travisCI -> GHA

.Rbuildignore

@@ -7,3 +7,5 @@ cran-comment
 ^appveyor\.yml$
 revdep
 ^cran-comments\.md$
+^CRAN-RELEASE$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        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
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1

.gitignore

@@ -11,4 +11,5 @@
 Rprof.out
 defaultmonitor.txt
 cran-comment
-revdep
+revdep
+*.DS_Store

R/summary.DPMMclust.R

@@ -10,7 +10,7 @@
 #'Default is \code{1}, i.e. no thining.
 #'
 #'@param lossFn character string specifying the loss function to be used.
-#'Either "F-measure" or "Binder" (see Details). Default is "F-measure".
+#'Either "F-measure" or "Binder" (see Details). Default is "Binder".
 #'
 #'@param gs optional vector of length \code{n} containing the gold standard
 #'partition of the \code{n} observations to compare to the point estimate
@@ -64,7 +64,7 @@
 #'@seealso \code{\link{similarityMat}} \code{\link{similarityMatC}}
 #'
 
-summary.DPMMclust <- function(object, burnin=0, thin=1, gs=NULL, lossFn="F-measure",
+summary.DPMMclust <- function(object, burnin=0, thin=1, gs=NULL, lossFn="Binder",
                               posterior_approx=FALSE, ...){
 
   x_invar <- burn.DPMMclust(object, burnin = burnin, thin=thin)

README.Rmd

@@ -15,8 +15,7 @@ knitr::opts_chunk$set(
 # `NPflow`
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/NPflow)](https://cran.r-project.org/package=NPflow)
-[![Travis-CI Build Status](https://travis-ci.org/borishejblum/NPflow.svg?branch=CRANrelease)](https://travis-ci.org/borishejblum/NPflow)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/borishejblum/NPflow?branch=CRANrelease&svg=true)](https://ci.appveyor.com/project/borishejblum/NPflow)
+[![R-CMD-check](https://github.com/borishejblum/NPflow/workflows/R-CMD-check/badge.svg)](https://github.com/borishejblum/NPflow/actions)
 [![Downloads](https://cranlogs.r-pkg.org/badges/NPflow?color=blue)](https://www.r-pkg.org/pkg/NPflow)
 
 

README.md

@@ -3,18 +3,16 @@
 
 # `NPflow`
 
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/NPflow)](https://cran.r-project.org/package=NPflow)
-[![Travis-CI Build
-Status](https://travis-ci.org/borishejblum/NPflow.svg?branch=CRANrelease)](https://travis-ci.org/borishejblum/NPflow)
-[![AppVeyor Build
-Status](https://ci.appveyor.com/api/projects/status/github/borishejblum/NPflow?branch=CRANrelease&svg=true)](https://ci.appveyor.com/project/borishejblum/NPflow)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/NPflow)](https://cran.r-project.org/package=NPflow)
+[![R-CMD-check](https://github.com/borishejblum/NPflow/workflows/R-CMD-check/badge.svg)](https://github.com/borishejblum/NPflow/actions)
 [![Downloads](https://cranlogs.r-pkg.org/badges/NPflow?color=blue)](https://www.r-pkg.org/pkg/NPflow)
 
 ## Overview
 
 `NPflow` is a package for performing **Bayesian estimation of Dirichlet
-process mixtures of multivariate skew \(t\)-distributions**. It is
-especially oriented towards flow-cytometry data preprocessing
+process mixtures of multivariate skew
+![t](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;t "t")-distributions**.
+It is especially oriented towards flow-cytometry data preprocessing
 applications, but can be useful for numerous other applications.
 
 The main function of the package is `DPMpost()`.
@@ -25,9 +23,9 @@ article:
 > Hejblum BP, Alkhassim C, Gottardo R, Caron F and Thiebaut R (2019).
 > Sequential Dirichlet Process Mixtures of Multivariate Skew
 > t-distributions for Model-based Clustering of Flow Cytometry Data.
-> *The Annals of Applied Statistics*, **13**(1):638-660.
-> [\<doi: 10.1214/18-AOAS1209\>](https://doi.org/10.1214/18-AOAS1209)
-> [\<arXiv: 1702.04407\>](https://arxiv.org/abs/1702.04407)
+> *The Annals of Applied Statistics*, **13**(1):638-660. [\<doi:
+> 10.1214/18-AOAS1209\>](https://doi.org/10.1214/18-AOAS1209) [\<arXiv:
+> 1702.04407\>](https://arxiv.org/abs/1702.04407)
 
 ## Installation
 

cran-comments.md

@@ -1,14 +1,16 @@
 # This is an update of the NPflow package  
 
 ## Test environments  
-* local macOS 10.15.2 install, R 3.6.2
-* macOS 10.13.6 (on travis-ci), R devel and release
-* ubuntu 16.04.11 (on travis-ci), R devel and release
-* Windows Visual Studio 2015 (on appveyor), R devel and release
+ * local R installation, R 4.1.2 on macOS 12.2.1
+ * 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
+for NPflow.
+
 ## Reverse dependencies  
 There are no reverse dependencies.