more fix tests and warnings

Author: lgatto

R/methods-MSnExp.R

@@ -588,7 +588,7 @@ setMethod("combineSpectra", "MSnExp", function(object, fcol = "fileIdx",
     BPPARAM <- getBpParam(object, BPPARAM = BPPARAM)
     fns <- fileNames(object)
     if (is(object, "MSnExp") && fcol == "fileIdx")
-        fData(object)$fileIdx <- fromFile(object)
+        fData(object)[, "fileIdx"] <- fromFile(object)
     objs <- split(object, fromFile(object))
     dots <- list(...)
     res <- bplapply(objs, function(z, fcol, fns, dots) {

R/utils.R

@@ -587,7 +587,7 @@ nologging <- function(object, n = 1) {
   ## removes the last n entries from
   ## object@processingData@processing
   l <- length(object@processingData@processing)
-  x <- seq(l, length = n, by = -1)
+  x <- seq(l, length.out = n, by = -1)
   object@processingData@processing <-
     object@processingData@processing[-x]
   stopifnot(length(object@processingData@processing) == (l - n))

tests/testthat/test_nadata.R

@@ -34,11 +34,11 @@ test_that("makeNAdata", {
 test_that("makeNAdata2", {
     expect_error(makeNaData2(1))
     expect_error(makeNaData2(dunkley2006))
-    expect_error(makeNaData2(dunkley2006, nRows = 1:10, nNA = 1:2))
+    expect_error(makeNaData2(dunkley2006, nRows = 1:10, nNAs = 1:2))
 
 
     tmp <- makeNaData2(dunkley2006[1:56],
-                       nRows = 1:10, nNA = 1:10,
+                       nRows = 1:10, nNAs = 1:10,
                        exclude = 1)
     expect_true(!anyNA(tmp[1, ]))
     expect_true(all(apply(exprs(tmp[-1, ]), 1, function(x) any(is.na(x)))))
@@ -48,7 +48,7 @@ test_that("makeNAdata2", {
     k <- logical(56)
     k[1] <- TRUE
     tmp <- makeNaData2(dunkley2006[1:56],
-                       nRows = 1:10, nNA = 1:10,
+                       nRows = 1:10, nNAs = 1:10,
                        exclude = k)
     expect_true(!anyNA(tmp[1, ]))
     expect_true(all(apply(exprs(tmp[-1, ]), 1, function(x) any(is.na(x)))))
@@ -57,14 +57,14 @@ test_that("makeNAdata2", {
 
     k <- featureNames(dunkley2006)[1]
     tmp <- makeNaData2(dunkley2006[1:56],
-                       nRows = 1:10, nNA = 1:10,
+                       nRows = 1:10, nNAs = 1:10,
                        exclude = k)
     expect_true(!anyNA(tmp[1, ]))
     expect_true(all(apply(exprs(tmp[-1, ]), 1, function(x) any(is.na(x)))))
     nna <- table(apply(exprs(tmp[-1, ]), 1, function(x) sum(is.na(x))))
     expect_identical(as.vector(nna), 1:10)
 
-    tmp <- makeNaData2(dunkley2006, nRows = 1:10, nNA = 1:10)
+    tmp <- makeNaData2(dunkley2006, nRows = 1:10, nNAs = 1:10)
     expect_identical(sum(is.na(exprs(tmp))), sum(1:10 * 1:10))
 })