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smped · Feb 8, 2024 · f013846 · f013846
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -54,8 +54,8 @@ jobs:
         config:
           - { os: ubuntu-latest, r: 'next', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
           ## Dockers for macOS and Windows can't handle r: 'next' at this stage
-          - { os: macOS-latest, r: 'next', bioc: 'devel'}
-          - { os: windows-latest, r: 'next', bioc: 'devel'}
+          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
+          - { os: windows-latest, r: '4.3', bioc: '3.18'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,7 +19,7 @@ Description: This package provides methods and object classes for parsing
     objects.
 URL: https://github.com/smped/ngsReports
 BugReports: https://github.com/smped/ngsReports/issues
-License: file LICENSE
+License: LGPL-3
 Encoding: UTF-8
 Depends:
   R (>= 4.2.0),
@@ -40,7 +40,6 @@ Imports:
     lubridate,
     methods,
     plotly (>= 4.9.4),
-    readr,
     reshape2,
     rlang,
     rmarkdown,
@@ -111,6 +110,7 @@ Suggests:
   DT,
   knitr,
   pander,
+  readr,
   testthat,
   truncnorm
 biocViews: QualityControl, ReportWriting

diff --git a/R/FastpData.R b/R/FastpData.R
@@ -36,19 +36,19 @@
 #' @rdname FastpData
 #' @aliases FastpData-class
 setClass(
-  "FastpData",
-  slots = c(
-    Summary = "list",
-    Adapters = "data.frame",
-    Duplication = "data.frame",
-    Insert_size = "data.frame",
-    Before_filtering = "list",
-    After_filtering = "list",
-    paired = "logical",
-    command = "character",
-    version = "character",
-    path = "character"
-  )
+    "FastpData",
+    slots = c(
+        Summary = "list",
+        Adapters = "data.frame",
+        Duplication = "data.frame",
+        Insert_size = "data.frame",
+        Before_filtering = "list",
+        After_filtering = "list",
+        paired = "logical",
+        command = "character",
+        version = "character",
+        path = "character"
+    )
 )
 setValidity("FastpData", .isValidFastpData)
 
@@ -57,28 +57,30 @@ setValidity("FastpData", .isValidFastpData)
 #' @rdname FastpData
 #' @export
 FastpData <- function(x){
-  stopifnot(!is.null(x))
-  fl <- .FastpFile(x)
-  as(fl, "FastpData")
+    stopifnot(!is.null(x))
+    fl <- .FastpFile(x)
+    as(fl, "FastpData")
 }
 
 ## The show method doesn't need exporting
 setMethod(
-  "show",
-  "FastpData",
-  function(object){
-    isPaired <- object@paired
-    reads <- object@Summary$Before_filtering$total_reads
-    cat("Source Fastp file is located in", object@path)
-    cat(
-      "\nSource Fastq file(s) contains",
-      ifelse(
-        isPaired,
-        paste(c(scales::comma(reads/2, 1), "paired-end"), collapse = " "),
-        paste(c(scales::comma(reads, 1), "single-end"), collapse = " ")
-      ),
-      "reads.\n"
-    )
-  }
+    "show",
+    "FastpData",
+    function(object){
+        isPaired <- object@paired
+        reads <- object@Summary$Before_filtering$total_reads
+        cat("Source Fastp file is located in", object@path)
+        cat(
+            "\nSource Fastq file(s) contains",
+            ifelse(
+                isPaired,
+                paste(
+                    c(scales::comma(reads/2, 1), "paired-end"), collapse = " "
+                ),
+                paste(c(scales::comma(reads, 1), "single-end"), collapse = " ")
+            ),
+            "reads.\n"
+        )
+    }
 )
 
diff --git a/R/PwfCols.R b/R/PwfCols.R
@@ -17,6 +17,8 @@
 #' @slot MAX A vector of length 1, defining the colour for an extreme FAIL or
 #' NA in rgb format. Defaults to rgb(1, 1, 1)
 #'
+#' @return An S4 object of class PwfCols
+#'
 #' @include validationFunctions.R
 #' @aliases PwfCols
 setClass("PwfCols", slots = c(
@@ -30,4 +32,4 @@ setValidity("PwfCols", .isValidPwf)
 # The default method for show. Doesn't need exporting
 setMethod("show", "PwfCols",  function(object){
     cat("An object of class PwfCols.\n")
-})
+})
diff --git a/R/estGcDistn.R b/R/estGcDistn.R
@@ -40,7 +40,7 @@
 #' @export
 #' @rdname estGcDistn
 setGeneric("estGcDistn", function(
-    x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
+        x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
     standardGeneric("estGcDistn")
 })
 #' @export
@@ -53,29 +53,28 @@ setMethod("estGcDistn", "ANY", function(x, ...){
 #' @export
 #' @rdname estGcDistn
 #' @aliases estGcDistn
-setMethod("estGcDistn", "character", function(
-    x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
+setMethod(
+    "estGcDistn", "character",
+    function(x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
 
-    stopifnot(file.exists(x))
-    errMsg <- "Supplied File not in FASTA format"
-    x <- tryCatch(
-        readDNAStringSet(x, format = "fasta"),
-        error = function(e) {stop(errMsg)}
-    )
-    estGcDistn(x, n, rl, fl, fragSd, bins)
-})
+        stopifnot(file.exists(x))
+        errMsg <- "Supplied File not in FASTA format"
+        x <- tryCatch(
+            readDNAStringSet(x, format = "fasta"),
+            error = function(e) {stop(errMsg)}
+        )
+        estGcDistn(x, n, rl, fl, fragSd, bins)
+    })
 #' @export
 #' @rdname estGcDistn
 #' @aliases estGcDistn
 setMethod("estGcDistn", "DNAStringSet", function(
-    x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
+        x, n = 1e6, rl = 100, fl = 200, fragSd = 30, bins = 101, ...) {
 
-    if (!requireNamespace("truncnorm", quietly = TRUE)){
+    if (!requireNamespace("truncnorm", quietly = TRUE)) {
         stop(
-            paste(
-                "The package truncnorm is required for this function.",
-                "Please install it using BiocManager::install('truncnorm')"
-            )
+            "The package truncnorm is required for this function.\n",
+            "Please install it using BiocManager::install('truncnorm')"
         )
     }
 

diff --git a/R/getSummary.R b/R/getSummary.R
@@ -73,9 +73,7 @@ setMethod("getSummary", ".FastqcFile", function(object){
         ## Check in case it has been deleted post-instantiation though
         fl <- file.path(path, "summary.txt")
         if (!file.exists(fl)) stop("'summary.txt' could not be found.")
-        summaryData <- suppressMessages(
-            readr::read_tsv(fl, col_names = FALSE)
-        )
+        summaryData <- utils::read.delim(fl, header = FALSE)
     }
     colnames(summaryData) <- c("Status", "Category", "Filename")
     if (!any(modules %in% summaryData$Category))