Prepare package for re-upload to CRAN

diff --git a/comments.md b/comments.md
new file mode 100644 (file)
index 0000000..14b8ba5
--- /dev/null
+++ b/comments.md
@@ -0,0 +1,14 @@
+There were 3 NOTEs:
+
+1. "New submission / Package was archived on CRAN"
+   - This version addresses all previous issues that led to archiving, at least as far as I can check (R CMD check --as-cran is OK). I forgot the previous issues.
+
+2. "checking for future file timestamps ... NOTE: unable to verify current time"
+   - This appears to be an environmental issue on my machine during check and is not a property of the package files themselves (I reset all timestamps with "find . -exec touch {} +" )
+
+3. "checking compilation flags used ... NOTE: Compilation used the following non-portable flag(s): ..."
+   - These flags are the default configuration of the R installation on my machine. They are not hardcoded in the package's src/Makevars.
+
+====
+
+The version only changes to 1.0.5 because I just added the pvalue() function to the file R/utils.R.

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index d3b5427..0fb4a38 100644 (file)
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -5,12 +5,17 @@ Description: Mixture of logistic regressions parameters (H)estimation with
     (U)spectral methods. The main methods take d-dimensional inputs and a vector
     of binary outputs, and return parameters according to the GLMs mixture model
     (General Linear Model). For more details see chapter 3 in the PhD thesis of
     (U)spectral methods. The main methods take d-dimensional inputs and a vector
     of binary outputs, and return parameters according to the GLMs mixture model
     (General Linear Model). For more details see chapter 3 in the PhD thesis of

-               Mor-Absa Loum: <https://www.theses.fr/s156435>, available here
+               Mor-Absa Loum: <https://theses.fr/s156435>, available here

                <https://theses.hal.science/tel-01877796/document>.
                <https://theses.hal.science/tel-01877796/document>.

-Version: 1.0-4
-Author: Benjamin Auder <Benjamin.Auder@u-psud.fr> [aut,cre],
-    Mor-Absa Loum <Mor-Absa.Loum@u-psud.fr> [aut]
-Maintainer: Benjamin Auder <Benjamin.Auder@u-psud.fr>
+Version: 1.0-5
+Authors@R: c(person(given = "Benjamin",
+                    family = "Auder",
+                    role = c("aut", "cre"),
+                    email = "benjamin.auder@universite-paris-saclay.fr"),
+             person(given = "Mor-Absa",
+                    family = "Loum",
+                    role = "aut",
+                    email = "morabsa.loum@univ-thies.sn"))

 Depends:
     R (>= 3.5.0),
 Imports:
 Depends:
     R (>= 3.5.0),
 Imports:


@@ -25,7 +30,7 @@ Suggests:
     testthat (>= 3.0.0),
     roxygen2
 License: MIT + file LICENSE
     testthat (>= 3.0.0),
     roxygen2
 License: MIT + file LICENSE

-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

 URL: https://github.com/yagu0/morpheus
 Collate:
     'utils.R'
 URL: https://github.com/yagu0/morpheus
 Collate:
     'utils.R'

diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 2c6f6a1..75c3ec6 100644 (file)
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -10,19 +10,9 @@ export(optimParams)
 export(plotBox)
 export(plotCoefs)
 export(plotHist)
 export(plotBox)
 export(plotCoefs)
 export(plotHist)

-importFrom(graphics,barplot)
-importFrom(graphics,boxplot)
-importFrom(graphics,hist)
-importFrom(graphics,matplot)
-importFrom(graphics,par)
+importFrom(graphics,barplot,boxplot,hist,matplot,par)

 importFrom(jointDiag,ajd)
 importFrom(methods,new)
 importFrom(pracma,integral)
 importFrom(jointDiag,ajd)
 importFrom(methods,new)
 importFrom(pracma,integral)

-importFrom(stats,integrate)
-importFrom(stats,pnorm)
-importFrom(stats,rbinom)
-importFrom(stats,rmultinom)
-importFrom(stats,rnorm)
-importFrom(stats,runif)
-importFrom(stats,sd)
+importFrom(stats,integrate,pnorm,rbinom,rmultinom,rnorm,runif,sd,pchisq,var)

 useDynLib(morpheus, .registration = TRUE)
 useDynLib(morpheus, .registration = TRUE)

diff --git a/pkg/R/A_NAMESPACE.R b/pkg/R/A_NAMESPACE.R
index ab9ea34..ebe0135 100644 (file)
--- a/pkg/R/A_NAMESPACE.R
+++ b/pkg/R/A_NAMESPACE.R
@@ -3,7 +3,7 @@
 #' @useDynLib morpheus, .registration = TRUE
 #'
 #' @importFrom jointDiag ajd
 #' @useDynLib morpheus, .registration = TRUE
 #'
 #' @importFrom jointDiag ajd

-#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate sd
+#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate sd var pchisq

 #' @importFrom graphics boxplot barplot hist par matplot
 #' @importFrom methods new
 #' @importFrom pracma integral
 #' @importFrom graphics boxplot barplot hist par matplot
 #' @importFrom methods new
 #' @importFrom pracma integral

diff --git a/pkg/R/utils.R b/pkg/R/utils.R
index e39119e..06fe25f 100644 (file)
--- a/pkg/R/utils.R
+++ b/pkg/R/utils.R
@@ -27,7 +27,8 @@ normalize <- function(x)
 #' @return The matrix of p-values (same size as mr[[1]])
 #'
 #' @examples
 #' @return The matrix of p-values (same size as mr[[1]])
 #'
 #' @examples

-#' mr <- multiRun(...) #cf ?multiRun
+#' # Next line should be a real call to multiRun()
+#' mr <- list( list(matrix(c(1,2,3,4),ncol=2),matrix(c(2,2,1,1),ncol=2)) )

 #' p <- pvalue(mr[[1]])
 #' @export
 pvalue <- function(mr)
 #' p <- pvalue(mr[[1]])
 #' @export
 pvalue <- function(mr)