Validation Report - EnvStats@3.0.0

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 EnvStats

Metric based risk assessment

The following metrics are derived from the riskmetric R package.

has_news 0
exported_namespace 305
has_vignettes 0
export_help 305
has_website TRUE
has_maintainer Alexander Kowarik
bugs_status package DESCRIPTION does not have a BugReports field
has_source_control https://github.com/alexkowa/EnvStats
has_bug_reports_url 0
downloads_1yr 208784
reverse_dependencies 41
has_examples 0.9416446
dependencies 3
license GPL (>= 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 MASS Imports
2 ggplot2 Imports
3 nortest Imports

Package dependencies

Reverse dependencies

Overall the package has 41 reverse dependencies:

admix, AnnuityRIR, AZIAD, bgev, CellTrails, depCensoring, dTBM, Ecfun, epidecodeR, eva, fitteR, FMAdist, FuzzyClass, GeomxTools, ggplot2.utils, GWEX, hermes, httk, HyMETT, LRTesteR, mem, mevr, NADA2, nett, OVtool, PLreg, PSS.Health, r6qualitytools, ramr, remaCor, simPop, smam, SmCCNet, snSMART, ssdtools, statBasics, SWMPrExtension, ThermalSampleR, TidyDensity, varTestnlme, VTShiny

Namespace

Overall the package has 305 exported objects. 305 are documented:

                                      anovaPE 
                                         TRUE 
                                         aovN 
                                         TRUE 
                                     aovPower 
                                         TRUE 
                                         base 
                                         TRUE 
                                       boxcox 
                                         TRUE 
                               boxcoxCensored 
                                         TRUE 
                              boxcoxTransform 
                                         TRUE 
                                    calibrate 
                                         TRUE 
                                   cdfCompare 
                                         TRUE 
                           cdfCompareCensored 
                                         TRUE 
                                      cdfPlot 
                                         TRUE 
                                    chenTTest 
                                         TRUE 
                             ciBinomHalfWidth 
                                         TRUE 
                                     ciBinomN 
                                         TRUE 
                              ciNormHalfWidth 
                                         TRUE 
                                      ciNormN 
                                         TRUE 
                              ciNparConfLevel 
                                         TRUE 
                                      ciNparN 
                                         TRUE 
                                  ciTableMean 
                                         TRUE 
                                  ciTableProp 
                                         TRUE 
                                           cv 
                                         TRUE 
                                         dchi 
                                         TRUE 
                                         demp 
                                         TRUE 
                      detectionLimitCalibrate 
                                         TRUE 
                                         devd 
                                         TRUE 
                                    dgammaAlt 
                                         TRUE 
                                        dgevd 
                                         TRUE 
                                   distChoose 
                                         TRUE 
                           distChooseCensored 
                                         TRUE 
                                      dlnorm3 
                                         TRUE 
                                    dlnormAlt 
                                         TRUE 
                                    dlnormMix 
                                         TRUE 
                                 dlnormMixAlt 
                                         TRUE 
                                  dlnormTrunc 
                                         TRUE 
                               dlnormTruncAlt 
                                         TRUE 
                                     dnormMix 
                                         TRUE 
                                   dnormTrunc 
                                         TRUE 
                                      dpareto 
                                         TRUE 
                                         dtri 
                                         TRUE 
                                     dzmlnorm 
                                         TRUE 
                                  dzmlnormAlt 
                                         TRUE 
                                      dzmnorm 
                                         TRUE 
                                        ebeta 
                                         TRUE 
                                       ebinom 
                                         TRUE 
                                     ecdfPlot 
                                         TRUE 
                             ecdfPlotCensored 
                                         TRUE 
                                         eevd 
                                         TRUE 
                                         eexp 
                                         TRUE 
                                       egamma 
                                         TRUE 
                                    egammaAlt 
                                         TRUE 
                            egammaAltCensored 
                                         TRUE 
                               egammaCensored 
                                         TRUE 
                                        egeom 
                                         TRUE 
                                        egevd 
                                         TRUE 
                                       ehyper 
                                         TRUE 
                                       elnorm 
                                         TRUE 
                                      elnorm3 
                                         TRUE 
                                    elnormAlt 
                                         TRUE 
                            elnormAltCensored 
                                         TRUE 
                               elnormCensored 
                                         TRUE 
                                       elogis 
                                         TRUE 
                                      enbinom 
                                         TRUE 
                                        enorm 
                                         TRUE 
                                enormCensored 
                                         TRUE 
                                        enpar 
                                         TRUE 
                                enparCensored 
                                         TRUE 
                                      epareto 
                                         TRUE 
                                     epdfPlot 
                                         TRUE 
                                        epois 
                                         TRUE 
                                epoisCensored 
                                         TRUE 
                                       eqbeta 
                                         TRUE 
                                      eqbinom 
                                         TRUE 
                                        eqevd 
                                         TRUE 
                                        eqexp 
                                         TRUE 
                                      eqgamma 
                                         TRUE 
                                   eqgammaAlt 
                                         TRUE 
                                       eqgeom 
                                         TRUE 
                                       eqgevd 
                                         TRUE 
                                      eqhyper 
                                         TRUE 
                                      eqlnorm 
                                         TRUE 
                                     eqlnorm3 
                                         TRUE 
                              eqlnormCensored 
                                         TRUE 
                                      eqlogis 
                                         TRUE 
                                     eqnbinom 
                                         TRUE 
                                       eqnorm 
                                         TRUE 
                               eqnormCensored 
                                         TRUE 
                                       eqnpar 
                                         TRUE 
                                     eqpareto 
                                         TRUE 
                                       eqpois 
                                         TRUE 
                                       equnif 
                                         TRUE 
                                    eqweibull 
                                         TRUE 
                                    eqzmlnorm 
                                         TRUE 
                                 eqzmlnormAlt 
                                         TRUE 
                                     eqzmnorm 
                                         TRUE 
                                     errorBar 
                                         TRUE 
                                        eunif 
                                         TRUE 
                               evNormOrdStats 
                                         TRUE 
                         evNormOrdStatsScalar 
                                         TRUE 
                                     eweibull 
                                         TRUE 
                                     ezmlnorm 
                                         TRUE 
                                  ezmlnormAlt 
                                         TRUE 
                                      ezmnorm 
                                         TRUE 
                              geom_stripchart 
                                         TRUE 
                                      geoMean 
                                         TRUE 
                                        geoSD 
                                         TRUE 
                                 gofGroupTest 
                                         TRUE 
                                      gofTest 
                                         TRUE 
                              gofTestCensored 
                                         TRUE 
                    gpqCiNormMultiplyCensored 
                                         TRUE 
                      gpqCiNormSinglyCensored 
                                         TRUE 
                gpqTolIntNormMultiplyCensored 
                                         TRUE 
                  gpqTolIntNormSinglyCensored 
                                         TRUE 
                      inversePredictCalibrate 
                                         TRUE 
                                          iqr 
                                         TRUE 
                     kendallSeasonalTrendTest 
                                         TRUE 
                             kendallTrendTest 
                                         TRUE 
                                     kurtosis 
                                         TRUE 
                             linearTrendTestN 
                                         TRUE 
                         linearTrendTestPower 
                                         TRUE 
                     linearTrendTestScaledMds 
                                         TRUE 
                                      lMoment 
                                         TRUE 
                                   longToWide 
                                         TRUE 
                                 newsEnvStats 
                                         TRUE 
                     oneSamplePermutationTest 
                                         TRUE 
                                         pchi 
                                         TRUE 
                                      pdfPlot 
                                         TRUE 
                                         pemp 
                                         TRUE 
                                         pevd 
                                         TRUE 
                                    pgammaAlt 
                                         TRUE 
                                        pgevd 
                                         TRUE 
                                      plnorm3 
                                         TRUE 
                                    plnormAlt 
                                         TRUE 
                                    plnormMix 
                                         TRUE 
                                 plnormMixAlt 
                                         TRUE 
                                  plnormTrunc 
                                         TRUE 
                               plnormTruncAlt 
                                         TRUE 
                                  plot.boxcox 
                                         TRUE 
                          plot.boxcoxCensored 
                                         TRUE 
                                plot.boxcoxLm 
                                         TRUE 
                                     plot.gof 
                                         TRUE 
                             plot.gofCensored 
                                         TRUE 
                                plot.gofGroup 
                                         TRUE 
                            plot.gofTwoSample 
                                         TRUE 
                         plot.permutationTest 
                                         TRUE 
                                plotAovDesign 
                                         TRUE 
                            plotCiBinomDesign 
                                         TRUE 
                             plotCiNormDesign 
                                         TRUE 
                             plotCiNparDesign 
                                         TRUE 
                    plotLinearTrendTestDesign 
                                         TRUE 
plotPredIntLnormAltSimultaneousTestPowerCurve 
                                         TRUE 
            plotPredIntLnormAltTestPowerCurve 
                                         TRUE 
                        plotPredIntNormDesign 
                                         TRUE 
    plotPredIntNormSimultaneousTestPowerCurve 
                                         TRUE 
                plotPredIntNormTestPowerCurve 
                                         TRUE 
                        plotPredIntNparDesign 
                                         TRUE 
            plotPredIntNparSimultaneousDesign 
                                         TRUE 
    plotPredIntNparSimultaneousTestPowerCurve 
                                         TRUE 
                           plotPropTestDesign 
                                         TRUE 
                         plotTolIntNormDesign 
                                         TRUE 
                         plotTolIntNparDesign 
                                         TRUE 
                              plotTTestDesign 
                                         TRUE 
                      plotTTestLnormAltDesign 
                                         TRUE 
                                     pnormMix 
                                         TRUE 
                                   pnormTrunc 
                                         TRUE 
                                    pointwise 
                                         TRUE 
                                      ppareto 
                                         TRUE 
                              ppointsCensored 
                                         TRUE 
                                      predict 
                                         TRUE 
                              predict.default 
                                         TRUE 
                                   predict.lm 
                                         TRUE 
                                 predIntGamma 
                                         TRUE 
                              predIntGammaAlt 
                                         TRUE 
                  predIntGammaAltSimultaneous 
                                         TRUE 
                     predIntGammaSimultaneous 
                                         TRUE 
                                 predIntLnorm 
                                         TRUE 
                              predIntLnormAlt 
                                         TRUE 
                  predIntLnormAltSimultaneous 
                                         TRUE 
         predIntLnormAltSimultaneousTestPower 
                                         TRUE 
                     predIntLnormAltTestPower 
                                         TRUE 
                     predIntLnormSimultaneous 
                                         TRUE 
                                  predIntNorm 
                                         TRUE 
                         predIntNormHalfWidth 
                                         TRUE 
                                 predIntNormK 
                                         TRUE 
                                 predIntNormN 
                                         TRUE 
                      predIntNormSimultaneous 
                                         TRUE 
                     predIntNormSimultaneousK 
                                         TRUE 
             predIntNormSimultaneousTestPower 
                                         TRUE 
                         predIntNormTestPower 
                                         TRUE 
                                  predIntNpar 
                                         TRUE 
                         predIntNparConfLevel 
                                         TRUE 
                                 predIntNparN 
                                         TRUE 
                      predIntNparSimultaneous 
                                         TRUE 
             predIntNparSimultaneousConfLevel 
                                         TRUE 
                     predIntNparSimultaneousN 
                                         TRUE 
             predIntNparSimultaneousTestPower 
                                         TRUE 
                                  predIntPois 
                                         TRUE 
                                 print.boxcox 
                                         TRUE 
                         print.boxcoxCensored 
                                         TRUE 
                               print.boxcoxLm 
                                         TRUE 
                               print.estimate 
                                         TRUE 
                       print.estimateCensored 
                                         TRUE 
                                    print.gof 
                                         TRUE 
                            print.gofCensored 
                                         TRUE 
                               print.gofGroup 
                                         TRUE 
                             print.gofOutlier 
                                         TRUE 
                           print.gofTwoSample 
                                         TRUE 
                          print.htestCensored 
                                         TRUE 
                          print.htestEnvStats 
                                         TRUE 
                        print.permutationTest 
                                         TRUE 
                           print.summaryStats 
                                         TRUE 
                                  propTestMdd 
                                         TRUE 
                                    propTestN 
                                         TRUE 
                                propTestPower 
                                         TRUE 
                                         ptri 
                                         TRUE 
                                     pwMoment 
                                         TRUE 
                                     pzmlnorm 
                                         TRUE 
                                  pzmlnormAlt 
                                         TRUE 
                                      pzmnorm 
                                         TRUE 
                                         qchi 
                                         TRUE 
                                         qemp 
                                         TRUE 
                                         qevd 
                                         TRUE 
                                    qgammaAlt 
                                         TRUE 
                                        qgevd 
                                         TRUE 
                                      qlnorm3 
                                         TRUE 
                                    qlnormAlt 
                                         TRUE 
                                    qlnormMix 
                                         TRUE 
                                 qlnormMixAlt 
                                         TRUE 
                                  qlnormTrunc 
                                         TRUE 
                               qlnormTruncAlt 
                                         TRUE 
                                     qnormMix 
                                         TRUE 
                                   qnormTrunc 
                                         TRUE 
                                      qpareto 
                                         TRUE 
                                       qqPlot 
                                         TRUE 
                               qqPlotCensored 
                                         TRUE 
                                qqPlotGestalt 
                                         TRUE 
                                         qtri 
                                         TRUE 
                                 quantileTest 
                                         TRUE 
                           quantileTestPValue 
                                         TRUE 
                                     qzmlnorm 
                                         TRUE 
                                  qzmlnormAlt 
                                         TRUE 
                                      qzmnorm 
                                         TRUE 
                                         rchi 
                                         TRUE 
                                         remp 
                                         TRUE 
                                         revd 
                                         TRUE 
                                    rgammaAlt 
                                         TRUE 
                                        rgevd 
                                         TRUE 
                                      rlnorm3 
                                         TRUE 
                                    rlnormAlt 
                                         TRUE 
                                    rlnormMix 
                                         TRUE 
                                 rlnormMixAlt 
                                         TRUE 
                                  rlnormTrunc 
                                         TRUE 
                               rlnormTruncAlt 
                                         TRUE 
                                     rnormMix 
                                         TRUE 
                                   rnormTrunc 
                                         TRUE 
                                   rosnerTest 
                                         TRUE 
                                      rpareto 
                                         TRUE 
                                         rtri 
                                         TRUE 
                                     rzmlnorm 
                                         TRUE 
                                  rzmlnormAlt 
                                         TRUE 
                                      rzmnorm 
                                         TRUE 
                        serialCorrelationTest 
                                         TRUE 
                                     signTest 
                                         TRUE 
                             simulateMvMatrix 
                                         TRUE 
                               simulateVector 
                                         TRUE 
                                     skewness 
                                         TRUE 
                            stat_mean_sd_text 
                                         TRUE 
                         stat_median_iqr_text 
                                         TRUE 
                                  stat_n_text 
                                         TRUE 
                               stat_test_text 
                                         TRUE 
                               StatMeanSDText 
                                         TRUE 
                            StatMedianIQRText 
                                         TRUE 
                                    StatNText 
                                         TRUE 
                                 StatTestText 
                                         TRUE 
                                   stripChart 
                                         TRUE 
                                  summaryFull 
                                         TRUE 
                                 summaryStats 
                                         TRUE 
                                  tolIntGamma 
                                         TRUE 
                               tolIntGammaAlt 
                                         TRUE 
                                  tolIntLnorm 
                                         TRUE 
                               tolIntLnormAlt 
                                         TRUE 
                          tolIntLnormCensored 
                                         TRUE 
                                   tolIntNorm 
                                         TRUE 
                           tolIntNormCensored 
                                         TRUE 
                          tolIntNormHalfWidth 
                                         TRUE 
                                  tolIntNormK 
                                         TRUE 
                                  tolIntNormN 
                                         TRUE 
                                   tolIntNpar 
                                         TRUE 
                          tolIntNparConfLevel 
                                         TRUE 
                           tolIntNparCoverage 
                                         TRUE 
                                  tolIntNparN 
                                         TRUE 
                                   tolIntPois 
                                         TRUE 
                                   tTestAlpha 
                                         TRUE 
                               tTestLnormAltN 
                                         TRUE 
                           tTestLnormAltPower 
                                         TRUE 
                    tTestLnormAltRatioOfMeans 
                                         TRUE 
                                       tTestN 
                                         TRUE 
                                   tTestPower 
                                         TRUE 
                               tTestScaledMdd 
                                         TRUE 
                      twoSampleLinearRankTest 
                                         TRUE 
              twoSampleLinearRankTestCensored 
                                         TRUE 
             twoSamplePermutationTestLocation 
                                         TRUE 
           twoSamplePermutationTestProportion 
                                         TRUE 
                                 varGroupTest 
                                         TRUE 
                                      varTest 
                                         TRUE 
                               zTestGevdShape 
                                         TRUE 

Examples

There are 355 help pages with examples, from 377 (94.16 %).

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 24.04.1 LTS
Platform x86_64-pc-linux-gnu
System x86_64, linux-gnu
Execution Time 2025-02-19 04:12:54 UTC

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

R Session Info

Information about the R environment and capabilities:

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 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_4.4.2         fastmap_1.2.0         
 [4] cli_3.6.4              htmltools_0.5.8.1      yaml_2.3.10           
 [7] rmarkdown_2.29         knitr_1.49             jsonlite_1.8.9        
[10] xfun_0.50              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/27.2.12479018
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
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_c412a26f-cd8a-499e-b689-b0767882aa5e
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_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_PATH             /home/runner/work/_temp/_runner_file_commands/add_path_c412a26f-cd8a-499e-b689-b0767882aa5e
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           13404668958
GITHUB_RUN_NUMBER       96
GITHUB_SERVER_URL       https://github.com
GITHUB_SHA              a8b95a62e6dc098bb3af41043304208245a9ed4a
GITHUB_STATE            /home/runner/work/_temp/_runner_file_commands/save_state_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_STEP_SUMMARY     /home/runner/work/_temp/_runner_file_commands/step_summary_c412a26f-cd8a-499e-b689-b0767882aa5e
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     a8b95a62e6dc098bb3af41043304208245a9ed4a
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/1.23.6/x64
GRADLE_HOME             /usr/share/gradle-8.12.1
HOME                    /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
                        3650
HOMEBREW_NO_AUTO_UPDATE
                        1
ImageOS                 ubuntu24
ImageVersion            20250209.1.0
INVOCATION_ID           8bd4b7db4d15432e8df0477a564753c1
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          8:7410
LANG                    C.UTF-8
LD_LIBRARY_PATH         /opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.2/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        1000
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/RtmpZYt03y
POWERSHELL_DISTRIBUTION_CHANNEL
                        GitHub-Actions-ubuntu24
PROCESSX_PS1d457cdd2b20_1739938368
                        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/4.4.2/lib/R/doc
R_GZIPCMD               /usr/bin/gzip
R_HOME                  /opt/R/4.4.2/lib/R
R_INCLUDE_DIR           /opt/R/4.4.2/lib/R/include
R_LIB_FOR_PAK           /opt/R/4.4.2/lib/R/site-library
R_LIBS_SITE             /opt/R/4.4.2/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/RtmpDoKlD8
R_SHARE_DIR             /opt/R/4.4.2/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 2
RUNNER_OS               Linux
RUNNER_PERFLOG          /home/runner/perflog
RUNNER_TEMP             /home/runner/work/_temp
RUNNER_TOOL_CACHE       /opt/hostedtoolcache
RUNNER_TRACKING_ID      github_40220c0a-4f03-4847-8b7e-3a374b87939a
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        837
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: 0x5631f8e26910>
<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: 0x5631f8305060>
<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/4.4.2 R (4.4.2 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/4.4.2/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: 0x5631f82fe520>


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

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

$tikzMetricsDictionary
[1] "validation_report_EnvStats_v3.0.0-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