test no drop

.github/workflows/check-bioc.yml

@@ -247,8 +247,8 @@ jobs:
         run: |
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
-              args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-build-vignettes", "--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              args = c("--no-manual", "--timings", "--no-vignettes", "--ignore-vignettes"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data", "--no-build-vignettes"),
               error_on = "warning",
               check_dir = "check"
           )

.gitignore

@@ -41,3 +41,5 @@ doc
 Meta
 .Rproj.user
 FRASER_output
+/doc/
+/Meta/

DESCRIPTION

@@ -28,7 +28,7 @@ biocViews:
 License: MIT + file LICENSE
 URL: https://github.com/gagneurlab/FRASER
 BugRepots: https://github.com/gagneurlab/FRASER/issues
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 VignetteBuilder: knitr
 Depends:

R/AllGenerics.R

@@ -236,12 +236,12 @@ setReplaceMethod("nonSplicedReads", "FraserDataSet", function(object, value){
 #' @return A subsetted \code{FraserDataSet} object
 #' @examples
 #'     fds <- createTestFraserDataSet()
-#'     fds[1:10,2:3,,drop=FALSE]
-#'     fds[,samples(fds) %in% c("sample1", "sample2"),,drop=FALSE]
-#'     fds[1:10,by="ss",,drop=FALSE]
+#'     fds[1:10,2:3]
+#'     fds[,samples(fds) %in% c("sample1", "sample2")]
+#'     fds[1:10,by="ss"]
 #'
 #' @rdname subset
-subset.FRASER <- function(x, i, j, by=c("j", "ss"), drop = FALSE){
+subset.FRASER <- function(x, i, j, by=c("j", "ss"), drop=FALSE){
     if(length(by) == 1){
         by <- whichReadType(x, by)
     }
@@ -673,7 +673,7 @@ FRASER.results <- function(object, sampleIDs, fdrCutoff, zscoreCutoff,
         ans <- lapply(seq_along(sampleChunks), function(idx){
             message(date(), ": Process chunk: ", idx, " for: ", type)
             sc <- sampleChunks[[idx]]
-            tmp_x <- object[,sc,,drop=FALSE]
+            tmp_x <- object[,sc]
 
             # extract values
             rawCts       <- as.matrix(K(tmp_x))
@@ -865,7 +865,7 @@ mapSeqlevels <- function(fds, style="UCSC", ...){
         nonSplicedReads(fds) <- keepStandardChromosomes(nonSplicedReads(fds))
         validObject(fds)
     }
-    fds <- fds[as.vector(seqnames(fds)) %in% names(mappings),,,drop=FALSE]
+    fds <- fds[as.vector(seqnames(fds)) %in% names(mappings),]
 
     seqlevels(fds) <- as.vector(mappings)
     seqlevels(nonSplicedReads(fds)) <- as.vector(mappings)

R/countRNAseqData.R

@@ -231,7 +231,7 @@ getSplitReadCountsForAllSamples <- function(fds, NcpuPerSample=1,
                     "remove this folder: \n", outDir)
             # create summarized object for counts
             h5 <- saveAsHDF5(fds, "rawCountsJ", 
-                            assay(splitCounts)[,samples(fds),drop=FALSE])
+                            assay(splitCounts)[,samples(fds)])
             colnames(h5) <- samples(fds)
             final_splitCounts <- SummarizedExperiment(
                 colData=colData(fds),
@@ -337,7 +337,7 @@ getNonSplitReadCountsForAllSamples <- function(fds, splitCountRanges,
                     "the non-split reads again, use the option recount=TRUE ",
                     "or remove this folder: \n", outDir)
             h5 <- saveAsHDF5(fds, "rawCountsSS",
-                                assay(siteCounts)[,samples(fds), drop=FALSE])
+                                assay(siteCounts)[,samples(fds)])
             colnames(h5) <- samples(fds)
             final_nonSplicedCounts <- SummarizedExperiment(
                 colData=colData(fds),
@@ -459,8 +459,8 @@ getSplitCountCacheFile <- function(sampleID, settings){
 #' @export
 countSplitReads <- function(sampleID, fds, NcpuPerSample=1, genome=NULL, 
                     recount=FALSE, keepNonStandardChromosomes=TRUE,
-                    bamfile=bamFile(fds[,sampleID,,drop=FALSE]),
-                    pairedend=pairedEnd(fds[,sampleID,,drop=FALSE]),
+                    bamfile=bamFile(fds[,sampleID]),
+                    pairedend=pairedEnd(fds[,sampleID]),
                     strandmode=strandSpecific(fds),
                     cacheFile=getSplitCountCacheFile(sampleID, fds),
                     scanbamparam=scanBamParam(fds),
@@ -856,11 +856,11 @@ countNonSplicedReads <- function(sampleID, splitCountRanges, fds,
     }
 
 
-    bamFile <- bamFile(fds[,samples(fds) == sampleID,,drop=FALSE])[[1]]
+    bamFile <- bamFile(fds[,samples(fds) == sampleID])[[1]]
 
     # unstranded case: for counting only non spliced reads we 
     # skip this information
-    isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID,,drop=FALSE])[[1]]
+    isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID])[[1]]
     doAutosort <- isPairedEnd
 
     # check cache if available

src/Makevars

@@ -1,4 +1,4 @@
-CXX_STD = CXX11
+# CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,4 +1,4 @@
-CXX_STD = CXX11
+# CXX_STD = CXX11
 
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)