Move some code outside \donttest{} to prevent BiocCheck() error a…

…bout missing examples
neurogenomics · Aug 10, 2024 · 9a1eb4a · 9a1eb4a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: MotifPeeker
 Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
-Version: 0.99.3
+Version: 0.99.4
 Authors@R: c( 
     person(given = "Hiranyamaya",
            family = "Dash",

diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,8 @@
 ## Miscellaneous
 
 * Switch to a smaller file to download in `check_ENCODE` example.
+* Move some code outside `\donttest{}` to prevent `BiocCheck()` error about
+  missing examples.
 
 
 # MotifPeeker 0.99.3

diff --git a/R/MotifPeeker.R b/R/MotifPeeker.R
@@ -120,28 +120,29 @@
 #' value can also reduce the runtime significantly.
 #' 
 #' @examples
-#' \donttest{
-#'     peaks <- list(
-#'         system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
-#'               package = "MotifPeeker"),
-#'         system.file("extdata", "CTCF_TIP_peaks.narrowPeak",
+#' peaks <- list(
+#'     system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
+#'                 package = "MotifPeeker"),
+#'     system.file("extdata", "CTCF_TIP_peaks.narrowPeak",
 #'                 package = "MotifPeeker")
-#'     )
+#' )
 #' 
-#'     alignments <- list(
-#'         system.file("extdata", "CTCF_ChIP_alignment.bam",
+#' alignments <- list(
+#'     system.file("extdata", "CTCF_ChIP_alignment.bam",
 #'                 package = "MotifPeeker"),
-#'         system.file("extdata", "CTCF_TIP_alignment.bam",
+#'     system.file("extdata", "CTCF_TIP_alignment.bam",
 #'                 package = "MotifPeeker")
-#'     )
+#' )
 #' 
-#'     motifs <- list(
-#'         system.file("extdata", "motif_MA1930.2.jaspar",
+#' motifs <- list(
+#'     system.file("extdata", "motif_MA1930.2.jaspar",
 #'                 package = "MotifPeeker"),
-#'         system.file("extdata", "motif_MA1102.3.jaspar",
+#'     system.file("extdata", "motif_MA1102.3.jaspar",
 #'                 package = "MotifPeeker")
-#'     )
+#' )
 #' 
+#' \donttest{
+#'     # MotifPeeker takes time to run
 #'     MotifPeeker(
 #'         peak_files = peaks,
 #'         reference_index = 1,

diff --git a/R/find_motifs.R b/R/find_motifs.R
@@ -20,8 +20,9 @@
 #' @inherit memes::runTomTom return
 #' 
 #' @examples
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#'     
 #' \donttest{
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/R/get_df_enrichment.R b/R/get_df_enrichment.R
@@ -26,25 +26,25 @@
 #' }
 #' 
 #' @examples
-#' \donttest{
-#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
-#'     data("motif_MA1102.3", package = "MotifPeeker")
-#'     data("motif_MA1930.2", package = "MotifPeeker")
-#'     input <- list(
-#'         peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'         exp_type = c("ChIP", "TIP"),
-#'         exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'         read_count = c(150, 200),
-#'         peak_count = c(100, 120)
-#'     )
-#'     segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#'     motifs <- list(
-#'         motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'         motif_labels = list("MA1930.2", "MA1102.3")
-#'     )
-#'     reference_index <- 1
+#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' data("motif_MA1102.3", package = "MotifPeeker")
+#' data("motif_MA1930.2", package = "MotifPeeker")
+#' input <- list(
+#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
+#'     exp_type = c("ChIP", "TIP"),
+#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
+#'     read_count = c(150, 200),
+#'     peak_count = c(100, 120)
+#' )
+#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
+#' motifs <- list(
+#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
+#'     motif_labels = list("MA1930.2", "MA1102.3")
+#' )
+#' reference_index <- 1
 #' 
+#' \donttest{
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/R/motif_enrichment.R b/R/motif_enrichment.R
@@ -24,10 +24,10 @@
 #' to the proportion of peaks with a motif.
 #'
 #' @examples
-#' \donttest{
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
-#'     data("motif_MA1102.3", package = "MotifPeeker")
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' data("motif_MA1102.3", package = "MotifPeeker")
 #' 
+#' \donttest{
 #'     res <- motif_enrichment(
 #'         peak_input = CTCF_TIP_peaks,
 #'         motif = motif_MA1102.3,

diff --git a/R/motif_similarity.R b/R/motif_similarity.R
@@ -30,10 +30,10 @@
 #' The list is repeated for each set of comparison groups in input.
 #' 
 #' @examples
-#' \donttest{
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
-#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' 
+#' \donttest{
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/R/plot_enrichment_individual.R b/R/plot_enrichment_individual.R
@@ -24,23 +24,24 @@
 #' instead.
 #' 
 #' @examples
+#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' data("motif_MA1102.3", package = "MotifPeeker")
+#' data("motif_MA1930.2", package = "MotifPeeker")
+#' input <- list(
+#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
+#'     exp_type = c("ChIP", "TIP"),
+#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
+#'     read_count = c(150, 200),
+#'     peak_count = c(100, 120)
+#' )
+#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
+#' motifs <- list(
+#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
+#'     motif_labels = list("MA1930.2", "MA1102.3")
+#' )
+#'     
 #' \donttest{
-#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
-#'     data("motif_MA1102.3", package = "MotifPeeker")
-#'     data("motif_MA1930.2", package = "MotifPeeker")
-#'     input <- list(
-#'         peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'         exp_type = c("ChIP", "TIP"),
-#'         exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'         read_count = c(150, 200),
-#'         peak_count = c(100, 120)
-#'     )
-#'     segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#'     motifs <- list(
-#'         motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'         motif_labels = list("MA1930.2", "MA1102.3")
-#'     )
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/R/plot_enrichment_overall.R b/R/plot_enrichment_overall.R
@@ -22,23 +22,24 @@
 #' }
 #' 
 #' @examples
+#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' data("motif_MA1102.3", package = "MotifPeeker")
+#' data("motif_MA1930.2", package = "MotifPeeker")
+#' input <- list(
+#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
+#'     exp_type = c("ChIP", "TIP"),
+#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
+#'     read_count = c(150, 200),
+#'     peak_count = c(100, 120)
+#' )
+#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
+#' motifs <- list(
+#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
+#'     motif_labels = list("MA1930.2", "MA1102.3")
+#' )
+#'     
 #' \donttest{
-#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
-#'     data("motif_MA1102.3", package = "MotifPeeker")
-#'     data("motif_MA1930.2", package = "MotifPeeker")
-#'     input <- list(
-#'         peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'         exp_type = c("ChIP", "TIP"),
-#'         exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'         read_count = c(150, 200),
-#'         peak_count = c(100, 120)
-#'     )
-#'     segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#'     motifs <- list(
-#'         motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'         motif_labels = list("MA1930.2", "MA1102.3")
-#'     )
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@ style="height: 300px !important;" />
 
 [![License: GPL (\>=
 3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://cran.r-project.org/web/licenses/GPL%20(%3E=%203))
-[![](https://img.shields.io/badge/devel%20version-0.99.2-black.svg)](https://github.com/neurogenomics/MotifPeeker)
+[![](https://img.shields.io/badge/devel%20version-0.99.4-black.svg)](https://github.com/neurogenomics/MotifPeeker)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/MotifPeeker.svg)](https://github.com/neurogenomics/MotifPeeker)
 [![](https://img.shields.io/github/last-commit/neurogenomics/MotifPeeker.svg)](https://github.com/neurogenomics/MotifPeeker/commits/master)
 <br> [![R build

diff --git a/man/MotifPeeker.Rd b/man/MotifPeeker.Rd
diff --git a/man/find_motifs.Rd b/man/find_motifs.Rd
diff --git a/man/get_df_enrichment.Rd b/man/get_df_enrichment.Rd
diff --git a/man/motif_enrichment.Rd b/man/motif_enrichment.Rd
diff --git a/man/motif_similarity.Rd b/man/motif_similarity.Rd