final tweaks before 1.2.1 submission

NAMESPACE

@@ -106,9 +106,12 @@ import(checkmate)
 importFrom(stats,aggregate)
 importFrom(stats,reshape)
 importFrom(stats,runif)
+importFrom(utils,Rprof)
+importFrom(utils,capture.output)
 importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,read.csv)
+importFrom(utils,summaryRprof)
 importFrom(utils,tail)
 importFrom(utils,unzip)
 useDynLib(icd9)

R/benchmark.R

@@ -243,6 +243,7 @@ icd9BenchComorbidParallel <- function() {
 #' importance, after correctness. R package test code is for correctness,
 #' whereas this script stresses the core functions, and looks for bottlenecks.
 #' @keywords internal
+#' @importFrom utils Rprof capture.output Rprof summaryRprof
 icd9Benchmark <- function() {
   # generate large data set: this is copied from test-ICD9.R for now...
   set.seed(1441)

R/datadocs.R

@@ -61,7 +61,6 @@ NULL
 #'   \url{http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html}
 #'    This page has versions 23 to 32 (2005 to 2014). At present, only the 2014
 #'   data is included in this package.
-#' @source \url{http://wonder.cdc.gov/wonder/help/icd.html}
 #' @source
 #' \url{http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9abb.asp}
 #' @source

R/zzz.R

@@ -39,7 +39,7 @@ install_github(\"jackwasey/icd9\")
 release_questions <- function() {
   c(
     "Have you checked all TODO comments",
-    "Is there any commented code? (lint for this now possible)",
+    "Have you removed any commented code? (lint for this now possible)",
     "Have tests been run with do_slow_tests turned on?",
     "Are there skipped tests which should be run?",
     "Do all examples look ok (not just run without errors)?",
@@ -54,7 +54,9 @@ release_questions <- function() {
     "Does every file have correct licence information?",
     "Have you linted?",
     "Does it compile and check fine on travis?",
-    "Have you checked on Windows, win_builder (if possible with configure step), Mac, Ubuntu, ASAN, and UBSAN rocker, and updated my docker image which resembles a CRAN maintainers environment?",
+    "Have you checked on Windows, win_builder (if possible with configure step),
+    Mac, Ubuntu, ASAN, and UBSAN rocker, and updated my docker image which
+    resembles a CRAN maintainers environment?",
     "Are all NOTES from R CMD check documented in cran-comments.md",
     "Have all unnecessary files been ignored in built archive? Especially thinking of autoconfigure stuff."
   )

cran-comments.md

@@ -4,15 +4,16 @@
 ## Test environments
 * Ubuntu 15.04 R 3.2.2, clang 3.6.0 and gcc 4.9.2
 * Ubuntu 12.04 (on travis-ci) R 3.2, gcc 4.6.3
-* Debian jessie in docker with UBSAN and clang, R 3.1.2
+* Debian jessie in docker with UBSAN and clang, R 3.2.2
 * Windows 7 64 bit R 3.2 with gcc from Rtools32
+* Windows 7 64 bit R 3.3 devel with gcc from Rtools33
 
-## R CMD check results
+# R CMD check results
 
 There is one note:
 
 * checking data for non-ASCII characters ... NOTE
   Note: found 14 marked Latin-1 strings
   Note: found 39 marked UTF-8 strings
 
-These are integral to included data which has accented characters in some disease names.
+These are integral to included data which have accented characters in some disease names.

icd9.Rproj

@@ -17,7 +17,7 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageInstallArgs: --force-biarch --with-keep.source --install-tests
-PackageBuildBinaryArgs: --install-tests --force-biarch
-PackageCheckArgs: --multiarch
+PackageInstallArgs: --with-keep.source --install-tests
+PackageBuildBinaryArgs: --install-tests
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,namespace

man/icd9Hierarchy.Rd

@@ -14,8 +14,6 @@ Rich text descriptions here:
    This page has versions 23 to 32 (2005 to 2014). At present, only the 2014
   data is included in this package.
 
-\url{http://wonder.cdc.gov/wonder/help/icd.html}
-
 \url{http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9abb.asp}
 
 \url{http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9cm.asp}

tests/testthat/test-comorbid.R

@@ -585,8 +585,13 @@ test_that("diff comorbid works", {
 
   expect_that(resq <- icd9DiffComorbid(quanElixComorbid, quanDeyoComorbid, show = TRUE),
               testthat::not(gives_warning()))
-  # TODO: actually do a test here?
-  utils::capture.output(resq <- icd9DiffComorbid(quanElixComorbid, quanDeyoComorbid, show = TRUE))
+
+  expect_that(
+    utils::capture.output(
+      resq <- icd9DiffComorbid(quanElixComorbid, quanDeyoComorbid, show = TRUE)
+      ),
+    testthat::not(throws_error())
+  )
 
 })