splitting tests

NEWS.md

@@ -25,8 +25,12 @@
   `$DATA` and `$INPUT` sections based on a data set. Previously a data
   object had to be passed to the function. Now also just a path to the
   data set on file can be used.
+
 
 ## Bugfixes
+* `NMreadExt()` was incorrectly calculating blocksize for some
+  OMEGAs. Thanks to Brian Reilly for proposing a bugfix!
+
 * `mat2dt()` was doing the opposite to what was specified by the
   `triangle` argument and returned the upper triangle when
   `triangle=lower` and vice versa.
@@ -39,7 +43,7 @@
 * `dt2mat()` would only work on `data.table`s. Support for other
   `data.frame`s added.
 
-## Other improvements
+## Other minor improvements
 * `addTAPD()` has a few improvements on documentations and the following
   improvements on code. Together they imply that `by` defaults to
   `NMdataConf()$col.id`.
@@ -51,6 +55,10 @@
 * `NMcheckData()` did not check for missing (NA) values on dose
   events. Checks now capture this.
 
+* `NMgenText()` now looks up `col.flagn` using `NMdataConf()` for
+  default value.
+
+
 # NMdata 0.1.8
 
 ## New features

R/NMreadInits.R

@@ -446,5 +446,5 @@ initsToExt <- function(elements){
     pars <- pars[,.(par.type,parameter,par.name,i,j,iblock,blocksize,init,lower,upper,FIX)]
     pars <- pars[order(match(par.type,c("THETA","OMEGA","SIGMA")),i,j)]
 
-    pars
+    pars[]
 }

tests/testthat/test_NMreadInits.R

@@ -11,12 +11,15 @@ test_that("basic",{
     lines <- readLines(file.mod)
     res1 <- NMreadInits(lines=lines,return="all")
 
-    ## res1$lines[grepl("^ +$",text.before),text.before:=""]
+    res1$lines[grepl("^ +$",text.before),text.before:=""]
 
 ## cat(paste(res1$lines$text.before,collapse=":"),"\n")
 ## cat(paste(readRDS(fileRef)$lines$text.before,collapse=":"),"\n")
 
-    expect_equal_to_reference(res1,fileRef)
+    ## expect_equal_to_reference(res1,fileRef)
+    expect_equal_to_reference(res1$pars,fnAppend(fileRef,"pars"))
+    expect_equal_to_reference(res1$elements,fnAppend(fileRef,"elems"))
+    expect_equal_to_reference(res1$lines,fnAppend(fileRef,"lines"))
 
 
 })
@@ -29,7 +32,10 @@ test_that("with OMEGA block",{
     file.mod <- "testData/nonmem/xgxr133.mod"
     res1 <- NMreadInits(file=file.mod,return="all")
 
-    expect_equal_to_reference(res1,fileRef)
+    ## expect_equal_to_reference(res1,fileRef)
+    expect_equal_to_reference(res1$pars,fnAppend(fileRef,"pars"))
+    expect_equal_to_reference(res1$elements,fnAppend(fileRef,"elems"))
+    expect_equal_to_reference(res1$lines,fnAppend(fileRef,"lines"))
 
 })
 
@@ -49,5 +55,10 @@ $OMEGA  BLOCK(1) SAME")
 
     res1 <- NMreadInits(lines=text,return="all")
 
-    expect_equal_to_reference(res1,fileRef)
+    ## expect_equal_to_reference(res1,fileRef)
+    expect_equal_to_reference(res1$pars,fnAppend(fileRef,"pars"))
+    expect_equal_to_reference(res1$elements,fnAppend(fileRef,"elems"))
+    expect_equal_to_reference(res1$lines,fnAppend(fileRef,"lines"))
+
+
 })