Fix CI (#55)

.Rbuildignore

@@ -1,3 +1,4 @@
+\.git/.*$
 \.ipynb_checkpoints/.*$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.github/workflows/check-bioc.yml

@@ -83,6 +83,13 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v2
 
+      ## Setup Python and nbconvert
+      - name: Setup Python for nbconvertR
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+      - run: pip install nbconvert
+
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
@@ -201,7 +208,7 @@ jobs:
           ## This pass does not use AnVIL and will thus update any packages
           ## that have seen been updated in Bioconductor
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics

DESCRIPTION

@@ -11,7 +11,7 @@ Authors@R: c(
 	person('Carsten', 'Marr', NULL, '[email protected]', 'ctb', comment = c(ORCID = '0000-0003-2154-4552')),
 	person('Florian', 'Büttner', NULL, '[email protected]', 'ctb', comment = c(ORCID = '0000-0001-5587-6761')))
 Description: Create and plot diffusion maps.
-License: GPL
+License: GPL-3
 URL:
 	https://theislab.github.io/destiny/,
 	https://github.com/theislab/destiny/,
@@ -26,6 +26,7 @@ Imports:
     methods,
     graphics,
     grDevices,
+    grid,
     utils,
     stats,
     Matrix,

R/dpt-methods-matrix.r

@@ -24,6 +24,7 @@ NULL
 #' @rdname DPT-matrix-methods
 NULL
 
+#' @return \code{[} returns a dense matrix or (if applicable and \code{isTRUE(drop)}) a vector.
 #' @rdname DPT-matrix-methods
 #' @export
 setMethod('[', c('DPT', 'index', 'index', 'logicalOrMissing'), function(x, i, j, ..., drop = TRUE) {
@@ -68,6 +69,7 @@ setMethod('[', c('DPT', 'missing', 'missing', 'logicalOrMissing'), function(x, i
 	x[seq_len(nrow(x)), seq_len(nrow(x)), ..., drop = drop]
 })
 
+#' @return \code{[[} returns single distance value
 #' @rdname DPT-matrix-methods
 #' @export
 setMethod('[[', c('DPT', 'index', 'index'), function(x, i, j, ...) {
@@ -76,6 +78,7 @@ setMethod('[[', c('DPT', 'index', 'index'), function(x, i, j, ...) {
 	x[i, j, ...]
 })
 
+#' @return \code{nrow} and \code{ncol} return the number of cells
 #' @importFrom BiocGenerics nrow
 #' @rdname DPT-matrix-methods
 #' @export
@@ -86,6 +89,7 @@ setMethod('nrow', 'DPT', function(x) length(x@dm@d))
 #' @export
 setMethod('ncol', 'DPT', function(x) length(x@dm@d))
 
+#' @return \code{dim} returns \code{c(n_cells, n_cells)}
 #' @rdname DPT-matrix-methods
 #' @export
 setMethod('dim', 'DPT', function(x) c(nrow(x), ncol(x)))

R/projection-dist.r

@@ -9,6 +9,8 @@
 #'                  or \link[SingleCellExperiment]{SingleCellExperiment}.
 #' @param verbose   If \code{\link{TRUE}}, log additional info to the console.
 #' 
+#' @return A vector of distances each new data point has to the existing data.
+#' 
 #' @examples
 #' data(guo_norm)
 #' g2_32 <- guo_norm[, guo_norm$num_cells < 64]

README.md

@@ -12,6 +12,6 @@ An R package for diffusion maps, with additional features for large-scale and si
 builds
 ------
 
-- [![Travis](https://travis-ci.org/theislab/destiny.svg?branch=master)](https://travis-ci.org/theislab/destiny) – Travis
+- [![R-CMD-check-bioc](https://github.com/theislab/destiny/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/theislab/destiny/actions/workflows/check-bioc.yml)
 - [![Bioconductor stable](https://bioconductor.org/shields/build/release/bioc/destiny.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/destiny/) – Bioconductor stable
 - [![Bioconductor devel](https://bioconductor.org/shields/build/devel/bioc/destiny.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/) – Bioconductor devel