Address CRAN comments

nlmixr2 · May 26, 2023 · b83b678 · b83b678
1 parent fd222f8
commit b83b678
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Showing 20 changed files with 50 additions and 32 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,4 @@
 ^docs$
 ^pkgdown$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/R/nonmem2rx.R b/R/nonmem2rx.R
@@ -508,14 +508,15 @@
 #' # a faster way to import a dataset (and allows the CRAN machines to
 #' # run a quick example)
 #' 
-#' mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE,
-#'      validate=FALSE, compress=FALSE)
+#' mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res",
+#'                 save=FALSE, validate=FALSE, compress=FALSE)
 #'
 #' \donttest{
 #'
 #' # Though by default you likely wish to validate the input
 #'
-#' mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE)
+#' mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"),
+#'                  lst=".res", save=FALSE)
 #'
 #' mod
 #'

diff --git a/R/plot.R b/R/plot.R
@@ -4,6 +4,7 @@
 #' @param page number of page(s) for the individual plots, by default
 #'   (`FALSE`) no pages are print; You can use `TRUE` for all pages to
 #'   print, or list which pages you want to print
+#' @return a ggplot2 object
 #' @inheritParams rxode2::plot.rxSolve
 #' @inheritParams ggplot2::autoplot
 #' @inheritParams ggforce::facet_wrap_paginate

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,14 @@
+> Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g.
+> \value{No return value, called for side effects} or similar) Missing Rd-tags:
+>      autoplot.nonmem2rx.Rd: \value
+
+Added value
+
+> Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies.
+> Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().
+
+Turned off saving in tests/examples/vignettes. This should fix it
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note

diff --git a/man/autoplot.nonmem2rx.Rd b/man/autoplot.nonmem2rx.Rd
diff --git a/man/nonmem2rx.Rd b/man/nonmem2rx.Rd
diff --git a/tests/testthat/test-abbrev.R b/tests/testthat/test-abbrev.R
@@ -288,8 +288,8 @@ test_that("test abbrev", {
     # test if1
     .ae("IF (EMAX>0) pope0=pope0*EXP(etae0)", "if (EMAX > 0) POPE0 <- theta1 * exp(eta1)", "pope0")
     withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{
-      .ext <- nonmem2rx(system.file("TheopdExt.ctl", package="nonmem2rx"), extended=TRUE)
-      .nonExt <- nonmem2rx(system.file("Theopd.ctl", package="nonmem2rx"))
+      .ext <- nonmem2rx(system.file("TheopdExt.ctl", package="nonmem2rx"), extended=TRUE, save=FALSE)
+      .nonExt <- nonmem2rx(system.file("Theopd.ctl", package="nonmem2rx"), save=FALSE)
       .ext1 <- sub("extended", "compare", deparse(as.function(.ext)))
       .ext2 <- sub("standard", "compare",deparse(as.function(.nonExt)))
       expect_equal(.ext1, .ext2)

diff --git a/tests/testthat/test-bauer-2019.R b/tests/testthat/test-bauer-2019.R
@@ -32,7 +32,7 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
                            nonmem2rx.extended=FALSE),{
                              lapply(files,function(x) {
                                test_that(paste(x, ", regular"), {
-                                 expect_error(nonmem2rx(system.file(x, package="nonmem2rx")), NA)
+                                 expect_error(nonmem2rx(system.file(x, package="nonmem2rx"), save=FALSE), NA)
                                })
                              })
                            })

diff --git a/tests/testthat/test-bauer-2021.R b/tests/testthat/test-bauer-2021.R
@@ -24,7 +24,7 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
                            nonmem2rx.extended=FALSE),{
                              lapply(files,function(x) {
                                test_that(paste(x, ", regular"), {
-                                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(system.file(x, package="nonmem2rx")))), NA)
+                                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(system.file(x, package="nonmem2rx"), save=FALSE))), NA)
                                })
                              })
                            })

diff --git a/tests/testthat/test-ddmore.R b/tests/testthat/test-ddmore.R
@@ -185,7 +185,7 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
                                unzip(system.file("ddmore.zip", package="nonmem2rx"))
                                lapply(files,function(x) {
                                  test_that(paste(x, ", extended"), {
-                                   expect_error(suppressMessages(suppressWarnings(nonmem2rx(x))), NA)
+                                   expect_error(suppressMessages(suppressWarnings(nonmem2rx(x, save=FALSE))), NA)
                                  })
                                })
                              })

diff --git a/tests/testthat/test-external-models.R b/tests/testthat/test-external-models.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{

diff --git a/tests/testthat/test-full-parsing.R b/tests/testthat/test-full-parsing.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressMessages(nonmem2rx(...))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressMessages(nonmem2rx(..., save=FALSE))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE,

diff --git a/tests/testthat/test-linCmt.R b/tests/testthat/test-linCmt.R
@@ -1,4 +1,4 @@
 test_that("linCmt read test(s)", {
   skip_on_cran()
-  expect_error(nonmem2rx(system.file("mods/err/run000.lst", package="nonmem2rx")), NA)
+  expect_error(nonmem2rx(system.file("mods/err/run000.lst", package="nonmem2rx"), save=FALSE), NA)
 })
diff --git a/tests/testthat/test-model-load.R b/tests/testthat/test-model-load.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{

diff --git a/tests/testthat/test-nm75.R b/tests/testthat/test-nm75.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{

diff --git a/tests/testthat/test-piping.R b/tests/testthat/test-piping.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{

diff --git a/tests/testthat/test-psn.R b/tests/testthat/test-psn.R
@@ -220,14 +220,14 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
       lapply(.files,
              function(file) {
                test_that(file, {
-                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(file, strictLst=TRUE))), NA)
+                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(file, strictLst=TRUE, save=FALSE))), NA)
                })
              })
 
       lapply(.fileError,
              function(file) {
                test_that(paste0("error for ", file), {
-                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(file, strictLst=TRUE))))
+                 expect_error(suppressMessages(suppressWarnings(nonmem2rx(file, strictLst=TRUE, save=FALSE))))
                })
              })
 

diff --git a/tests/testthat/test-read-nonmemData.R b/tests/testthat/test-read-nonmemData.R
@@ -8,17 +8,17 @@ withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.o
       file.copy(system.file("mods/cpt/Bolus_2CPT.csv", package="nonmem2rx"),
                 file.path(getwd(), "Bolus_2CPT.csv"))
 
-      f <- nonmem2rx("runODE032.ctl")
+      f <- nonmem2rx("runODE032.ctl", save=FALSE)
       expect_true(is.null(f$nonmemData))
-      f <- nonmem2rx("runODE032.ctl", nonmemData=TRUE)
+      f <- nonmem2rx("runODE032.ctl", nonmemData=TRUE, save=FALSE)
       expect_true(inherits(f$nonmemData, "data.frame"))
     })
   })
 
   test_that("read in data without phi, lower case id", {
     skip_on_cran()
-    expect_error(nonmem2rx(system.file("mods/err/run002.res", package="nonmem2rx"), lst=".res", usePhi = FALSE), NA)
-    tmp <- nonmem2rx(system.file("mods/err/run002.res", package="nonmem2rx"), lst=".res", usePhi = FALSE)
+    expect_error(nonmem2rx(system.file("mods/err/run002.res", package="nonmem2rx"), lst=".res", usePhi = FALSE, save=FALSE), NA)
+    tmp <- nonmem2rx(system.file("mods/err/run002.res", package="nonmem2rx"), lst=".res", usePhi = FALSE, save=FALSE)
     expect_true(inherits(tmp$iwresAtol, "numeric"))
     expect_true(length(tmp$iwresAtol) == 1L)
   })

diff --git a/tests/testthat/test-rename.R b/tests/testthat/test-rename.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE),{

diff --git a/tests/testthat/test-rxsolve.R b/tests/testthat/test-rxsolve.R
@@ -1,5 +1,5 @@
-.nonmem2rx <- function(...) {
-  suppressWarnings(suppressMessages(nonmem2rx(...)))
+.nonmem2rx <- function(..., save=FALSE) {
+  suppressWarnings(suppressMessages(nonmem2rx(..., save=FALSE)))
 }
 
 .rxSolve <-  function(...) {