ROBUSTNESS: Assert future (>= 1.22.1) [#101]

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: QDNAseq
-Version: 1.31.0-9000
+Version: 1.31.0-9001
 Title: Quantitative DNA Sequencing for Chromosomal Aberrations
 Depends: R (>= 3.1.0)
 Imports:
@@ -44,3 +44,4 @@ biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
 License: GPL
 URL: https://github.com/ccagc/QDNAseq
 BugReports: https://github.com/ccagc/QDNAseq/issues
+RoxygenNote: 7.1.2

NEWS

@@ -1,9 +1,12 @@
 Package: QDNAseq
 ----------------
 
-Version: 1.31.0-9000 [2021-10-27]
+Version: 1.31.0-9001 [2021-11-25]
 
- * ...
+MISCELLANEOUS:
+
+ * Now the package gives an informative error message when an outdated version
+   of the 'future' package is used.  It requires future (>= 1.22.1).
 
 
 Version: 1.31.0 [2021-10-27]

R/binReadCounts.R

@@ -193,6 +193,8 @@ binReadCounts <- function(bins, bamfiles=NULL, path=NULL, ext='bam',
         isSecondaryAlignment, isNotPassingQualityControls, isDuplicate, minMapq,
         verbose=getOption("QDNAseq::verbose", TRUE)) {
 
+    assert_future_version() ## Until future.apply (>= 1.9.0) is on CRAN
+
     binSize <- (bins$end[1L]-bins$start[1L]+1)/1000
 
     bamfile <- normalizePath(bamfile)

R/createBinAnnotations.R

@@ -65,6 +65,8 @@
 createBins <- function(bsgenome, binSize, ignoreMitochondria=TRUE,
     excludeSeqnames=NULL, verbose=getOption("QDNAseq::verbose", TRUE)) {
 
+    assert_future_version() ## Until future.apply (>= 1.9.0) is on CRAN
+
     oopts <- options("QDNAseq::verbose"=verbose)
     on.exit(options(oopts))
 

R/estimateCorrection.R

@@ -68,6 +68,8 @@ setMethod("estimateCorrection", signature=c(object="QDNAseqReadCounts"),
     adjustIncompletes=TRUE, maxIter=1, cutoff=4.0,
     variables=c("gc", "mappability"), ...,
     verbose=getOption("QDNAseq::verbose", TRUE)) {
+
+    assert_future_version() ## Until future.apply (>= 1.9.0) is on CRAN
 
     oopts <- options("QDNAseq::verbose"=verbose)
     on.exit(options(oopts))

R/segmentBins.R

@@ -98,6 +98,8 @@ setMethod("segmentBins", signature=c(object="QDNAseqCopyNumbers"),
     transformFun="log2",
     segmentStatistic="seg.mean", storeSegmentObjects=FALSE,
     ..., verbose=getOption("QDNAseq::verbose", TRUE)) {
+
+    assert_future_version() ## Until future.apply (>= 1.9.0) is on CRAN
 
     if ("seeds" %in% names(list(...))) {
       .Defunct("Argument 'seeds' (integer) is no longer supported and ignored.")

R/utils.R

@@ -14,3 +14,19 @@ suppressVerbose <- function(expr, envir = parent.frame(), suppress = TRUE) {
   res <- eval(expr, envir=envir, enclos=baseenv())
   if (res$visible) res$value else invisible(res$value)
 }
+
+
+#' @importFrom utils packageVersion
+future_version <- local({
+  ver <- NULL
+  function() {
+    if (is.null(ver)) ver <<- packageVersion("future")
+    ver
+  }
+})
+
+assert_future_version <- function() {
+  if (future_version() >= "1.22.1") return()
+  stop(sprintf("This function requires future (>= 1.22.1). Please update: %s",
+               future_version()))
+}

man/QDNAseq-package.Rd

@@ -16,12 +16,12 @@
 
 \description{
     Quantitative DNA sequencing for chromosomal aberrations.
-    The genome is divided into non-overlapping fixed-sized bins, number of
-    sequence reads in each counted, adjusted with a simultaneous
-    two-dimensional loess correction for sequence mappability and GC
-    content, and filtered to remove spurious regions in the genome.
-    Downstream steps of segmentation and calling are also implemented via
-    packages DNAcopy and CGHcall, respectively.
+The genome is divided into non-overlapping fixed-sized bins, number of
+sequence reads in each counted, adjusted with a simultaneous
+two-dimensional loess correction for sequence mappability and GC
+content, and filtered to remove spurious regions in the genome.
+Downstream steps of segmentation and calling are also implemented via
+packages DNAcopy and CGHcall, respectively.
 }
 
 \section{Details}{