From: Benjamin Auder <benjamin.auder@somewhere>
Date: Thu, 19 Apr 2018 08:21:16 +0000 (+0200)
Subject: Adjustments to pass R CMD check --as-cran
X-Git-Url: https://git.auder.net/%7B%7B%20asset%28%27mixstore/css/user/doc/pieces/%7B%7B%20pkg.url%20%7D%7D?a=commitdiff_plain;h=cf673dee64ab0ce02ccaaba0fb63a9a4589ee8aa;p=morpheus.git

Adjustments to pass R CMD check --as-cran
---

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index eb5e6f6..e1050a3 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -16,6 +16,7 @@ Imports:
     methods,
     pracma
 Suggests:
+    devtools,
     flexmix,
     parallel,
     testthat,
diff --git a/pkg/R/A_NAMESPACE.R b/pkg/R/A_NAMESPACE.R
index ea2711e..0a45138 100644
--- a/pkg/R/A_NAMESPACE.R
+++ b/pkg/R/A_NAMESPACE.R
@@ -3,8 +3,8 @@
 #' @useDynLib morpheus
 #'
 #' @importFrom jointDiag ajd
-#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate
-#' @importFrom graphics boxplot barplot hist par
+#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate sd
+#' @importFrom graphics boxplot barplot hist par matplot
 #' @importFrom methods new
 #' @importFrom pracma integral
 #'
diff --git a/pkg/R/multiRun.R b/pkg/R/multiRun.R
index 0a2a833..1cebaab 100644
--- a/pkg/R/multiRun.R
+++ b/pkg/R/multiRun.R
@@ -11,6 +11,7 @@
 #' @param prepareArgs Prepare arguments for the functions inside estimParams
 #' @param N Number of runs
 #' @param ncores Number of cores for parallel runs (<=1: sequential)
+#' @param agg Aggregation method (default: lapply)
 #' @param verbose TRUE to indicate runs + methods numbers
 #'
 #' @return A list of nf aggregates of N results (matrices).
diff --git a/pkg/R/optimParams.R b/pkg/R/optimParams.R
index 9185efb..1ef1494 100644
--- a/pkg/R/optimParams.R
+++ b/pkg/R/optimParams.R
@@ -56,11 +56,6 @@ optimParams = function(K, link=c("logit","probit"), optargs=list())
 		M <- computeMoments(optargs$X,optargs$Y)
 	}
 
-	# TODO: field?!
-	exactComp <<- optargs$exact
-	if (is.null(exactComp))
-		exactComp <<- FALSE
-
 	# Build and return optimization algorithm object
 	methods::new("OptimParams", "li"=link, "M1"=as.double(M[[1]]),
 		"M2"=as.double(M[[2]]), "M3"=as.double(M[[3]]), "K"=as.integer(K))
@@ -249,6 +244,8 @@ setRefClass(
 	# link="probit"; order=2; λ=c(531.8099,586.8893,523.5816); b=c(-118.512674,-3.488020,2.109969)
 	# Switch to pracma package for that (but it seems slow...)
 
+	exactComp <- FALSE #TODO: global, or argument...
+
 	if (exactComp && link == "probit")
 	{
 		# Use exact computations
diff --git a/pkg/R/plot.R b/pkg/R/plot.R
index 0097607..265f1cd 100644
--- a/pkg/R/plot.R
+++ b/pkg/R/plot.R
@@ -115,6 +115,9 @@ plotCoefs <- function(mr, params)
 #' Draw 3D map of objective function values
 #'
 #' @param N Number of starting points
+#' @param n Number of points in sample
+#' @param p Vector of proportions
+#' @param b Vector of biases
 #' @param β Regression matrix (target)
 #' @param link Link function (logit or probit)
 #'
diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R
index 539a565..3b28538 100644
--- a/pkg/tests/testthat.R
+++ b/pkg/tests/testthat.R
@@ -1,5 +1,10 @@
 library(testthat)
-#library(morpheus)
-load_all()
+
+# Locally:
+#library(devtools)
+#load_all("../")
+
+# With R CMD check:
+library(morpheus)
 
 test_check("morpheus")
diff --git a/to-cran.sh b/to-cran.sh
index b7e0ccd..16d4407 100755
--- a/to-cran.sh
+++ b/to-cran.sh
@@ -9,6 +9,7 @@ for file in `find -name *.R`; do
 	if [ -f $file ]; then
 		sed -i 's/μ/mu/g' $file
 		sed -i 's/β/beta/g' $file
+		sed -i 's/ρ/rho/g' $file
 		sed -i 's/λ/lambda/g' $file
 		sed -i 's/Σ/Sigma/g' $file
 	fi