Working on docs

Makefile

@@ -48,3 +48,7 @@ docker-check-all:
 		APHYLO_ATLAS_TEST=true \
 		R CMD check --ignore-vignettes aphylo_*.tar.gz
 
+docker-interactive:
+	podman run --mount type=bind,source=$(PWD),target=/mnt -w /mnt -it \
+		rocker/geospatial:4.4.0 bash
+

R/aphylo-package.R

@@ -72,10 +72,9 @@ release_questions <- function() {
 #' 
 #' Statistical Inference in Annotated Phylogenetic Trees
 #' 
-#' @docType package
 #' @name aphylo-package
 #' 
-NULL
+"_PACKAGE"
 
 .onLoad <- function(libname, pkgname) {
   options(

R/data-management.R

@@ -19,8 +19,8 @@
 #' \item{pseq}{Integer vector. The pruning sequence (postorder).}
 #' \item{reduced_pseq}{Integer vector. The reduced version of `pseq`.}
 #' \item{Ntips.annotated}{Integer. Number of tips with annotations.}
-#' \item{tip.type}{Binary of length [Ntip()]. 0 means duplication and 1 speciation.}
-#' \item{tip.type}{Binary of length [Nnode()]. 0 means duplication and 1 speciation.}
+#' \item{tip.type}{Binary of length [ape::Ntip()]. 0 means duplication and 1 speciation.}
+#' \item{tip.type}{Binary of length [ape::Nnode()]. 0 means duplication and 1 speciation.}
 #' 
 #' @examples 
 #' # A simple example ----------------------------------------------------------

docker/Makefile

@@ -1,13 +1,17 @@
+ifndef CNTR
+	CNTR = docker
+endif
+
 build:
-	docker build -t uscbiostats/aphylo:release -f Dockerfile . && \
-		docker build -t uscbiostats/aphylo:devel -f Dockerfile.dev .
+	$(CNTR) build -t uscbiostats/aphylo:release -f Dockerfile . && \
+		$(CNTR) build -t uscbiostats/aphylo:devel -f Dockerfile.dev .
 
 clang:
-	docker build -t uscbiostats/aphylo:clang -f Dockerfile-clang .
+	$(CNTR) build -t uscbiostats/aphylo:clang -f Dockerfile-clang .
 
 flexiblas:
-	docker build -t uscbiostats/aphylo:flexiblas -f Dockerfile.flexiblas .
+	$(CNTR) build -t uscbiostats/aphylo:flexiblas -f Dockerfile.flexiblas .
 
 push: build
-	docker push uscbiostats/aphylo:release && \
-		docker push uscbiostats/aphylo:devel
+	$(CNTR) push uscbiostats/aphylo:release && \
+		$(CNTR) push uscbiostats/aphylo:devel

inst/NEWS

@@ -1,3 +1,7 @@
+Changes in aphylo version 0.3-4
+
+-   Fixing documentation (CRAN request).
+
 Changes in aphylo version 0.3-3
 
 -   Removing C++ requirement as requested by CRAN.