fix(spectronaut): Fix spectronaut converter to account for anomaly detection updates

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+# Motivation and Context
+
+Please include relevant motivation and context of the problem along with a short summary of the solution.
+
+## Changes
+
+Please provide a detailed bullet point list of your changes.
+
+- 
+
+## Testing
+
+Please describe any unit tests you added or modified to verify your changes.
+
+## Checklist Before Requesting a Review
+- [ ] I have read the MSstats [contributing guidelines](https://github.com/Vitek-Lab/MSstatsConvert/blob/master/.github/CONTRIBUTING.md)
+- [ ] My changes generate no new warnings
+- [ ] Any dependent changes have been merged and published in downstream modules
+- [ ] I have run the devtools::document() command after my changes and committed the added files

.github/workflows/dry-run-build.yml

@@ -0,0 +1,18 @@
+name: Dry runs for PRs
+on: 
+  pull_request:
+    branches: [devel]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: devel
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Build, Install, Check
+        uses: grimbough/bioc-actions/build-install-check@v1

DESCRIPTION

@@ -31,4 +31,4 @@ BugReports: https://github.com/Vitek-Lab/MSstatsLiP/issues
 Encoding: UTF-8
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/MSstatsLiP.R

@@ -39,6 +39,6 @@
 #'   coverage.
 #' }
 #'
-#' @docType package
 #' @name MSstatsLiP
-NULL
+#' @keywords internal
+"_PACKAGE"

R/SpectronauttoMSstatsLiPFormat.R

@@ -1,7 +1,7 @@
-#' Converts raw LiP MS data from Spectronautt into the format needed for
+#' Converts raw LiP MS data from Spectronaut into the format needed for
 #' MSstatsLiP.
 #'
-#' Takes as as input both raw LiP and Trp outputs from Spectronautt.
+#' Takes as as input both raw LiP and Trp outputs from Spectronaut.
 #'
 #' @export
 #' @importFrom MSstats SpectronauttoMSstatsFormat
@@ -143,26 +143,40 @@ SpectronauttoMSstatsLiPFormat <- function(LiP.data,
 
   getOption("MSstatsLog")("INFO", "Formatting LiP data..")
   ## MSstats process
-  df.lip <- SpectronauttoMSstatsFormat(LiP.data, annotation, intensity,
-                                       filter_with_Qvalue, qvalue_cutoff,
-                                       useUniquePeptide, removeFewMeasurements,
-                                       removeProtein_with1Feature,
-                                       summaryforMultipleRows, use_log_file,
-                                       append, verbose, log_file_path = path,
-                                       base)
+  df.lip <- SpectronauttoMSstatsFormat(
+      LiP.data, 
+      annotation = annotation, 
+      intensity = intensity,
+      filter_with_Qvalue = filter_with_Qvalue,
+      qvalue_cutoff = qvalue_cutoff,
+      useUniquePeptide = useUniquePeptide,
+      removeFewMeasurements = removeFewMeasurements,
+      removeProtein_with1Feature = removeProtein_with1Feature,
+      summaryforMultipleRows = summaryforMultipleRows,
+      use_log_file = use_log_file,
+      append = append, 
+      verbose = verbose,
+      log_file_path = path
+  )
   df.lip <- as.data.table(as.matrix(df.lip))
   if (!is.null(Trp.data)){
 
     getOption("MSstatsLog")("INFO", "Formatting TrP data..")
-    df.trp <- SpectronauttoMSstatsFormat(as.data.frame(Trp.data), annotation,
-                                         intensity,
-                                         filter_with_Qvalue, qvalue_cutoff,
-                                         useUniquePeptide,
-                                         removeFewMeasurements,
-                                         removeProtein_with1Feature,
-                                         summaryforMultipleRows, use_log_file,
-                                         append, verbose, log_file_path = path,
-                                         base)
+    df.trp <- SpectronauttoMSstatsFormat(
+        as.data.frame(Trp.data), 
+        annotation = annotation, 
+        intensity = intensity,
+        filter_with_Qvalue = filter_with_Qvalue,
+        qvalue_cutoff = qvalue_cutoff,
+        useUniquePeptide = useUniquePeptide,
+        removeFewMeasurements = removeFewMeasurements,
+        removeProtein_with1Feature = removeProtein_with1Feature,
+        summaryforMultipleRows = summaryforMultipleRows,
+        use_log_file = use_log_file,
+        append = append, 
+        verbose = verbose,
+        log_file_path = path
+    )
     df.trp <- as.data.table(as.matrix(df.trp))
   }