Run examples and tests conditionally based on MEME Suite installation…

… status

NEWS.md

@@ -5,6 +5,8 @@
 * Remove `cat()` calls in functions.
 * Implement helper `check_input()` to validate input before passing them to
   other functions.
+* Run examples and tests only if MEME Suite is detected (only for functions
+which require MEME Suite).
 
 
 # MotifPeeker 0.99.5 / 0.99.6

R/MotifPeeker.R

@@ -142,6 +142,7 @@
 #' )
 #' 
 #' \donttest{
+#'     if (memes::meme_is_installed()) {
 #'     # MotifPeeker takes time to run
 #'     MotifPeeker(
 #'         peak_files = peaks,
@@ -163,6 +164,7 @@
 #'         quiet = TRUE,
 #'         verbose = FALSE
 #'     )
+#'     }
 #' }
 #' 
 #' @export

R/denovo_motifs.R

@@ -36,6 +36,7 @@
 #' associated metadata.
 #' 
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
 #'     genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
@@ -48,6 +49,7 @@
 #'                         out_dir = tempdir())
 #'     print(res[[1]]$consensus)
 #' }
+#' }
 #' @export
 denovo_motifs <- function(seqs,
                             trim_seq_width,

R/find_motifs.R

@@ -23,6 +23,7 @@
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #'     
 #' \donttest{
+#'     if (memes::meme_is_installed()) {
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
@@ -37,6 +38,7 @@
 #'                             out_dir = tempdir())
 #'         print(res2)
 #'     }
+#'     }
 #' }
 #' 
 #' @export

R/get_df_distances.R

@@ -35,6 +35,7 @@
 #' }
 #' 
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' data("motif_MA1102.3", package = "MotifPeeker")
 #' data("motif_MA1930.2", package = "MotifPeeker")
@@ -56,6 +57,7 @@
 #'                          workers = 1)
 #'     print(distances_df)
 #' }
+#' }
 #' 
 #' @family generate data.frames
 #' 

R/get_df_enrichment.R

@@ -26,6 +26,7 @@
 #' }
 #' 
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #' data("motif_MA1102.3", package = "MotifPeeker")
@@ -55,6 +56,7 @@
 #'         )
 #'     }
 #' }
+#' }
 #' 
 #' @family generate data.frames
 #' 

R/motif_enrichment.R

@@ -24,6 +24,7 @@
 #' to the proportion of peaks with a motif.
 #'
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #' data("motif_MA1102.3", package = "MotifPeeker")
 #' 
@@ -36,6 +37,7 @@
 #'     )
 #'     print(res)
 #' }
+#' }
 #'
 #' @seealso \code{\link[memes]{runAme}}
 #' 

R/motif_similarity.R

@@ -30,6 +30,7 @@
 #' The list is repeated for each set of comparison groups in input.
 #' 
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #' data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' 
@@ -49,6 +50,7 @@
 #'         print(similarity_matrices)
 #'     }
 #' }
+#' }
 #' 
 #' @export
 motif_similarity <- function(streme_out,

R/summit_to_motif.R

@@ -30,6 +30,7 @@
 #' distances for each valid peak.
 #'
 #' @examples
+#' if (memes::meme_is_installed()) {
 #' data("CTCF_TIP_peaks", package = "MotifPeeker")
 #' data("motif_MA1102.3", package = "MotifPeeker")
 #' 
@@ -40,6 +41,7 @@
 #'     genome_build = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
 #' )
 #' print(res)
+#' }
 #'
 #' @seealso \code{\link[memes]{runAme}}
 #' 

README.md

@@ -18,7 +18,7 @@ status](https://github.com/neurogenomics/MotifPeeker/workflows/rworkflows/badge.
 
 **Authors:** ***Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan
 Skene***  
-**Updated:** ***Nov-01-2024***
+**Updated:** ***Nov-04-2024***
 
 ## Introduction
 
@@ -380,12 +380,12 @@ utils::sessionInfo()
     ## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
     ## [22] munsell_0.5.1       pillar_1.9.0        RColorBrewer_1.1-3 
     ## [25] rlang_1.1.4         utf8_1.2.4          badger_0.2.4       
-    ## [28] xfun_0.48           fs_1.6.4            cli_3.6.3          
+    ## [28] xfun_0.49           fs_1.6.5            cli_3.6.3          
     ## [31] magrittr_2.0.3      rworkflows_1.0.2    digest_0.6.37      
     ## [34] grid_4.4.1          rstudioapi_0.17.1   lifecycle_1.0.4    
     ## [37] vctrs_0.6.5         evaluate_1.0.1      glue_1.8.0         
     ## [40] data.table_1.16.2   fansi_1.0.6         colorspace_2.1-1   
-    ## [43] rmarkdown_2.28      tools_4.4.1         pkgconfig_2.0.3    
+    ## [43] rmarkdown_2.29      tools_4.4.1         pkgconfig_2.0.3    
     ## [46] htmltools_0.5.8.1
 
 </details>