen = Rcpp::wrap(set_threads(num_threads));
+    return rcpp_result_gen;
 END_RCPP
 }
 

src/polyK/polyK_setup.cpp

@@ -1,10 +1,10 @@
 
 
 // necessary things to run in R
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wignored-attributes"
+// #pragma GCC diagnostic push
+// #pragma GCC diagnostic ignored "-Wignored-attributes"
 #include <RcppEigen.h>
-#pragma GCC diagnostic pop
+// #pragma GCC diagnostic pop
 
 #include "polyK_animal.h"
 #include "polyK_setup.h"

src/polyK/polyK_setup.h

@@ -2,10 +2,10 @@
 #include <array>
 #include <list>
 #include <vector>
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wignored-attributes"
+// #pragma GCC diagnostic push
+// #pragma GCC diagnostic ignored "-Wignored-attributes"
 #include <RcppEigen.h>
-#pragma GCC diagnostic pop
+// #pragma GCC diagnostic pop
 #include <RcppGSL.h>
 
 #include "polyK_animal.h"

src/set_omp_threads.cpp

@@ -11,20 +11,25 @@ using namespace Rcpp;
 // function: set_threads
 // purpose: takes an integer value and set the number of
 // openmp threads to that value
-// output: none
+// output: integer representing if openMP is supported and set correctely
 // [[Rcpp::export(".set_threads")]]
-void set_threads(int num_threads) {
+int set_threads(int num_threads) {
   #ifndef NO_OMP
   if(omp_get_max_threads() > 1){
     if (num_threads > omp_get_num_threads()) {
       Seeder* s = Seeder::getInstance();
       omp_set_num_threads(num_threads);
       s->reset_max_threads(num_threads);
+      // Rcpp::Rcout << "OpenMP threads set to " << num_threads << std::endl;
+      return 1;
     }
   }else{
-    Rcout << "OMP will not be used for parallelization.";
+    return 0;
+    // Rcpp::Rcout << "OMP will not be used for parallelization.";
   }
   #else
-  Rcpp::Rcout << "OpenMP not supported on this architecure." << std::endl;
+  return -1;
+  // Rcpp::Rcout << "OpenMP not supported on this architecure." << std::endl;
   #endif
+  return -1;
 }