Fixed mclapply error on Windows

.Rbuildignore

@@ -1,2 +1,4 @@
+^Meta$
+^doc$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.gitignore

@@ -1,3 +1,5 @@
+Meta
+doc
 .Rproj.user
 .Rhistory
 .RData

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: proteus
 Type: Package
 Title: Downstream analysis of the MaxQuant output
-Version: 0.2.10
+Version: 0.2.11
 Depends: R (>= 3.4)
 Authors@R: c(
   person("Marek", "Gierlinski", email="[email protected]", role=c("aut", "cre")),

R/func.R

@@ -258,9 +258,11 @@ readColumnNames <- function(file) {
 #' @return Data frame with selected columns from the evidence file.
 #'
 #' @examples
+#' \dontrun{
 #' library(proteusLabelFree)
 #' evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
 #' evi <- readEvidenceFile(evidenceFile)
+#' }
 #'
 #' @export
 readEvidenceFile <- function(file, measure.cols=measureColumns, data.cols=evidenceColumns, zeroes.are.missing=TRUE) {
@@ -446,9 +448,11 @@ parameterString <- function(...) {
 #'   metadata.
 #'
 #' @examples
+#' \dontrun{
 #' library(proteusLabelFree)
 #' data(proteusLabelFree)
 #' pepdat <- makePeptideTable(evi, meta, ncores=2)
+#' }
 #'
 #' @export
 makePeptideTable <- function(evi, meta, sequence.col=c("sequence", "modified_sequence"),
@@ -460,6 +464,12 @@ makePeptideTable <- function(evi, meta, sequence.col=c("sequence", "modified_seq
   protein.col <- match.arg(protein.col)
   experiment.type <- match.arg(experiment.type)
 
+  # mclapply doesn't work on Windows, so force 1 core
+  if(Sys.info()[['sysname']] == "Windows") {
+    ncores <- 1
+    warning("Multicore processing not available in Windows. Using ncores=1")
+  }
+
   # check if measure.cols, sequence.col and protein.col are in the evidence file
   measures <- names(measure.cols)
   for(col in c(measures, sequence.col, protein.col)) {
@@ -605,6 +615,12 @@ makeProteinTable <- function(pepdat, aggregate.fun=aggregateHifly, ...,
                              min.peptides=2, ncores=4) {
   if(!is(pepdat, "proteusData")) stop ("Input data must be of class proteusData.")
 
+  # mclapply doesn't work on Windows, so force 1 core
+  if(Sys.info()[['sysname']] == "Windows") {
+    ncores <- 1
+    warning("Multicore processing not available in Windows. Using ncores=1")
+  }
+
   meta <- pepdat$metadata
   tab <- pepdat$tab
 

vignettes/proteus.Rmd

@@ -38,6 +38,7 @@ data(proteusLabelFree)
 Here is a minimal example of data analysis in *Proteus*. You will need the evidence file from *MaxQuant* and a very simple text file with metadata  (see below how to create it). Then, you can get from the evidence file to differential expression in just a few steps.
 
 ```{r quick_start, eval=FALSE}
+library(proteus)
 evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
 metadataFile <- system.file("extdata", "metadata.txt", package="proteusLabelFree")