appveyor refresh

appveyor

git stuff

appveyor.yml

appveyor

appveyor

appveyor

.gitattributes

@@ -1,5 +1,9 @@
 # Auto detect text files and perform LF normalization
 * text=auto
+data/* binary
+src/* text=lf
+R/* text=lf
+tools/* text=lf
 *.rtf	 diff=astextplain
 *.RTF	 diff=astextplain
 
@@ -10,6 +14,7 @@
 *.png diff=png
 *.pdf diff=pdf
 
+## after my bug report, I think Rcpp is now more deterministic
 ## git config diff.nodiff.command /usr/bin/true or /bin/true
 # *RcppExports* diff=nodiff
 # *.Rd diff=nodiff

.gitconfig

@@ -1,6 +1,7 @@
 [diff "png"]
     textconv = identify -quiet -format "%#"
 [diff "pdf"]
+    # or consider pdftotext
     textconv = identify -quiet -format "%#"
 [diff "nodiff"]
     command = /bin/true

appveyor.yml

@@ -1,4 +1,8 @@
+# vim: set shiftwidth=2 tabstop=2 softtabstop=-1 expandtab:
 # DO NOT CHANGE the "init" and "install" sections below
+#
+# https://github.com/krlmlr/r-appveyor
+# for many environment variables to configure
 
 # Download script file from GitHub
 init:
@@ -10,55 +14,59 @@ init:
 install:
   ps: Bootstrap
 
-# temporarily disable cache if error?
 cache:
-- C:\RLibrary
-
-# Adapt as necessary starting from here
-
-platform:
-  - x86
-  - x64
+  - C:\RLibrary
 
 before_build:
-#  - ls -aR
+  - ls -aR
+  - bash tools/dump-env.sh
   - rm .Rinstignore  # do install everything for testing
   - sed -i'' -e '/.*[Dd]ata.*/d' .Rbuildignore # do include data for testing, some data not in github though
-  # make sure Rcpp generated code is made, if not checked in to repo
-  - Rscript -e "install.packages(c('remotes', 'Rcpp', 'knitr'), repos = 'https://cloud.r-project.org/'); Rcpp::compileAttributes()"
-  # temporarily used while latest icd.data is not on CRAN
-  #- Rscript -e "remotes::install_github(\"jackwasey/icd.data\", ref = \"WHO\")"
-  # CRAN of course doesn't do this, but Travis has build without nhds available
-  - Rscript -e "remotes::install_github(\"jackwasey/nhds\")"
-
-build_script:
-  - travis-tool.sh install_deps
 
 environment:
-  # APPVEYOR_CACHE_SKIP_RESTORE: true
-  WARNINGS_ARE_ERRORS: 1
+  # env vars that may need to be set, at least temporarily, from time to time
+  # see https://github.com/krlmlr/r-appveyor#readme for details
+  # USE_RTOOLS: true
+  NOT_CRAN: true
+  WARNINGS_ARE_ERRORS: 0
   _R_CHECK_EXIT_ON_FIRST_ERROR_: true
   USE_RTOOLS: true
-  R_BUILD_ARGS: ""
-  NOT_CRAN: true
+  R_BUILD_ARGS: "--no-manual --no-build-vignettes"
+  R_CHECK_ARGS: "--no-manual --ignore-vignettes --no-build-vignettes"
+  # TODO: use an environment script in tools/env
+  #_R_CHECK_FORCE_SUGGESTS_: false
   ICD_DATA_VERBOSE: true
   ICD_DATA_OFFLINE: true
   ICD_DATA_INTERACT: false
-# by default, don't set environment, to be more like CRAN?
-#  ICD_DATA_ABSENT_ACTION: 'message'
+  # KEEP_VIGNETTES: ""
+  # by default, don't set environment, to be more like CRAN?
+  #  ICD_DATA_ABSENT_ACTION: 'message'
+  #  R_REMOTES_STANDALONE: Set this to true if builds are failing due to the inability to update infrastructure packages such as curl, git2r and rlang. Read more in the docs for the remotes package.
+
   matrix:
+    - R_VERSION: patched
+      MINI_BENCH: "no"
+
     - R_VERSION: release
       MINI_BENCH: "yes"
+
     - R_VERSION: devel
+      MINI_BENCH: "no"
+
+platform:
+  - x86
+  - x64
 
 matrix:
   fast_finish: false
-#  allow_failures:
-#    - platform: x64
-#      MINI_BENCH: "yes"
-#  exclude:
-#    - platform: x86
-#      MINI_BENCH: "yes"
+  allow_failures:
+    - platform: x64
+      MINI_BENCH: "yes"
+
+build_script:
+  - travis-tool.sh install_deps
+  #- see https://github.com/craigcitro/r-travis/wiki#configuration-options
+  #- travis-tool.sh install_github r-lib/covr
 
 test_script:
   - travis-tool.sh run_tests
@@ -67,12 +75,12 @@ on_failure:
   - 7z a failure.zip *.Rcheck\*
   - appveyor PushArtifact failure.zip
 
-after_build:
-  - pwd
-  - IF NOT "%MINI_BENCH%"=="" cd benchmarks/icd-JSS3447-replication
-  - IF NOT "%MINI_BENCH%"=="" make bench3
-#  - IF NOT "%MINI_BENCH%"=="" make replmat # needs to call Rscript on appveyor path.
-  - IF NOT "%MINI_BENCH%"=="" cd ../..
+on_success:
+  - IF "%MINI_BENCH%"=="yes" cd benchmarks/icd-JSS3447-replication
+  - IF "%MINI_BENCH%"=="yes" make bench3
+    #  - IF NOT "%MINI_BENCH%"=="" make replmat # needs to call Rscript on appveyor path.
+  - IF "%MINI_BENCH%"=="yes" cd ../..
+  #- Rscript -e "covr::codecov()"
 
 artifacts:
   - path: '*.Rcheck\**\*.log'
@@ -94,11 +102,11 @@ artifacts:
     name: Bits
 
 notifications:
- - provider: Email
-   to:
-     - [email protected]
-#   subject: 'r-appveyor build {{status}}'                  # optional
-#   message: "https://ci.appveyor.com/project/krlmlr/r-appveyor"    # optional
-   on_build_success: false
-   on_build_failure: true
-   on_build_status_changed: true
+  - provider: Email
+    to:
+      - [email protected]
+        #   subject: 'r-appveyor build {{status}}'                  # optional
+        #   message: "https://ci.appveyor.com/project/krlmlr/r-appveyor"    # optional
+    on_build_success: false
+    on_build_failure: true
+    on_build_status_changed: true

tools/appveyor-yaml-check.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+ruby -ryaml -e "p YAML.load(STDIN.read)" <"${ICD_HOME?}/appveyor.yml" >/dev/null

tools/githooks/pre-commit

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-set -xu
+set -u
 declare -i ok=0
 declare -i wcres=0