r 4.0 (r-devel) changes

.Rbuildignore

@@ -32,6 +32,7 @@
 ^data-raw$
 ^doc$
 ^docs$
+^Dockerfile$
 ^icd.*\.out$
 ^icd\.Rcheck$
 ^icd_.*tar\.gz

.travis.yml

@@ -4,7 +4,7 @@ language: r
 # https://docs.travis-ci.com/user/ci-environment/
 
 # for RcppEigen to compile, (but disable if brew gcc on mac to avoid conflict)
-# fortran: true # set explicitly in each stanza
+# fortran: true # set explicitly in each stanza? but not recognized by an "include" group.
 
 # may need this for clang:
 # export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH
@@ -16,15 +16,18 @@ language: r
 #
 # https://docs.travis-ci.com/user/languages/cpp/
 
-sudo: false
+# assert the defaults for os and dist - will add macos and bionic etc. later
+os: linux
+dist: xenial
+
 cache:
   - packages
   - ccache
 
-addons:
-  apt:
-    packages:
-      - valgrind
+#addons:
+#  apt:
+#    packages:
+#      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 
 #r_packages:
@@ -36,103 +39,60 @@ cran: https://cloud.r-project.org
 r_check_args: ""
 warnings_are_errors: true
 
-# try to speed up compilation time
 before_install:
+  # - set -o allexport; source tools/env/travis-global; set +o allexport;
   # May need to set the R library directory so R CMD check finds packages
   # installed by travis (automatically, and in my scripts) and by R itself
   # https://stackoverflow.com/questions/31879011/r-cant-find-packages-installed-by-travis
   # - mkdir -p "$HOME/R.icd.lib"
   # - echo R_LIBS=$HOME/R.icd.lib:/usr/lib/R/site-library/" > ~/.Renviron
   # - sudo chmod 2777 "$HOME/R.icd.lib"
-  #
-  # Work-around r-lib/remotes bug which prevents travis building.
-  # https://github.com/r-lib/devtools/issues/2020#issuecomment-481219296
-  - Rscript -e 'source("https://install-github.me/r-lib/remotes")'
-  # ready for Makevars
   - mkdir -p ~/.R ;
-  - echo 'CXXFLAGS=-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option' >> ~/.R/Makevars ;
-  - echo 'CXX11FLAGS=-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option' >> ~/.R/Makevars ;
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then
-      echo 'CFLAGS=-O0' >> ~/.R/Makevars ;
-      echo 'CXXFLAGS=-O0' >> ~/.R/Makevars ;
-      echo 'CXX11FLAGS=-O0' >> ~/.R/Makevars ;
-      fi
-  # ignore the stubs for the pre-built vignettes, as the latex environments on
-  # travis are heterogeneous!
+  - if [[ $TRAVIS_R_VERSION_STRING == devel ]]; then cat tools/mk/travis-debug.mk >> ~/.R/Makevars; fi;
+  # this is one of oldrel, release or devel per https://docs.travis-ci.com/user/languages/r#configuration-options
+  - cat tools/mk/travis-nowarn.mk >> ~/.R/Makevars
+  # ignore the stubs for the pre-built vignettes, as the latex environments on travis are heterogeneous!
   - echo '^vignettes\/.*-vignette\.Rnw$' >> .Rbuildignore
-  # Homebrew GCC currently version 8.3 from
+
   # https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb
-  - if [[ "$(uname -s)" = 'Darwin' && x"$ICD_USE_XCODE_CLANG" != 'xtrue' ]]; then
-      brew upgrade gcc;
-      command -v g++-9 >/dev/null 2>&1 || brew install gcc && echo 'CC=gcc-9' >> ~/.R/Makevars && echo 'CXX=g++-9' >> ~/.R/Makevars && echo 'CXX11=g++-9' >> ~/.R/Makevars && Rscript -e 'install.packages("Rcpp", type = "source")';
+  # I think PKG_CXX etc only needed if Makevars in the package itself, not ~/.R/Makevars
+  # openblas may need brew linking. may be best NOT to overwrite gfortran?
+  - export HOMEBREW_NO_INSTALL_CLEANUP=1 && if [[ "$(uname -s)" = 'Darwin' ]] && [[ $ICD_USE_XCODE_CLANG != 'true' ]]; then
+      brew upgrade ;
+      brew install gcc ;
+      brew link --overwrite gcc ;
+      cat tools/mk/travis-macos.mk  >> ~/.R/Makevars ;
+      Rscript -e 'install.packages("Rcpp", type = "source")' ;
     fi
   - cat ~/.R/Makevars
   - cat .Rbuildignore
-  - Rscript -e '.libPaths()'
+  - Rscript -e '.libPaths(); getOption("repos")'
   - pwd
-  - ls -R
   # for the pre-built static vignette stubs to include the actual vignettes.
-  # Make sure travis latex option is not false for relevant builds.
-  # - Rscript -e 'if (!require("tinytex")) {quit(status=1)} else {tinytex::install_tinytex(); tinytex::tlmgr_install("pdfpages", "ae")}' || hash tlmgr 2>/dev/null && { tlmgr --usermode install pdfpages ae; }
+  # Make sure travis latex: true is set just for relevant builds. Official way to add latex packages is:
+  # before_install:
+  #   - tlmgr install index
+  # and/or? something like:
+  # - Rscript -e 'if (!require("tinytex", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)) {quit(status=1)} else {tinytex::install_tinytex(); tinytex::tlmgr_install("pdfpages", "ae")}' || hash tlmgr 2>/dev/null && { tlmgr --usermode install pdfpages ae; }
 
-env:
-  global:
-    - _R_CHECK_CRAN_INCOMING_=FALSE
-    - _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
-    - _R_CHECK_FORCE_SUGGESTS_=FALSE
-    - _R_CHECK_USE_INSTALL_LOG_=TRUE
-    - _R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
-    - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
-    - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
-    # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=FALSE
-    - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
-    # the following are to simulate cran, and
-    # help debugging if we didn't use --as-cran
-    - _R_CHECK_ALL_NON_ISO_C_=TRUE
-    - _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
-    - _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
-    - _R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
-    - _R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
-    - _R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
-    - _R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
-    - _R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
-    - _R_CHECK_RD_LINE_WIDTHS_=true
-    - _R_CHECK_TESTS_NLINES_=0
-    - _R_CHECK_USE_INSTALL_LOG_=TRUE
-    - _R_CHECK_VIGNETTES_NLINES_=0
-    - _R_CHECK_PKG_SIZES_THRESHOLD_=50
-    - ICD_COVERAGE=false
-    - ICD_MINI_BENCH=false
-    - ICD_DATA_VERBOSE=true
-    - ICD_DATA_OFFLINE=true
-    - ICD_DATA_INTERACT=false
-    # 4 is the official travis suggestion, but the docker images only seem to
-    # have access to two cores/threads.
-    - OMP_NUM_THREADS=2
+#env: #  global: instead of defining here, source tools/env/travis-global
 
-matrix:
+jobs:
   fast_finish: true
   include:
   - r: devel
-    os: linux
-    dist: xenial
-    compiler:
-      - gcc
-      - clang
+    dist: bionic
+    # note that the default compilers are quite far behind, e.g. bionic is only gcc 7 by default. See:
+    # https://docs.travis-ci.com/user/languages/c/#choosing-compilers-to-test-against
+    compiler: gcc
     env:
       - ICD_MINI_BENCH=true
   - r: release
-    os: linux
-    compiler:
-      - gcc
-      - clang
-    dist: xenial
+    compiler: clang
+    dist: bionic
     env:
       - ICD_MINI_BENCH=true
-  # https://docs.travis-ci.com/user/languages/c/#gcc-on-macos
   - r: release
-    os: linux
     compiler: gcc
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
@@ -142,48 +102,68 @@ matrix:
     - ICD_MINI_BENCH=false
     - ICD_TEST_SLOW=true
   - r: oldrel
-    os: linux
-    dist: trusty
+    compiler: gcc
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
-  # MacOS:
+  # MacOS: https://docs.travis-ci.com/user/languages/c/#gcc-on-macos
   - r: release
     os: osx
     # xcode image is needed so things like _stdio.h are available to GCC.
-    osx_image: xcode10.1
+    osx_image: xcode10.3
 #    compiler: gcc # redundant: done by logic in before_intall
-    fortran: false
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     env:
       - ICD_MINI_BENCH=true
   - r: devel
     os: osx
-    osx_image: xcode10.2
+    osx_image: xcode10.3
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
 #    compiler: gcc # redundant: done by logic in before_intall
-    fortran: false
   - r: devel
     os: osx
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     # as of May 2019, default osx image is 9.4.1
     # https://docs.travis-ci.com/user/reference/osx#xcode-version
     # compiler: clang # redundant
-    fortran: true
     env: ICD_USE_XCODE_CLANG=true
   - r: release
     os: osx
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     # compiler: clang # redundant
-    fortran: true
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
     env:
     - ICD_USE_XCODE_CLANG=true
     - ICD_MINI_BENCH=true
+  - r: release
+    arch: arm64
+    r_build_args: --no-build-vignettes --no-manual --resave-data=no
+    r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
+    env:
+    - ICD_MINI_BENCH=true
+    - ICD_TEST_SLOW=true
   allow_failures:
   # allow any osx to fail for now: error prone tool chain
   - os: osx
+  - arch: arm64
+  - arch: ppc64le
+  - arch: s390x
   - r: oldrel
   - r: release
-    os: linux
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
@@ -193,6 +173,14 @@ matrix:
     - ICD_TEST_SLOW=true
 
 before_script:
+# n.b., before_install bash exports are not preserved beyond each shell invocation.
+ - set -o allexport; source tools/env/travis-global; set +o allexport;
+ - set
+ - echo "$LD_LIBRARY_PATH"
+# qpdf debugging start
+ - which qpdf || true
+ - which gs || true
+# qpdf debugging end
  - if [ x"$ICD_TEST_SLOW" = x"true" ]; then
      Rscript -e 'source("tools/split-tests.R"); testthat_split();';
    fi

DESCRIPTION

@@ -71,6 +71,7 @@ LinkingTo:
     RcppEigen
 VignetteBuilder: 
     knitr
+Biarch: true
 Classification/ACM-2012: Social and professional topics~Medical
     records, Applied computing~Health care information systems, Applied
     computing~Health informatics, Applied computing~Bioinformatics
@@ -79,4 +80,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0

NAMESPACE

@@ -161,6 +161,7 @@ export(as.icd_long_data)
 export(as.icd_short_diag)
 export(as.icd_wide_data)
 export(as.short_diag)
+export(categorize_simple)
 export(chapters_to_map)
 export(charlson)
 export(charlson_from_comorbid)

R/categorize.R

@@ -35,6 +35,7 @@
 #' u$icd10 <- decimal_to_short(u$icd10)
 #' j <- icd:::categorize_simple(u, m, id_name = "case", code_name = "icd10")
 #' @keywords internal
+#' @export
 categorize_simple <- function(x,
                               map,
                               id_name,

R/cim-10-fr.R

@@ -8,7 +8,7 @@
       "https://www.atih.sante.fr",
       "plateformes-de-transmission-et-logiciels",
       "logiciels-espace-de-telechargement",
-      "telecharger/gratuit/11616/456"
+      "telecharger/gratuit/13332/456"
     ),
     file_name = "LIBCIM10MULTI.TXT",
     dl_msg = "Working on ICD-10-FR (CIM-10-FR)",

R/icd10be.R

@@ -6,7 +6,7 @@
                             ...) {
   site_file_2017 <-
     "fy2017_reflist_icd-10-be.xlsx_last_updatet_28-07-2017_1.xlsx"
-  fnp <- .download_to_data_raw(
+  fnp <- .download_to_data_cache(
     paste(.icd10be_site,
       .icd10be_url_path,
       site_file_2017,
@@ -28,7 +28,7 @@
   }
   site_file <- "fy2014_reflist_icd-10-be.xlsx"
   .msg("Downloading or getting cached icd10be2014 data")
-  .download_to_data_raw(
+  .download_to_data_cache(
     paste(.icd10be_site,
       .icd10be_url_path,
       site_file,
@@ -58,7 +58,7 @@
 #' \url{https://www.health.belgium.be/sites/default/files/uploads/fields/fpshealth_theme_file/fy2017_reflist_icd-10-be.xlsx_last_updatet_28-07-2017_1.xlsx}
 # nolint end
 #' \url{https://www.health.belgium.be/fr/fy2014reflisticd-10-bexlsx}
-#' @param ... passed to \code{.download_to_data_raw}, e.g., \code{offline =
+#' @param ... passed to \code{.download_to_data_cache}, e.g., \code{offline =
 #'   FALSE}.
 #' @seealso \code{link{parse_icd10be2014_be}}
 #' @keywords internal
@@ -133,7 +133,7 @@
 #'   \url{https://www.health.belgium.be/fr/sante/organisation-des-soins-de-sante/hopitaux/systemes-denregistrement/icd-10-be}
 # nolint end
 #'    \url{https://www.health.belgium.be/fr/fy2014reflisticd-10-bexlsx}
-#' @param ... passed to \code{.download_to_data_raw}, e.g., \code{offline =
+#' @param ... passed to \code{.download_to_data_cache}, e.g., \code{offline =
 #'   FALSE}.
 #' @seealso \code{link{parse_icd10be2014_be}}
 #' @keywords internal

R/util-file.R

@@ -121,7 +121,7 @@
 #' @param url URL of a zip file
 #' @param file_name file name of the resource within the zip file
 #' @param save_path file path to save the first file from the zip
-#' @param insecure Logical value, wil disable certificate check which fails on
+#' @param insecure Logical value, will disable certificate check which fails on
 #'   some platforms for some ICD data from CDC and CMS, probably because of TLS
 #'   version or certificate key length issues. Default is \code{TRUE}.
 #' @param ... additional arguments passed to \code{utils::download.file}

R/util.R

@@ -398,7 +398,8 @@ capitalize_first <- function(x) {
 #' @noRd
 #' @keywords internal
 get_raw_data_dir <- function() {
-  system.file("data-raw", package = "icd")
+  # use mustWork = TRUE to throw an error if the directory is not found
+  system.file("data-raw", package = "icd", mustWork = TRUE)
 }
 
 .stopifnot_year <- function(year) {

R/who.R

@@ -19,7 +19,7 @@
   # memoise package has given me problems and crashes. DIY
   mem_file_name <- paste(
     "WHO", year, lang,
-    gsub("JsonGetChildrenConcepts\\?ConceptId=|&useHtml=false", "", resource),
+    gsub("JsonGetChildrenConcepts\\?ConceptId=|(&|\\?)useHtml=false", "", resource),
     "json",
     sep = "."
   )
@@ -70,8 +70,7 @@
       )
     }
   } # end 400+
-  json_data <- rawToChar(http_response$content)
-  jsonlite::fromJSON(json_data)
+  httr::content(http_response, simplifyDataFrame=TRUE)
 }
 
 #' Use WHO API to discover chapters
@@ -91,7 +90,7 @@
 }
 
 #' Get the children of a concept (ICD-10 chapter, code or range)
-#' @param concept_id NULl for root, concept string for any leaf or intermediate.
+#' @param concept_id NULL for root, concept string for any leaf or intermediate.
 #' @examples
 #' .dl_icd10who_children("XXII")
 #' .dl_icd10who_children("U84")

appveyor.yml

@@ -36,6 +36,7 @@ build_script:
 
 environment:
   # APPVEYOR_CACHE_SKIP_RESTORE: true
+  R_REMOTES_STANDALONE: true
   WARNINGS_ARE_ERRORS: 1
   _R_CHECK_EXIT_ON_FIRST_ERROR_: true
   USE_RTOOLS: true