reducing examples to less than 5s #26

kassambara · Feb 18, 2023 · 6542243 · 6542243
1 parent ec54581
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: fastqcr
 Type: Package
 Title: Quality Control of Sequencing Data
 Version: 0.1.3
-Date: 2023-02-17
+Date: 2023-02-18
 Authors@R: c(
  person("Alboukadel", "Kassambara", role = c("aut", "cre"), email = "[email protected]")
  )

diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,7 @@
 - Using `select()` in place of the deprecated `select_()` function in `qc_aggregate()` and `qc_problems()` (#24)
 - Using `arrange()` and `group_by()` in place of the deprecated `arrange_()` and `group_by()_` functions in `qc_problems()`
 - Changing http to https for urls concerning fastc installation and documentation
+- `qc_read_collection()` and `qc_plot_collection()` examples reduced to less than 5 seconds 
 
 ## Bug fixes
 

diff --git a/R/qc_plot_collection.R b/R/qc_plot_collection.R
@@ -28,26 +28,28 @@ NULL
 #' @examples
 # extract paths to the demo files
 #' qc.dir <- system.file("fastqc_results", package = "fastqcr")
-#' qc.files <- list.files(qc.dir, full.names = TRUE)[1:3]
+#' qc.files <- list.files(qc.dir, full.names = TRUE)[1:2]
 #' nb_samples <- length(qc.files)
 #' 
-#' # read all modules in all files
-#' qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:nb_samples, sep = ''))
+#' # read specific modules in all files
+#' # To read all modules, specify: modules = "all"
+#' modules <- c(
+#' "Per sequence GC content",
+#' "Per base sequence quality",
+#' "Per sequence quality scores"
+#' )
+#' qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:nb_samples, sep = ''),
+#' modules = modules)
 #'
 #' # Plot per sequence GC content
 #' qc_plot_collection(qc, "Per sequence GC content")
 #'
 #' # Per base sequence quality
 #' qc_plot_collection(qc, "Per base sequence quality")
-#'
+#' 
 #' # Per sequence quality scores
 #' qc_plot_collection(qc, "Per sequence quality scores")
 #'
-#' # Per base sequence content
-#' qc_plot_collection(qc, "Per base sequence content")
-#'
-#' # Sequence duplication levels
-#' qc_plot_collection(qc, "Sequence duplication levels")
 #'
 #' @export
 qc_plot_collection <- function(qc, modules = "all"){

diff --git a/R/qc_read_collection.R b/R/qc_read_collection.R
@@ -13,14 +13,12 @@
 #' @examples 
 #' # extract paths to the demo files
 #' qc.dir <- system.file("fastqc_results", package = "fastqcr")
-#' qc.files <- list.files(qc.dir, full.names = TRUE)[1:3]
+#' qc.files <- list.files(qc.dir, full.names = TRUE)[1:2]
 #' nb_samples <- length(qc.files)
 #' 
-#' # read all modules in all files
-#' qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:nb_samples, sep = ''))
-#' 
 #' 
 #' # read a specified module in all files
+#' # To read all modules, specify: modules = "all"
 #' qc <- qc_read_collection(qc.files, 
 #' sample_names = paste('S', 1:nb_samples, sep = ''),
 #' modules = "Per base sequence quality")

diff --git a/cran-comments.md b/cran-comments.md
@@ -10,6 +10,6 @@ There were no ERRORs, WARNINGs or NOTES.
 ## Downstream dependencies
 There are currently no downstream dependencies for this package
 
-## Update
+## Resubmission
 
-This is a new version fastqcr 0.1.3 (see NEWS.md)
+This is a resubmission of version fastqcr 0.1.3 (see NEWS.md). In this version all examples were reduced to less than 5 seconds to fix CRAN auto-check NOTES
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.7.3
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2023-02-17T07:09Z
+last_built: 2023-02-18T06:08Z
 
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
diff --git a/docs/reference/qc_aggregate.html b/docs/reference/qc_aggregate.html
diff --git a/docs/reference/qc_plot.html b/docs/reference/qc_plot.html
diff --git a/docs/reference/qc_plot_collection-1.png b/docs/reference/qc_plot_collection-1.png
diff --git a/docs/reference/qc_plot_collection-2.png b/docs/reference/qc_plot_collection-2.png
diff --git a/docs/reference/qc_plot_collection-3.png b/docs/reference/qc_plot_collection-3.png
diff --git a/docs/reference/qc_plot_collection.html b/docs/reference/qc_plot_collection.html
diff --git a/docs/reference/qc_problems.html b/docs/reference/qc_problems.html
diff --git a/docs/reference/qc_read.html b/docs/reference/qc_read.html