Added package doi

Author: fbertran

.DS_Store

@@ -1,32 +1,52 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+name: R-CMD-check
+
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [ main, master ]
   pull_request:
-    branches:
-      - main
-      - master
-
-name: R-CMD-check
+    branches: [ main, master ]
 
 jobs:
   R-CMD-check:
-    runs-on: macOS-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        r: ['devel', 'release', 'oldrel-1']
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      NOT_CRAN: true
+
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
+
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set up R ${{ matrix.r }}
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r }}
+          use-public-rspm: true
+
       - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
       - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          upload-snapshots: true
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: r-cmd-check-results-${{ runner.os }}-r${{ matrix.r }}
+          path: check

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

@@ -1,21 +1,22 @@
 Package: plsRglm
-Version: 1.5.1
-Date: 2023-03-14
+Version: 1.6.0
+Date: 2025-09-11
 Depends: R (>= 2.10)
 Imports: mvtnorm, boot, bipartite, car, MASS
 Enhances: pls
-Suggests: plsdof, R.rsp, chemometrics, plsdepot
+Suggests: chemometrics, plsdof, plsdepot, plspm, plsRcox, R.rsp, testthat (>= 3.0.0)
 Title: Partial Least Squares Regression for Generalized Linear Models
 Authors@R: c(
-	person(given = "Frederic", family= "Bertrand", role = c("cre", "aut"), email = "frederic.bertrand@utt.fr", comment = c(ORCID = "0000-0002-0837-8281")),
-	person(given = "Myriam", family= "Maumy-Bertrand", role = c("aut"), email = "myriam.maumy@utt.fr", comment = c(ORCID = "0000-0002-4615-1512")))
+	person(given = "Frederic", family= "Bertrand", role = c("cre", "aut"), email = "frederic.bertrand@lecnam.net", comment = c(ORCID = "0000-0002-0837-8281")),
+	person(given = "Myriam", family= "Maumy-Bertrand", role = c("aut"), email = "myriam.maumy@ehesp.fr", comment = c(ORCID = "0000-0002-4615-1512")))
 Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>)
-Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
-Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <arXiv:1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
+Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
+Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <doi:10.48550/arXiv.1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
 License: GPL-3
 Encoding: UTF-8
 URL: https://fbertran.github.io/plsRglm/, https://github.com/fbertran/plsRglm/
 BugReports: https://github.com/fbertran/plsRglm/issues/
 VignetteBuilder: R.rsp
 Classification/MSC: 62J12, 62J99
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
+Config/testthat/edition: 3

DESCRIPTION

@@ -1,3 +1,9 @@
+# plsRglm 1.6.0
+
+* Maintainer email update.
+* Added unit tests.
+* Fix package to get rid of CRAN check notes
+
 # plsRglm 1.5.1
 
 Fix to methods as requested by CRAN and remove escaped latex characters.

NEWS.md

@@ -9,7 +9,7 @@
 #' @param weights Weights of observations
 #' @return \item{real}{AIC value}
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link{loglikpls}} for loglikelihood computations for plsR
 #' models and \code{\link{AIC}} for AIC computation for a linear models

R/AICpls.R

@@ -96,7 +96,7 @@
 #' \code{ncol(dataX) * 1} matrix of the coefficients of the the eXplanatory
 #' variables}
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link{PLS_glm}} for more detailed results,
 #' \code{\link{PLS_glm_kfoldcv}} for cross-validating models and
@@ -106,7 +106,7 @@
 #' logistic PLS regression with qualitative predictors: application to
 #' allelotyping data. \emph{Journal de la Societe Francaise de Statistique},
 #' 151(2), pages 1-18.
-#' \url{http://publications-sfds.math.cnrs.fr/index.php/J-SFdS/article/view/47}
+#' \url{https://www.numdam.org/item/JSFS_2010__151_2_1_0/}
 #' @keywords models regression
 #' @examples
 #' 

R/PLS_glm_wvc.R

@@ -40,7 +40,7 @@
 #' @note Use \code{\link{PLS_lm_kfoldcv}} for a wrapper in view of
 #' cross-validation.
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link{PLS_lm}} for more detailed results,
 #' \code{\link{PLS_lm_kfoldcv}} for cross-validating models and
@@ -50,7 +50,7 @@
 #' logistic PLS regression with qualitative predictors: application to
 #' allelotyping data. \emph{Journal de la Societe Francaise de Statistique},
 #' 151(2), pages 1-18.
-#' \url{http://publications-sfds.math.cnrs.fr/index.php/J-SFdS/article/view/47}
+#' \url{https://www.numdam.org/item/JSFS_2010__151_2_1_0/}
 #' @keywords models regression
 #' @examples
 #' 

R/PLS_lm_wvc.R

@@ -19,7 +19,7 @@
 #' same as the length of \code{sigmahat}.
 #' @return \item{vector}{numerical values of the requested AIC, BIC or GMDL.}
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link{plsR.dof}} for degrees of freedom computation and
 #' \code{\link{infcrit.dof}} for computing information criteria directly from a

R/aic.dof.R

@@ -41,7 +41,7 @@
 #' @return An object of class \code{"boot"}. See the Value part of the help of
 #' the function \code{\link[boot:boot]{boot}}.
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link[boot:boot]{boot}}
 #' @references A. Lazraq, R. Cleroux, and J.-P. Gauchi. (2003). Selecting both

R/bootpls.R

@@ -41,7 +41,7 @@
 #' @return An object of class \code{"boot"}. See the Value part of the help of
 #' the function \code{\link[boot:boot]{boot}}.
 #' @author Frédéric Bertrand\cr
-#' \email{frederic.bertrand@@utt.fr}\cr
+#' \email{frederic.bertrand@@lecnam.net}\cr
 #' \url{https://fbertran.github.io/homepage/}
 #' @seealso \code{\link[boot:boot]{boot}}
 #' @references A. Lazraq, R. Cleroux, and J.-P. Gauchi. (2003). Selecting both