Validation Report - crunch@1.31.0

Context

This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:

  • Installation environment description
  • Testing coverage

It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.

Package crunch

Metric based risk assessment

The following metrics are derived from the riskmetric R package.

has_news 0
exported_namespace 308
has_vignettes 31
export_help 508
has_website TRUE
has_maintainer Greg Freedman Ellis
bugs_status 0.9
assess_size_codebase 14596
has_source_control https://github.com/Crunch-io/rcrunch
has_bug_reports_url 1
downloads_1yr 10799
reverse_dependencies 2
has_examples 0.9722222
dependencies 8
license LGPL (>= 3)

Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.

Dependencies

Overall the package has these dependencies:

package type
1 abind Imports
2 crayon Imports
3 curl Imports
4 grDevices Imports
5 httr (>= 1.0.0) Imports
6 httpcache (>= 0.1.4) Imports
7 jsonlite (>= 0.9.15) Imports
8 methods Imports

Package dependencies

Reverse dependencies

Overall the package has 2 reverse dependencies:

crplyr, crunchy

Namespace

Overall the package has 308 exported objects. 492 are documented:

                   %ornm%        AbstractCategories          AbstractCategory 
                    FALSE                      TRUE                      TRUE 
           addGeoMetadata            addSubvariable           addSubvariables 
                     TRUE                      TRUE                      TRUE 
           addSummaryStat              addVariables            alterArrayExpr 
                     TRUE                      TRUE                      TRUE 
      alterCategoriesExpr                  analyses                  analysis 
                     TRUE                      TRUE                      TRUE 
               analysis<-             appendDataset              appendStream 
                     TRUE                      TRUE                      TRUE 
          applyTransforms                   archive              are.Headings 
                     TRUE                      TRUE                      TRUE 
            are.Subtotals          are.SummaryStats           arraySelections 
                     TRUE                      TRUE                      TRUE 
          arraySubsetExpr                asSelected          availableGeodata 
                     TRUE                      TRUE                      TRUE 
 availableGeodataFeatures                   batches                       bin 
                     TRUE                      TRUE                      TRUE 
                 caseExpr              caseWhenExpr  CategoricalArrayVariable 
                     TRUE                      TRUE                      TRUE 
      CategoricalVariable                Categories      categoriesFromLevels 
                     TRUE                      TRUE                      TRUE 
                 Category                        cd          changeCategoryID 
                     TRUE                      TRUE                      TRUE 
       checkForNewVersion            cleanseBatches        collapseCategories 
                     TRUE                      TRUE                      TRUE 
                  combine         combineCategories          combineResponses 
                     TRUE                      TRUE                      TRUE 
              compareCols       compareColsPairwise           compareDatasets 
                     TRUE                      TRUE                      TRUE 
              compareDims       compareDimsPairwise               compareRows 
                     TRUE                      TRUE                      TRUE 
      compareRowsPairwise      conditionalTransform                   consent 
                     TRUE                      TRUE                      TRUE 
           ContextManager                      copy               copyFolders 
                     TRUE                      TRUE                      TRUE 
                copyOrder              copyVariable                  crDELETE 
                     TRUE                      TRUE                      TRUE 
            createDataset createWithMetadataAndFile    createWithPreparedData 
                     TRUE                      TRUE                      TRUE 
                    crGET                   crPATCH                    crPOST 
                     TRUE                      TRUE                      TRUE 
                    crPUT                    crtabs             crunch_sitrep 
                     TRUE                      TRUE                      TRUE 
        crunch_user_agent             crunchBetween                 crunchBox 
                     TRUE                      TRUE                      TRUE 
                CrunchBox             CrunchDataset              crunchdbFunc 
                     TRUE                      TRUE                      TRUE 
           crunchDifftime           CrunchGeography                      cube 
                     TRUE                      TRUE                      TRUE 
          cubeMeasureType                     cubes                 dashboard 
                     TRUE                      TRUE                      TRUE 
              dashboard<-              DatasetGroup              DatasetOrder 
                     TRUE                      TRUE                      TRUE 
         datasetReference                  datasets                datasets<- 
                     TRUE                      TRUE                      TRUE 
                    dates          datetimeFromCols          DatetimeVariable 
                     TRUE                      TRUE                      TRUE 
                    decks                   decks<-            defaultPalette 
                     TRUE                      TRUE                      TRUE 
            deleteDataset         deleteSubvariable        deleteSubvariables 
                     TRUE                      TRUE                      TRUE 
           deleteVariable           deleteVariables               deprivatise 
                     TRUE                      TRUE                      TRUE 
     deprivatiseVariables      deprivatizeVariables               deriveArray 
                     TRUE                      TRUE                      TRUE 
          displaySettings         displaySettings<-                  dropRows 
                     TRUE                      TRUE                      TRUE 
               duplicated            embedCrunchBox               envOrOption 
                     TRUE                      TRUE                      TRUE 
                exclusion               exclusion<-             exportDataset 
                     TRUE                      TRUE                      TRUE 
               exportDeck             extendDataset                    filter 
                     TRUE                      TRUE                      TRUE 
                 filter<-              flattenOrder                flipArrays 
                     TRUE                      TRUE                      TRUE 
                   folder      forceVariableCatalog               forkDataset 
                     TRUE                      TRUE                      TRUE 
      formulaToSlideQuery   fortify.CrunchDataFrame     fortify.CrunchDataset 
                     TRUE                      TRUE                      TRUE 
                  Geodata     getAccountUserCatalog               getDimTypes 
                     TRUE                      TRUE                      TRUE 
                 getTeams                   grouped                   Heading 
                     TRUE                      TRUE                      TRUE 
          hiddenVariables         hiddenVariables<-             hideVariables 
                     TRUE                      TRUE                      TRUE 
              index.table                 Insertion                Insertions 
                     TRUE                      TRUE                      TRUE 
        interactVariables                  is.Array                     is.CA 
                     TRUE                      TRUE                      TRUE 
           is.Categorical       is.CategoricalArray             is.CrunchExpr 
                     TRUE                      TRUE                      TRUE 
               is.dataset               is.Datetime                   is.Expr 
                     TRUE                      TRUE                      TRUE 
               is.Geodata                is.Heading                     is.MR 
                     TRUE                      TRUE                      TRUE 
              is.Multiple       is.MultipleResponse                is.Numeric 
                     TRUE                      TRUE                      TRUE 
          is.NumericArray                 is.script                  is.shoji 
                     TRUE                      TRUE                      TRUE 
              is.Subtotal            is.SummaryStat                   is.Text 
                     TRUE                      TRUE                      TRUE 
                 is.valid                 is.VarDef               is.variable 
                     TRUE                      TRUE                      TRUE 
    is.VariableDefinition                 is.weight         is.weightVariable 
                     TRUE                      TRUE                      TRUE 
             joinDatasets                  jsonprep              listDatasets 
                     TRUE                      TRUE                      TRUE 
              loadDataset                      lock                     login 
                     TRUE                      TRUE                      TRUE 
                   logout                 makeArray          makeCaseVariable 
                     TRUE                      TRUE                      TRUE 
     makeCaseWhenVariable          makeDimTransform                 makeFrame 
                     TRUE                      TRUE                      TRUE 
                   makeMR            makeMRFromText                makeWeight 
                     TRUE                      TRUE                      TRUE 
       markdownSlideImage            matchCatToFeat                        me 
                     TRUE                      TRUE                      TRUE 
                mergeFork                     mkdir     modifyWeightVariables 
                     TRUE                      TRUE                      TRUE 
 MultipleResponseVariable                        mv                newDataset 
                     TRUE                      TRUE                      TRUE 
       newDatasetByColumn        newDatasetFromFile                   newDeck 
                     TRUE                      TRUE                      TRUE 
        newExampleDataset                 newFilter          newMarkdownSlide 
                     TRUE                      TRUE                      TRUE 
            newMultitable                newProject                  newSlide 
                     TRUE                      TRUE                      TRUE 
       notifyIfNewVersion              noTransforms      NumericArrayVariable 
                     TRUE                      TRUE                      TRUE 
          NumericVariable                ownerNames                    owners 
                     TRUE                      TRUE                      TRUE 
                 palettes             pendingStream               permissions 
                     TRUE                      TRUE                      TRUE 
                       pk                      pk<-              pollProgress 
                     TRUE                      TRUE                      TRUE 
        preCrunchBoxCheck      prepareDataForCrunch          privateVariables 
                     TRUE                      TRUE                      TRUE 
       privateVariables<-                 privatise        privatiseVariables 
                     TRUE                      TRUE                      TRUE 
       privatizeVariables                  projects                   publish 
                     TRUE                      TRUE                      TRUE 
                  query<-              reassignUser         removeEmptyGroups 
                     TRUE                      TRUE                      TRUE 
            resetPassword                resolution              resolution<- 
                     TRUE                      TRUE                      TRUE 
           restoreVersion                     rmdir                    rollup 
                     TRUE                      TRUE                      TRUE 
         rollupResolution        rollupResolution<-                    rowAll 
                     TRUE                      TRUE                      TRUE 
                 rowAllNA                    rowAny                  rowAnyNA 
                     TRUE                      TRUE                      TRUE 
                 rowCount               rowDistinct                 rstandard 
                     TRUE                      TRUE                      TRUE 
      runCrunchAutomation               saveVersion            scoreCatToFeat 
                     TRUE                      TRUE                      TRUE 
           searchDatasets          selectCategories             selectedDepth 
                     TRUE                      TRUE                      TRUE 
                  session         set_crunch_config           set_crunch_opts 
                     TRUE                      TRUE                      TRUE 
             setCrunchAPI           setDashboardURL                   setName 
                     TRUE                      TRUE                      TRUE 
                 setNames                  setOrder                  settings 
                     TRUE                      TRUE                      TRUE 
               settings<-           setupCrunchAuth                     share 
                     TRUE                      TRUE                      TRUE 
   shojifyDatasetMetadata                  shojiURL          showScriptErrors 
                     TRUE                      TRUE                      TRUE 
          slideCategories             slideMarkdown           slideMarkdown<- 
                     TRUE                      TRUE                      TRUE 
            slideQueryEnv                    slides                  slides<- 
                     TRUE                      TRUE                      TRUE 
     straightlineResponse                 streaming               streaming<- 
                     TRUE                      TRUE                      TRUE 
                 subtitle                subtitle<-                 subtitles 
                     TRUE                      TRUE                      TRUE 
              subtitles<-                  Subtotal          subtypeInsertion 
                     TRUE                      TRUE                      TRUE 
        subtypeInsertions              Subvariables               SummaryStat 
                     TRUE                      TRUE                      TRUE 
                  tabBook                     table                      team 
                     TRUE                      TRUE                      TRUE 
                   team<-               temp.option              temp.options 
                     TRUE                      TRUE                      TRUE 
             TextVariable                    titles                  titles<- 
                     TRUE                      TRUE                      TRUE 
                   toJSON                 tokenAuth                toVariable 
                     TRUE                      TRUE                      TRUE 
               Transforms            TransformsList                      trim 
                     TRUE                      TRUE                      TRUE 
                   unbind                undoScript                 ungrouped 
                     TRUE                      TRUE                      TRUE 
          unhideVariables                    unlock                   unshare 
                     TRUE                      TRUE                      TRUE 
                   values                    VarDef        VariableDefinition 
                     TRUE                      TRUE                      TRUE 
            VariableGroup          variableMetadata             VariableOrder 
                     TRUE                      TRUE                      TRUE 
                variables                  versions                  vizSpecs 
                     TRUE                      TRUE                      TRUE 
               vizSpecs<-                    webApp                    weight 
                     TRUE                      TRUE                      TRUE 
                 weight<-           weightVariables              with_consent 
                     TRUE                      TRUE                      TRUE 
             write.csv.gz         writePreparedData 
                     TRUE                      TRUE 

Examples

There are 245 help pages with examples, from 252 (97.22 %).

NEWS

The package has NEWS file and it is current.

License

The package uses .

Installation environment

System Info

Field Value
Image rhub/ref-image
OS Ubuntu 24.04.2 LTS
Platform x86_64-pc-linux-gnu
System x86_64, linux-gnu
Execution Time 2025-03-19 03:26:49 UTC

System information. Table about the system used to check the package.

R Session Info

Information about the R environment and capabilities:

R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: UTC
tzcode source: system (glibc)

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

loaded via a namespace (and not attached):
 [1] riskreports_0.0.0.9003 compiler_4.4.3         fastmap_1.2.0         
 [4] cli_3.6.4              htmltools_0.5.8.1      yaml_2.3.10           
 [7] rmarkdown_2.29         knitr_1.50             jsonlite_1.9.1        
[10] xfun_0.51              digest_0.6.37          rlang_1.1.5           
[13] evaluate_1.0.3        

Platform used:

   OS.type   file.sep dynlib.ext        GUI     endian    pkgType   path.sep 
    "unix"        "/"      ".so"      "X11"   "little"   "source"        ":" 
    r_arch 
        "" 

R’s capabilities:

       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE       FALSE        TRUE       FALSE        TRUE 
        NLS       Rprof     profmem       cairo         ICU long.double 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
    libcurl 
       TRUE 

External software:

                                                     zlib 
                                                    "1.3" 
                                                    bzlib 
                                     "1.0.8, 13-Jul-2019" 
                                                       xz 
                                                  "5.4.5" 
                                               libdeflate 
                                                   "1.19" 
                                                     PCRE 
                                       "10.42 2022-12-11" 
                                                      ICU 
                                                   "74.2" 
                                                      TRE 
                                "TRE 0.8.0 R_fixes (BSD)" 
                                                    iconv 
                                             "glibc 2.39" 
                                                 readline 
                                                    "8.2" 
                                                     BLAS 
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" 

Graphics external software:

                   cairo                  cairoFT                    pango 
                "1.18.0"                       ""                 "1.52.1" 
                  libpng                     jpeg                  libtiff 
                "1.6.43"                    "8.0" "LIBTIFF, Version 4.5.1" 

Numerical characteristics of the machine:

               double.eps            double.neg.eps               double.xmin 
             2.220446e-16              1.110223e-16             2.225074e-308 
              double.xmax               double.base             double.digits 
            1.797693e+308              2.000000e+00              5.300000e+01 
          double.rounding              double.guard         double.ulp.digits 
             5.000000e+00              0.000000e+00             -5.200000e+01 
    double.neg.ulp.digits           double.exponent            double.min.exp 
            -5.300000e+01              1.100000e+01             -1.022000e+03 
           double.max.exp               integer.max               sizeof.long 
             1.024000e+03              2.147484e+09              8.000000e+00 
          sizeof.longlong         sizeof.longdouble            sizeof.pointer 
             8.000000e+00              1.600000e+01              8.000000e+00 
            sizeof.time_t            longdouble.eps        longdouble.neg.eps 
             8.000000e+00              1.084202e-19              5.421011e-20 
        longdouble.digits       longdouble.rounding          longdouble.guard 
             6.400000e+01              5.000000e+00              0.000000e+00 
    longdouble.ulp.digits longdouble.neg.ulp.digits       longdouble.exponent 
            -6.300000e+01             -6.400000e+01              1.500000e+01 
       longdouble.min.exp        longdouble.max.exp 
            -1.638200e+04              1.638400e+04 

Random number generation process:

[1] "Mersenne-Twister" "Inversion"        "Rejection"       

Information about the environment

Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report

_R_CHECK_SYSTEM_CLOCK_
                        FALSE
ACCEPT_EULA             Y
ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
                        /opt/actionarchivecache
AGENT_TOOLSDIRECTORY    /opt/hostedtoolcache
ANDROID_HOME            /usr/local/lib/android/sdk
ANDROID_NDK             /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_HOME        /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_LATEST_HOME
                        /usr/local/lib/android/sdk/ndk/28.0.13004108
ANDROID_NDK_ROOT        /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_SDK_ROOT        /usr/local/lib/android/sdk
ANT_HOME                /usr/share/ant
AZURE_EXTENSION_DIR     /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
                        1
BUNDLE_EXT              linux-amd64.deb
CHROME_BIN              /usr/bin/google-chrome
CHROMEWEBDRIVER         /usr/local/share/chromedriver-linux64
CI                      true
CONDA                   /usr/share/miniconda
DEBIAN_FRONTEND         noninteractive
DENO_DOM_PLUGIN         /opt/quarto/bin/tools/x86_64/deno_dom/libplugin.so
DENO_NO_UPDATE_CHECK    1
DENO_TLS_CA_STORE       system,mozilla
DEPLOYMENT_BASEPATH     /opt/runner
DOTNET_MULTILEVEL_LOOKUP
                        0
DOTNET_NOLOGO           1
DOTNET_SKIP_FIRST_TIME_EXPERIENCE
                        1
EDGEWEBDRIVER           /usr/local/share/edge_driver
EDITOR                  vi
GECKOWEBDRIVER          /usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX
                        /usr/local
GITHUB_ACTION           __run_2
GITHUB_ACTION_REF       
GITHUB_ACTION_REPOSITORY
                        
GITHUB_ACTIONS          true
GITHUB_ACTOR            llrs-roche
GITHUB_ACTOR_ID         185338939
GITHUB_API_URL          https://api.github.com
GITHUB_BASE_REF         
GITHUB_ENV              /home/runner/work/_temp/_runner_file_commands/set_env_2ce58585-a4b5-44f5-8f77-d87ad76a2637
GITHUB_EVENT_NAME       schedule
GITHUB_EVENT_PATH       /home/runner/work/_temp/_github_workflow/event.json
GITHUB_GRAPHQL_URL      https://api.github.com/graphql
GITHUB_HEAD_REF         
GITHUB_JOB              main
GITHUB_OUTPUT           /home/runner/work/_temp/_runner_file_commands/set_output_2ce58585-a4b5-44f5-8f77-d87ad76a2637
GITHUB_PATH             /home/runner/work/_temp/_runner_file_commands/add_path_2ce58585-a4b5-44f5-8f77-d87ad76a2637
GITHUB_REF              refs/heads/main
GITHUB_REF_NAME         main
GITHUB_REF_PROTECTED    false
GITHUB_REF_TYPE         branch
GITHUB_REPOSITORY       pharmaR/pharmapkgs
GITHUB_REPOSITORY_ID    798326913
GITHUB_REPOSITORY_OWNER
                        pharmaR
GITHUB_REPOSITORY_OWNER_ID
                        42115094
GITHUB_RETENTION_DAYS   90
GITHUB_RUN_ATTEMPT      1
GITHUB_RUN_ID           13938154436
GITHUB_RUN_NUMBER       139
GITHUB_SERVER_URL       https://github.com
GITHUB_SHA              e08b400d1a286e18e3bfb99262514016e0af1624
GITHUB_STATE            /home/runner/work/_temp/_runner_file_commands/save_state_2ce58585-a4b5-44f5-8f77-d87ad76a2637
GITHUB_STEP_SUMMARY     /home/runner/work/_temp/_runner_file_commands/step_summary_2ce58585-a4b5-44f5-8f77-d87ad76a2637
GITHUB_TRIGGERING_ACTOR
                        llrs-roche
GITHUB_WORKFLOW         Update package repositories
GITHUB_WORKFLOW_REF     pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA     e08b400d1a286e18e3bfb99262514016e0af1624
GITHUB_WORKSPACE        /home/runner/work/pharmapkgs/pharmapkgs
GOROOT_1_21_X64         /opt/hostedtoolcache/go/1.21.13/x64
GOROOT_1_22_X64         /opt/hostedtoolcache/go/1.22.12/x64
GOROOT_1_23_X64         /opt/hostedtoolcache/go/1.23.7/x64
GRADLE_HOME             /usr/share/gradle-8.13
HOME                    /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
                        3650
HOMEBREW_NO_AUTO_UPDATE
                        1
ImageOS                 ubuntu24
ImageVersion            20250309.1.0
INVOCATION_ID           6037dc8f08514ea9b696fae55211a51a
JAVA_HOME               /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_11_X64        /usr/lib/jvm/temurin-11-jdk-amd64
JAVA_HOME_17_X64        /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_21_X64        /usr/lib/jvm/temurin-21-jdk-amd64
JAVA_HOME_8_X64         /usr/lib/jvm/temurin-8-jdk-amd64
JOURNAL_STREAM          8:8201
LANG                    C.UTF-8
LD_LIBRARY_PATH         /opt/R/4.4.3/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.3/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server
LN_S                    ln -s
LOGGER_LOG_LEVEL        DEBUG
MAKE                    make
MEMORY_PRESSURE_WATCH   /sys/fs/cgroup/system.slice/runner-provisioner.service/memory.pressure
MEMORY_PRESSURE_WRITE   c29tZSAyMDAwMDAgMjAwMDAwMAA=
NOT_CRAN                true
NVM_DIR                 /home/runner/.nvm
PAGER                   /usr/bin/pager
PATH                    /snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PERFLOG_LOCATION_SETTING
                        RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
                        assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT        100
PHARMAPKGS_PLATFORM     ubuntu-22.04
PHARMAPKGS_R_VERSION    4.4
PHARMAPKGS_REMOTE_REPO
                        https://cloud.r-project.org/
PIPX_BIN_DIR            /opt/pipx_bin
PIPX_HOME               /opt/pipx
PKGCACHE_HTTP_VERSION   2
PKGLOAD_PARENT_TEMPDIR
                        /tmp/Rtmp3gFRHN
POWERSHELL_DISTRIBUTION_CHANNEL
                        GitHub-Actions-ubuntu24
PROCESSX_PS1c2c6d0f0160_1742354804
                        YES
PWD                     /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH         /opt/quarto/bin
QUARTO_DENO             /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH    /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE          
QUARTO_PROJECT_DIR      /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_PROJECT_ROOT     /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_ROOT             /
QUARTO_SHARE_PATH       /opt/quarto/share
R_ARCH                  
R_BROWSER               xdg-open
R_BZIPCMD               /usr/bin/bzip2
R_DOC_DIR               /opt/R/4.4.3/lib/R/doc
R_GZIPCMD               /usr/bin/gzip
R_HOME                  /opt/R/4.4.3/lib/R
R_INCLUDE_DIR           /opt/R/4.4.3/lib/R/include
R_LIB_FOR_PAK           /opt/R/4.4.3/lib/R/site-library
R_LIBS_SITE             /opt/R/4.4.3/lib/R/site-library
R_LIBS_USER             /home/runner/work/_temp/Library
R_PAPERSIZE             letter
R_PAPERSIZE_USER        letter
R_PDFVIEWER             /usr/bin/xdg-open
R_PLATFORM              x86_64-pc-linux-gnu
R_PRINTCMD              /usr/bin/lpr
R_RD4PDF                times,inconsolata,hyper
R_SESSION_TMPDIR        /tmp/RtmpcFJjEB
R_SHARE_DIR             /opt/R/4.4.3/lib/R/share
R_STRIP_SHARED_LIB      strip --strip-unneeded
R_STRIP_STATIC_LIB      strip --strip-debug
R_TEXI2DVICMD           /usr/bin/texi2dvi
R_UNZIPCMD              /usr/bin/unzip
R_ZIPCMD                /usr/bin/zip
RUNNER_ARCH             X64
RUNNER_ENVIRONMENT      github-hosted
RUNNER_NAME             GitHub-Actions-1000000597
RUNNER_OS               Linux
RUNNER_PERFLOG          /home/runner/perflog
RUNNER_TEMP             /home/runner/work/_temp
RUNNER_TOOL_CACHE       /opt/hostedtoolcache
RUNNER_TRACKING_ID      github_d51345bf-bdf6-4dd6-baca-3c2af67f55c1
RUNNER_USER             runner
RUNNER_WORKSPACE        /home/runner/work/pharmapkgs
SED                     /usr/bin/sed
SELENIUM_JAR_PATH       /usr/share/java/selenium-server.jar
SGX_AESM_ADDR           1
SHLVL                   1
STATS_D                 true
STATS_D_D               true
STATS_D_TC              true
STATS_EXT               true
STATS_EXTP              https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
STATS_PIP               false
STATS_RDCL              true
STATS_TRP               true
STATS_UE                true
STATS_V3PS              true
STATS_VMD               true
STATS_VMFE              true
SWIFT_PATH              /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID        830
TAR                     /usr/bin/tar
TZ                      UTC
USER                    runner
VCPKG_INSTALLATION_ROOT
                        /usr/local/share/vcpkg
XDG_CONFIG_HOME         /home/runner/.config
XDG_RUNTIME_DIR         /run/user/1001

These are the options set to generate the report:

$add.smooth
[1] TRUE

$bitmapType
[1] "cairo"

$browser
[1] "xdg-open"

$browserNLdisabled
[1] FALSE

$callr.condition_handler_cli_message
function (msg) 
{
    custom_handler <- getOption("cli.default_handler")
    if (is.function(custom_handler)) {
        custom_handler(msg)
    }
    else {
        cli_server_default(msg)
    }
}
<bytecode: 0x556de6bb7330>
<environment: namespace:cli>

$catch.script.errors
[1] FALSE

$CBoundsCheck
[1] FALSE

$check.bounds
[1] FALSE

$citation.bibtex.max
[1] 1

$continue
[1] "+ "

$contrasts
        unordered           ordered 
"contr.treatment"      "contr.poly" 

$covr.record_tests
[1] TRUE

$defaultPackages
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"  

$demo.ask
[1] "default"

$deparse.cutoff
[1] 60

$device
function (width = 7, height = 7, ...) 
{
    grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x556de6194db8>
<environment: namespace:knitr>

$device.ask.default
[1] FALSE

$digits
[1] 7

$dvipscmd
[1] "dvips"

$echo
[1] FALSE

$editor
[1] "vi"

$encoding
[1] "native.enc"

$example.ask
[1] "default"

$expressions
[1] 5000

$help.search.types
[1] "vignette" "demo"     "help"    

$help.try.all.packages
[1] FALSE

$htmltools.preserve.raw
[1] TRUE

$HTTPUserAgent
[1] "R/4.4.3 R (4.4.3 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions"

$internet.info
[1] 2

$keep.parse.data
[1] TRUE

$keep.parse.data.pkgs
[1] FALSE

$keep.source
[1] FALSE

$keep.source.pkgs
[1] FALSE

$knitr.in.progress
[1] TRUE

$locatorBell
[1] TRUE

$mailer
[1] "mailto"

$matprod
[1] "default"

$max.contour.segments
[1] 25000

$max.print
[1] 99999

$menu.graphics
[1] TRUE

$na.action
[1] "na.omit"

$Ncpus
[1] 1

$nwarnings
[1] 50

$OutDec
[1] "."

$pager
[1] "/opt/R/4.4.3/lib/R/bin/pager"

$papersize
[1] "letter"

$PCRE_limit_recursion
[1] NA

$PCRE_study
[1] FALSE

$PCRE_use_JIT
[1] TRUE

$pdfviewer
[1] "/usr/bin/xdg-open"

$pkgType
[1] "source"

$printcmd
[1] "/usr/bin/lpr"

$prompt
[1] "> "

$repos
                      CRAN 
"https://cran.rstudio.com" 

$rl_word_breaks
[1] " \t\n\"\\'`><=%;,|&{()}"

$rlang_trace_top_env
<environment: R_GlobalEnv>

$scipen
[1] 0

$show.coef.Pvalues
[1] TRUE

$show.error.messages
[1] TRUE

$show.signif.stars
[1] TRUE

$showErrorCalls
[1] TRUE

$showNCalls
[1] 50

$showWarnCalls
[1] FALSE

$str
$str$strict.width
[1] "no"

$str$digits.d
[1] 3

$str$vec.len
[1] 4

$str$list.len
[1] 99

$str$deparse.lines
NULL

$str$drop.deparse.attr
[1] TRUE

$str$formatNum
function (x, ...) 
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x556de6092688>


$str.dendrogram.last
[1] "`"

$texi2dvi
[1] "/usr/bin/texi2dvi"

$tikzMetricsDictionary
[1] "validation_report_crunch_v1.31.0-tikzDictionary"

$timeout
[1] 60

$try.outFile
A connection with                    
description ""      
class       "file"  
mode        "w+b"   
text        "binary"
opened      "opened"
can read    "yes"   
can write   "yes"   

$ts.eps
[1] 1e-05

$ts.S.compat
[1] FALSE

$unzip
[1] "/usr/bin/unzip"

$useFancyQuotes
[1] FALSE

$verbose
[1] FALSE

$warn
[1] 0

$warning.length
[1] 1000

$warnPartialMatchArgs
[1] FALSE

$warnPartialMatchAttr
[1] FALSE

$warnPartialMatchDollar
[1] FALSE

$width
[1] 80