Merge pull request #569 from assignUser/master

Add lintr support to super-lint

.automation/test/r/README.md

@@ -0,0 +1,13 @@
+# R Test Cases
+This folder holds the test cases for **R**.  
+
+## Additional Docs
+No Additional information is needed for this test case.
+
+## Good Test Cases
+The test cases denoted: `LANGUAGE_good_FILE.EXTENSION` are all valid, and should pass successfully when linted.
+- **Note:** They are linted utilizing the default linter rules.
+
+## Bad Test Cases
+The test cases denoted: `LANGUAGE_bad_FILE.EXTENSION` are **NOT** valid, and should trigger errors when linted.
+- **Note:** They are linted utilizing the default linter rules.

.automation/test/r/r_bad_1.r

@@ -0,0 +1,43 @@
+# Each of the default linters should throw at least one lint on this file
+
+# assignment
+# function_left_parentheses
+# closed_curly
+# commas
+# paren_brace
+f = function (x,y = 1){}
+
+# commented_code
+# some <- commented("out code")
+
+# cyclocomp
+# equals_na
+# infix_spaces
+# line_length
+# object_length
+# object_name
+# object_usage
+# open_curly
+someComplicatedFunctionWithALongCameCaseName <- function(x)
+{
+  y <- 1
+  if (1 > 2 && 2 > 3 && 3 > 4 && 4 > 5 && 5*10 > 6 && x == NA) {TRUE} else {FALSE}
+}
+
+# pipe_continuation
+# seq_linter
+# spaces_inside
+x <- 1:10
+x[ 2]
+1:length(x) %>% lapply(function(x) x*2) %>%
+  head()
+
+# single_quotes
+message('single_quotes')
+
+# spaces_left_parentheses
+# trailing_whitespace
+y <- 2 +(1:10)
+
+# trailing_blank_lines
+

.automation/test/r/r_good_1.r

@@ -0,0 +1,48 @@
+# Each of the default linters should throw at least one lint on this file
+
+# assignment
+# function_left_parentheses
+# closed_curly
+# commas
+# paren_brace
+f <- function(x, y = 1) {
+
+}
+
+# commented_code
+
+# cyclocomp
+# equals_na
+# infix_spaces
+# line_length
+# object_length
+# object_name
+# object_usage
+# open_curly
+short_snake <- function(x) {
+  y <- 1
+  y <- y^2
+  if (1 > 2 && 5 * 10 > 6 && is.na(x)) {
+    TRUE
+  } else {
+    FALSE
+  }
+}
+
+# pipe_continuation
+# seq_linter
+# spaces_inside
+x <- 1:10
+x[2]
+seq_len(x) %>%
+  lapply(function(x) x * 2) %>%
+  head()
+
+# single_quotes
+message("single_quotes")
+
+# spaces_left_parentheses
+# trailing_whitespace
+y <- 2 + (1:10)
+
+# trailing_blank_lines

.github/linters/.lintr

@@ -0,0 +1 @@
+linters: with_defaults(object_usage_linter = NULL)

Dockerfile

@@ -15,6 +15,7 @@ FROM yoheimuta/protolint:v0.26.0 as protolint
 FROM koalaman/shellcheck:v0.7.1 as shellcheck
 FROM wata727/tflint:0.19.0 as tflint
 FROM hadolint/hadolint:latest-alpine as dockerfile-lint
+FROM assignuser/lintr-lib:latest as lintr-lib
 
 ##################
 # Get base image #
@@ -60,7 +61,7 @@ RUN apk add --update --no-cache \
     go \
     icu-libs \
     jq \
-    libc-dev libxml2-utils \
+    libc-dev libxml2-dev libxml2-utils \
     make \
     musl-dev \
     npm nodejs-current \
@@ -69,6 +70,7 @@ RUN apk add --update --no-cache \
     php7 php7-phar php7-json php7-mbstring php-xmlwriter \
     php7-tokenizer php7-ctype php7-curl php7-dom php7-simplexml \
     py3-setuptools \
+    R \
     readline-dev \
     ruby ruby-dev ruby-bundler ruby-rdoc \
     gnupg 
@@ -240,6 +242,12 @@ RUN wget --tries=5 https://github.com/cvega/luarocks/archive/v3.3.1-super-linter
 
 RUN luarocks install luacheck
 
+#################
+# Install lintr #
+#################
+COPY --from=lintr-lib /usr/lib/R/library/ /home/r-library
+RUN R -e "install.packages(list.dirs('/home/r-library',recursive = FALSE), repos = NULL, type = 'source')"
+
 ###########################################
 # Load GitHub Env Vars for GitHub Actions #
 ###########################################
@@ -294,6 +302,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
     VALIDATE_PYTHON=${VALIDATE_PYTHON} \
     VALIDATE_PYTHON_PYLINT=${VALIDATE_PYTHON_PYLINT} \
     VALIDATE_PYTHON_FLAKE8=${VALIDATE_PYTHON_FLAKE8} \
+    VALIDATE_R=${VALIDATE_R} \
     VALIDATE_RAKU=${VALIDATE_RAKU} \
     VALIDATE_RUBY=${VALIDATE_RUBY} \
     VALIDATE_STATES=${VALIDATE_STATES} \

README.md

@@ -68,6 +68,7 @@ Developers on **GitHub** can call the **GitHub Action** to lint their code base
 | **PowerShell**                   | [PSScriptAnalyzer](https://github.com/PowerShell/Psscriptanalyzer)                                                                                                       |
 | **Protocol Buffers**             | [protolint](https://github.com/yoheimuta/protolint)                                                                                                                      |
 | **Python3**                      | [pylint](https://www.pylint.org/) [flake8](https://flake8.pycqa.org/en/latest/)                                                                                          |
+| **R**                            | [lintr](https://github.com/jimhester/lintr)                                                                                                                              |
 | **Raku**                         | [raku](https://raku.org)                                                                                                                                                 |
 | **Ruby**                         | [RuboCop](https://github.com/rubocop-hq/rubocop)                                                                                                                         |
 | **Shell**                        | [Shellcheck](https://github.com/koalaman/shellcheck)                                                                                                                     |
@@ -224,6 +225,7 @@ But if you wish to select or exclude specific linters, we give you full control
 | **VALIDATE_PYTHON_PYLINT**       | `true`                | Flag to enable or disable the linting process of the Python language. (Utilizing: pylint)                                                                                        |
 | **VALIDATE_PYTHON_FLAKE8**       | `true`                | Flag to enable or disable the linting process of the Python language. (Utilizing: flake8)                                                                                        |
 | **VALIDATE_POWERSHELL**          | `true`                | Flag to enable or disable the linting process of the Powershell language.                                                                                                        |
+| **VALIDATE_R**                   | `true`                | Flag to enable or disable the linting process of the R language.                                                                                                        |
 | **VALIDATE_RAKU**                | `true`                | Flag to enable or disable the linting process of the Raku language.                                                                                                              |
 | **VALIDATE_RUBY**                | `true`                | Flag to enable or disable the linting process of the Ruby language.                                                                                                              |
 | **VALIDATE_STATES**              | `true`                | Flag to enable or disable the linting process for AWS States Language.                                                                                                           |

TEMPLATES/.lintr

@@ -0,0 +1 @@
+linters: with_defaults(object_usage_linter = NULL)

docs/disabling-linters.md

@@ -42,6 +42,7 @@ For some linters it is also possible to override rules on a case by case level w
   - [Protocol Buffers](#protocol-buffers)
   - [Python3 pylint](#python3-pylint)
   - [Python3 flake8](#python3-flake8)
+  - [R](#r)
   - [Raku](#raku)
   - [Ruby](#ruby)
   - [Shell](#shell)
@@ -896,7 +897,40 @@ var = "terrible code down here..."
 ```
 
 ---
+## R
 
+- [lintr](https://github.com/jimhester/lintr)
+
+### lintr Config file
+
+- `.github/linters/.lintr`
+- You can pass multiple rules and overwrite default rules
+- You can use either one `.lintr` file in the root of your repository and/or additonal `.lintr` files in subdirectories. When linting a file lintr will look for config files from the file location upwards and will use the closest one.
+- Absolute paths for exclusions will not work due to the code being linted within the docker environment. Use paths relative to the `.lintr` file in which youare adding them.  
+- **Note:** The defaults adhere to the [tidyverse styleguide](https://style.tidyverse.org/)
+
+### lintr disable single line
+
+```r
+1++1/3+2 # nolint
+```
+
+### lintr disable code block
+
+```r
+ # nolint start
+ hotGarbage = 1++1/3+2
+    #a very long comment line
+ # nolint end
+```
+### lintr disable entire file
+
+Add files to exclude into the config file as  a list of filenames to exclude from linting. You can use a named item to exclude only certain lines from a file. Use paths relative to the location of the `.lintr` file.
+
+```r
+exclusions: list("inst/doc/creating_linters.R" = 1, "inst/example/bad.R", "tests/testthat/exclusions-test")
+```
+---
 ## Raku
 
 - [raku](https://raku.org)

lib/buildFileList.sh

@@ -355,6 +355,21 @@ function BuildFileList() {
       # Set the READ_ONLY_CHANGE_FLAG since this could be exec #
       ##########################################################
       READ_ONLY_CHANGE_FLAG=1
+    ####################
+    # Get the R files  #
+    ####################
+    elif [ "${FILE_TYPE}" == "r" ] || [ "${FILE_TYPE}" == "rmd" ]; then
+      ################################
+      # Append the file to the array #
+      ################################
+      FILE_ARRAY_R+=("${FILE}")
+      ##########################################################
+      # Set the READ_ONLY_CHANGE_FLAG since this could be exec #
+      ##########################################################
+      READ_ONLY_CHANGE_FLAG=1
+    ###########################
+    # Get the Terraform files #
+    ###########################
     ###########################
     # Get the Terraform files #
     ###########################

lib/linter.sh

@@ -107,6 +107,9 @@ PYTHON_PYLINT_FILE_NAME="${PYTHON_PYLINT_CONFIG_FILE:-.python-lint}"
 PYTHON_PYLINT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${PYTHON_PYLINT_FILE_NAME}" # Path to the python lint rules
 PYTHON_FLAKE8_FILE_NAME="${PYTHON_FLAKE8_CONFIG_FILE:-.flake8}"                   # Name of the file
 PYTHON_FLAKE8_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${PYTHON_FLAKE8_FILE_NAME}" # Path to the python lint rules
+# R Vars
+R_FILE_NAME='.lintr'                                                              # Name of the file
+R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}"                         # Path to the R lint rules
 # Ruby Vars
 RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}"            # Name of the file
 RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules
@@ -129,7 +132,7 @@ YAML_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${YAML_FILE_NAME}" # Path to the ya
 #######################################
 LINTER_ARRAY=('ansible-lint' 'arm-ttk' 'asl-validator' 'cfn-lint' 'checkstyle' 'clj-kondo' 'coffeelint'
   'dart' 'dockerfilelint' 'dotenv-linter' 'editorconfig-checker' 'eslint' 'flake8' 'golangci-lint'
-  'hadolint' 'htmlhint' 'jsonlint' 'ktlint' 'lua' 'markdownlint' 'npm-groovy-lint' 'perl' 'protolint'
+  'hadolint' 'htmlhint' 'jsonlint' 'ktlint' 'lintr' 'lua' 'markdownlint' 'npm-groovy-lint' 'perl' 'protolint'
   'pwsh' 'pylint' 'raku' 'rubocop' 'shellcheck' 'spectral' 'standard' 'stylelint' 'sql-lint'
   'terrascan' 'tflint' 'xmllint' 'yamllint')
 
@@ -140,7 +143,7 @@ LANGUAGE_ARRAY=('ANSIBLE' 'ARM' 'BASH' 'CLOUDFORMATION' 'CLOJURE' 'COFFEESCRIPT'
   'DART' 'DOCKERFILE' 'DOCKERFILE_HADOLINT' 'EDITORCONFIG' 'ENV' 'GO' 'GROOVY' 'HTML'
   'JAVA' 'JAVASCRIPT_ES' 'JAVASCRIPT_STANDARD' 'JSON' 'JSX' 'KOTLIN' 'LUA' 'MARKDOWN'
   'OPENAPI' 'PERL' 'PHP_BUILTIN' 'PHP_PHPCS' 'PHP_PHPSTAN' 'PHP_PSALM' 'POWERSHELL'
-  'PROTOBUF' 'PYTHON_PYLINT' 'PYTHON_FLAKE8' 'RAKU' 'RUBY' 'STATES' 'SQL' 'TERRAFORM'
+  'PROTOBUF' 'PYTHON_PYLINT' 'PYTHON_FLAKE8' 'R' 'RAKU' 'RUBY' 'STATES' 'SQL' 'TERRAFORM'
   'TERRAFORM_TERRASCAN' 'TSX' 'TYPESCRIPT_ES' 'TYPESCRIPT_STANDARD' 'XML' 'YAML')
 
 ############################################
@@ -197,6 +200,7 @@ VALIDATE_PHP_PSALM="${VALIDATE_PHP_PSALM}"                           # Boolean t
 VALIDATE_POWERSHELL="${VALIDATE_POWERSHELL}"                         # Boolean to validate language
 VALIDATE_PYTHON_PYLINT="${VALIDATE_PYTHON:-$VALIDATE_PYTHON_PYLINT}" # Boolean to validate language
 VALIDATE_PYTHON_FLAKE8="${VALIDATE_PYTHON_FLAKE8}"                   # Boolean to validate language
+VALIDATE_R="${VALIDATE_R}"                                           # Boolean to validate language
 VALIDATE_RAKU="${VALIDATE_RAKU}"                                     # Boolean to validate language
 VALIDATE_RUBY="${VALIDATE_RUBY}"                                     # Boolean to validate language
 VALIDATE_STATES="${VALIDATE_STATES}"                                 # Boolean to validate language
@@ -295,6 +299,7 @@ FILE_ARRAY_POWERSHELL=()          # Array of files to check
 FILE_ARRAY_PROTOBUF=()            # Array of files to check
 FILE_ARRAY_PYTHON_PYLINT=()       # Array of files to check
 FILE_ARRAY_PYTHON_FLAKE8=()       # Array of files to check
+FILE_ARRAY_R=()                   # Array of files to check
 FILE_ARRAY_RAKU=()                # Array of files to check
 FILE_ARRAY_RUBY=()                # Array of files to check
 FILE_ARRAY_STATES=()              # Array of files to check
@@ -375,6 +380,8 @@ ERRORS_FOUND_PYTHON_PYLINT=0            # Count of errors found
 export ERRORS_FOUND_PYTHON_PYLINT       # Workaround SC2034
 ERRORS_FOUND_PYTHON_FLAKE8=0            # Count of errors found
 export ERRORS_FOUND_PYTHON_FLAKE8       # Workaround SC2034
+ERRORS_FOUND_R=0                        # Count of errors found
+export ERRORS_FOUND_R                   # Workaround SC2034
 ERRORS_FOUND_RAKU=0                     # Count of errors found
 export ERRORS_FOUND_RAKU                # Workaround SC2034
 ERRORS_FOUND_RUBY=0                     # Count of errors found
@@ -442,6 +449,11 @@ GetLinterVersions() {
     elif [[ ${LINTER} == "protolint" ]] || [[ ${LINTER} == "editorconfig-checker" ]]; then
       # Need specific command for Protolint and editorconfig-checker
       mapfile -t GET_VERSION_CMD < <(echo "--version not supported")
+    elif [[ ${LINTER} == "lintr" ]]; then 
+      # Need specific command for lintr (--slave is deprecated in R 4.0 and replaced by --no-echo)
+      mapfile -t GET_VERSION_CMD < <(R --slave -e "r_ver <- R.Version()\$version.string; \
+                  lintr_ver <- packageVersion('lintr'); \
+                  glue::glue('lintr { lintr_ver } on { r_ver }')") 
     else
       # Standard version command
       mapfile -t GET_VERSION_CMD < <("${LINTER}" --version 2>&1)
@@ -1210,6 +1222,8 @@ GetLinterRules "POWERSHELL"
 GetLinterRules "PYTHON_PYLINT"
 # Get Python flake8 rules
 GetLinterRules "PYTHON_FLAKE8"
+# Get R rules
+GetLinterRules "R"
 # Get Ruby rules
 GetLinterRules "RUBY"
 # Get SQL rules
@@ -1688,6 +1702,25 @@ if [ "${VALIDATE_PYTHON_FLAKE8}" == "true" ]; then
   LintCodebase "PYTHON_FLAKE8" "flake8" "flake8 --config=${PYTHON_FLAKE8_LINTER_RULES}" ".*\.\(py\)\$" "${FILE_ARRAY_PYTHON_FLAKE8[@]}"
 fi
 
+################
+# R LINTING #
+################
+if [ "${VALIDATE_R}" == "true" ]; then
+  ##########################
+  # Check for local config #
+  ##########################
+  if [ ! -f "${GITHUB_WORKSPACE}/.lintr" ]; then 
+    info " "
+    info "No .lintr configuration file found, using defaults."
+    cp $R_LINTER_RULES "$GITHUB_WORKSPACE"
+  fi
+
+  ######################
+  # Lint the R files   #
+  ######################
+  LintCodebase  "R" "lintr" "lintr::lint(File)" ".*\.\(r\|R\|Rmd\|rmd\)\$" "${FILE_ARRAY_R[@]}"
+fi
+
 ################
 # RAKU LINTING #
 ################

lib/worker.sh

@@ -37,8 +37,12 @@ function LintCodebase() {
   #####################################
   # Validate we have linter installed #
   #####################################
+  # Edgecase for Lintr as it is a Package for R
+  if [[ ${LINTER_NAME} == *"lintr"* ]]; then
+    VALIDATE_INSTALL_CMD=$(command -v "R" 2>&1)
+  else
     VALIDATE_INSTALL_CMD=$(command -v "${LINTER_NAME}" 2>&1)
-
+  fi
   #######################
   # Load the error code #
   #######################
@@ -202,6 +206,23 @@ function LintCodebase() {
           cd "${GITHUB_WORKSPACE}" || exit
           ${LINTER_COMMAND} --path "${DIR_NAME}" --files "$FILE_NAME" 2>&1
         )
+      ###############################################################################
+      # Corner case for R as we have to pass it to R                                #
+      ###############################################################################
+      elif [[ ${FILE_TYPE} == "R" ]]; then
+        #######################################
+        # Lint the file with the updated path #
+        #######################################
+        if [ ! -f "${DIR_NAME}/.lintr" ]; then
+          r_dir="${GITHUB_WORKSPACE}"
+        else
+          r_dir="${DIR_NAME}"
+        fi
+        LINT_CMD=$(
+          cd "$r_dir" || exit
+          R --slave -e "errors <- lintr::lint('$FILE');print(errors);quit(save = 'no', status = if (length(errors) > 0) 1 else 0)" 2>&1 
+        )
+        #LINTER_COMMAND="lintr::lint('${FILE}')"
       else
         ################################
         # Lint the file with the rules #
@@ -285,7 +306,12 @@ function TestCodebase() {
   #####################################
   # Validate we have linter installed #
   #####################################
+  # Edgecase for Lintr as it is a Package for R
+  if [[ ${LINTER_NAME} == *"lintr"* ]]; then
+    VALIDATE_INSTALL_CMD=$(command -v "R" 2>&1)
+  else
     VALIDATE_INSTALL_CMD=$(command -v "${LINTER_NAME}" 2>&1)
+  fi
 
   #######################
   # Load the error code #
@@ -417,6 +443,17 @@ function TestCodebase() {
         cd "${GITHUB_WORKSPACE}" || exit
         ${LINTER_COMMAND} --path "${DIR_NAME}" --files "$FILE_NAME" 2>&1
       )
+    ###############################################################################
+    # Corner case for R as we have to pass it to R                                #
+    ###############################################################################
+    elif [[ ${FILE_TYPE} == "R" ]]; then
+      #######################################
+      # Lint the file with the updated path #
+      #######################################
+      LINT_CMD=$(
+        cd "${GITHUB_WORKSPACE}" || exit
+        R --slave -e "errors <- lintr::lint('$FILE');print(errors);quit(save = 'no', status = if (length(errors) > 0) 1 else 0)" 2>&1 
+      )    
     else
       ################################
       # Lint the file with the rules #
@@ -600,6 +637,7 @@ function RunTestCases() {
   TestCodebase "PROTOBUF" "protolint" "protolint lint --config_path ${PROTOBUF_LINTER_RULES}" ".*\.\(proto\)\$" "protobuf"
   TestCodebase "PYTHON_PYLINT" "pylint" "pylint --rcfile ${PYTHON_PYLINT_LINTER_RULES}" ".*\.\(py\)\$" "python"
   TestCodebase "PYTHON_FLAKE8" "flake8" "flake8 --config ${PYTHON_FLAKE8_LINTER_RULES}" ".*\.\(py\)\$" "python"
+  TestCodebase "R" "lintr" "lintr::lint()" ".*\.\(r\|rmd\)\$" "r"
   TestCodebase "RAKU" "raku" "raku -c" ".*\.\(raku\|rakumod\|rakutest\|pm6\|pl6\|p6\)\$" "raku"
   TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby"
   TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states"