cleaning tests. quiet flagsCount.

Author: philipdelff

R/flagsCount.R

@@ -40,6 +40,7 @@
 ##'     be written if file argument is supplied.
 ##' @param flagc.0 The character flag to assign to rows that are not
 ##'     matched by exclusion conditions (numerical flag 0).
+##' @param quiet Suppress non-critical messages? Default is `FALSE`.
 ##' @param as.fun The default is to return a data.table if input data
 ##'     is a data.table, and return a data.frame for all other input
 ##'     classes. Pass a function in as.fun to convert to something
@@ -88,7 +89,9 @@ flagsCount <- function(data,tab.flags,file,col.id="ID",
                        by=NULL, flags.increasing=FALSE,
                        flagc.0="Analysis set",
                        name.all.data="All available data",
-                       grp.incomp="EVID",save=TRUE,as.fun=NULL){
+                       grp.incomp="EVID",save=TRUE,
+                       quiet=FALSE,
+                       as.fun=NULL){
 
 #### Section start: Dummy variables, only not to get NOTE's in package checks ####
 
@@ -293,7 +296,7 @@ flagsCount <- function(data,tab.flags,file,col.id="ID",
 
     if(!is.null(file)&&save){
         fwrite(allres,file=file,quote=FALSE,row.names=F)
-        cat(paste0("Table written to ",file,"\n"))
+        if(!quiet) message(paste0("Table written to ",file,"\n"))
     }
 
 

man/flagsCount.Rd

@@ -6,7 +6,7 @@ test_that("basic",{
     file.mod <- "testData/nonmem/xgxr032.mod"
 
     NMdataConf(reset=T)
-    NMdataConf(as.fun="data.table")
+    ## NMdataConf(as.fun="data.table")
 
     lines <- readLines(file.mod)
     res1 <- NMreadInits(lines=lines,return="all")
@@ -31,7 +31,7 @@ test_that("with OMEGA block",{
 })
 
 test_that("OMEGA SAME",{
-
+    NMdataConf(reset=T)
     fileRef <- "testReference/NMreadInits_03.rds"
 
     text <- c("

tests/testthat/testReference/NMreadInits_01.rds

@@ -143,7 +143,7 @@ test_that("Writing data - data.frames",{
     pk <- flagsAssign(pk,subset.data="EVID==1",flagc.0="Dosing")
 
     ## all excluded due to below LLOQ
-    tab.count <- flagsCount(pk[pk$EVID==0,],dt.flags,flags.increasing=T,file=testOut)
+    tab.count <- flagsCount(pk[pk$EVID==0,],dt.flags,flags.increasing=T,file=testOut,quiet=TRUE)
 
     testRes <- fread(testOut,header=T)
 

tests/testthat/test_NMreadInits.R

@@ -5,7 +5,7 @@ test_that("basic",{
     fileRef <- "testReference/listMissings_1.rds"
 
     pk <- readRDS(file="testData/data/xgxr2.rds")
-    miss <- listMissings(pk)
+    miss <- listMissings(pk,quiet=TRUE)
 
     expect_equal_to_reference(miss,fileRef,version=2)