fixed try-catch error + update makevars etc

.github/workflows/R-CMD-check.yaml

@@ -1,10 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, CRANrelease]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, CRANrelease]
 
 name: R-CMD-check
 
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: NPflow
 Type: Package
 Title: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data
-Version: 0.13.3
-Date: 2020-02-06
+Version: 0.13.4
+Date: 2023-01-12
 Authors@R: c(person(c("Boris", "P"), "Hejblum", role = c("aut", "cre"),
     email = "[email protected]"),
     person("Chariff", "Alkhassim", role = c("aut"),
@@ -37,4 +37,4 @@ Description: Dirichlet process mixture of multivariate normal, skew normal or sk
 License: LGPL-3 | file LICENSE
 BugReports: https://github.com/borishejblum/NPflow/issues
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.0

NEWS.md

@@ -1,5 +1,8 @@
 # News about the `NPflow` R package
 
+### Main changes in Version 0.13.4 (2023-02-12) --- *this is only a minor release*:
+* bug fixed in try-catch syntax
+
 ### Main changes in Version 0.13.3 (2020-02-06) --- *this is only a minor release*:
 * bug fixed in documentation and compiling standards
 

R/NPflow-package.R

@@ -7,8 +7,8 @@
 #'\tabular{ll}{
 #'Package: \tab NPflow\cr
 #'Type: \tab Package\cr
-#'Version: \tab 0.13.3\cr
-#'Date: \tab 2020-02-06\cr
+#'Version: \tab 0.13.4\cr
+#'Date: \tab 2023-01-12\cr
 #'License:\tab \href{http://www.gnu.org/licenses/lgpl.txt}{LGPL-3}\cr
 #'}
 #'The main function in this package is \code{\link{DPMpost}}.
@@ -22,11 +22,10 @@
 #'13(1): 638-660. <doi: 10.1214/18-AOAS1209> <arXiv: 1702.04407> 
 #'\url{https://arxiv.org/abs/1702.04407} \url{https://doi.org/10.1214/18-AOAS1209}
 #'
-#'@docType package
 #'@name NPflow-package
 #'@aliases NPflow
 #'
 #'@useDynLib NPflow, .registration = TRUE
 #'@importFrom Rcpp evalCpp
 #'
-NULL
+"_PACKAGE"

R/plot_DPM.R

@@ -164,7 +164,7 @@ plot_DPM <- function(z, U_mu=NULL, U_Sigma=NULL, m, c, i, alpha="?", U_SS=NULL,
       message("unable to display 2D densities because 1 cluster has only 1 observation")
       upper_type <- GGally::wrap("points", alpha=0.1, size=0.2)
     }
-    p <- GGally::ggpairs(data = rpairplotdata, mapping = aes(color=Cluster),
+    p <- GGally::ggpairs(data = rpairplotdata, mapping = aes_string(color="Cluster"),
                          title = paste(n, " obs.",
                                        "\niteration ", i, ": ",
                                        length(fullCl)," clusters",

R/update_SSst.R

@@ -47,7 +47,7 @@ update_SSst <- function(z, S, ltn, scale, df, hyperprior=NULL){
 
   X <- matrix(c(sc_sr, sc_sr*ltn), ncol=2, byrow=FALSE)
   B <- try(solve(crossprod(X) + B0inv))
-  if(class(B)=="try-error"){
+  if(inherits(B, "try-error")){
     #   browser()
     stop("error in inverting B")
   }

cran-comments.md

@@ -1,14 +1,14 @@
 # This is an update of the NPflow package  
 
 ## Test environments  
- * local R installation, R 4.1.2 on macOS 12.2.1
+ * local R installation, R 4.3.2 on macOS 13.5.2
  * Linux (Ubuntu 20.04), macOS (11.6) and Windows (Server 2019 10.0), R devel and release (through GitHub Actions)
 
 ## R CMD check results  
 0 errors | 0 warnings | 0 note
 
 On some architectures, the large volume of compiled file may trigger a note.
-These compiled functions are necessary to ensure reasonnable computation time
+These compiled functions are necessary to ensure reasonable computation time
 for NPflow.
 
 ## Reverse dependencies  

src/Makevars

@@ -1,5 +1,5 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
 ## enable compilation with C++11 (where available)
 ##
 ## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
@@ -8,7 +8,12 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+##
+## R 4.0.0 made C++11 the default, R 4.1.0 switched to C++14, R 4.3.0 to C++17
+## _In general_ we should no longer need to set a standard as any recent R
+## installation will do the right thing. Should you need it, uncomment it and
+## set the appropriate value, possibly CXX17.
+#CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,5 +1,5 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
 ## enable compilation with C++11 (where available)
 ##
 ## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
@@ -8,7 +8,12 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+##
+## R 4.0.0 made C++11 the default, R 4.1.0 switched to C++14, R 4.3.0 to C++17
+## _In general_ we should no longer need to set a standard as any recent R
+## installation will do the right thing. Should you need it, uncomment it and
+## set the appropriate value, possibly CXX17.
+#CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/RcppExports.cpp

@@ -6,6 +6,11 @@
 
 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
+
 // FmeasureC
 double FmeasureC(const NumericVector& pred, const NumericVector& ref);
 RcppExport SEXP _NPflow_FmeasureC(SEXP predSEXP, SEXP refSEXP) {