Validation Report - fslr@2.25.3

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 fslr

Metric based risk assessment

The following metrics are derived from the riskmetric R package.

has_news 1
news_current TRUE
exported_namespace 257
has_vignettes 4
export_help 282
has_website FALSE
has_maintainer John Muschelli
bugs_status subscript out of bounds
assess_size_codebase 4765
has_bug_reports_url 1
downloads_1yr 5661
reverse_dependencies 1
has_examples 1
dependencies 8
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 methods Imports
2 R.utils Imports
3 graphics Imports
4 grDevices Imports
5 stats Imports
6 utils Imports
7 oro.nifti (>= 0.5.0) Depends
8 neurobase (>= 1.32.0) Depends

Package dependencies

Reverse dependencies

Overall the package has 1 reverse dependencies:

freesurfer

Namespace

Overall the package has 257 exported objects. 257 are documented:

            apply_topup              applytopup                 avscale 
                   TRUE                    TRUE                    TRUE 
             check_file                checkout              concat_xfm 
                   TRUE                    TRUE                    TRUE 
           deface_image                  dtifit                    eddy 
                   TRUE                    TRUE                    TRUE 
           eddy_correct            enforce_form                 epi_reg 
                   TRUE                    TRUE                    TRUE 
      face_removal_mask                    fast                fast_all 
                   TRUE                    TRUE                    TRUE 
            fast_nobias         fast_nobias_all               fast.help 
                   TRUE                    TRUE                    TRUE 
       fixscaleskew_xfm                   flirt             flirt_apply 
                   TRUE                    TRUE                    TRUE 
             flirt.help                   fnirt       fnirt_with_affine 
                   TRUE                    TRUE                    TRUE 
fnirt_with_affine_apply              fnirt.help                 fsl_abs 
                   TRUE                    TRUE                    TRUE 
               fsl_acos                 fsl_add                fsl_anat 
                   TRUE                    TRUE                    TRUE 
          fsl_anat.help                 fsl_and          fsl_applytopup 
                   TRUE                    TRUE                    TRUE 
          fsl_applywarp      fsl_applywarp.help                fsl_asin 
                   TRUE                    TRUE                    TRUE 
               fsl_atan           fsl_atlas_dir             fsl_avscale 
                   TRUE                    TRUE                    TRUE 
                fsl_bet         fsl_biascorrect                 fsl_bin 
                   TRUE                    TRUE                    TRUE 
            fsl_bin_tab                fsl_binv             fsl_cluster 
                   TRUE                    TRUE                    TRUE 
                fsl_cos            fsl_data_dir              fsl_deface 
                   TRUE                    TRUE                    TRUE 
               fsl_dice              fsl_dilate                 fsl_dir 
                   TRUE                    TRUE                    TRUE 
                fsl_div                fsl_edge             fsl_epi_reg 
                   TRUE                    TRUE                    TRUE 
              fsl_erode                 fsl_exp                fsl_fast 
                   TRUE                    TRUE                    TRUE 
        fsl_fast_nobias                fsl_fill               fsl_index 
                   TRUE                    TRUE                    TRUE 
                fsl_log                fsl_mask               fsl_maths 
                   TRUE                    TRUE                    TRUE 
              fsl_merge                 fsl_mul                 fsl_nan 
                   TRUE                    TRUE                    TRUE 
               fsl_nanm                  fsl_or                fsl_rand 
                   TRUE                    TRUE                    TRUE 
              fsl_randn               fsl_recip                 fsl_rem 
                   TRUE                    TRUE                    TRUE 
           fsl_resample           fsl_robustfov                 fsl_roi 
                   TRUE                    TRUE                    TRUE 
         fsl_slicetimer              fsl_smooth      fsl_smooth_in_mask 
                   TRUE                    TRUE                    TRUE 
          fsl_smoothest               fsl_split                 fsl_sqr 
                   TRUE                    TRUE                    TRUE 
               fsl_sqrt             fsl_std_dir            fsl_std_file 
                   TRUE                    TRUE                    TRUE 
                fsl_sub                fsl_sub2             fsl_swapdim 
                   TRUE                    TRUE                    TRUE 
                fsl_tan              fsl_thresh               fsl_topup 
                   TRUE                    TRUE                    TRUE 
             fsl_tsplot         fsl_tsplot.help             fsl_version 
                   TRUE                    TRUE                    TRUE 
        fsl_version_gt5                 fsl_xor                  fslabs 
                   TRUE                    TRUE                    TRUE 
            fslabs.help                 fslacos            fslacos.help 
                   TRUE                    TRUE                    TRUE 
                 fsladd             fsladd.help                  fsland 
                   TRUE                    TRUE                    TRUE 
                fslasin            fslasin.help                 fslatan 
                   TRUE                    TRUE                    TRUE 
           fslatan.help                  fslbet             fslbet.help 
                   TRUE                    TRUE                    TRUE 
                 fslbin             fslbin.help                 fslbinv 
                   TRUE                    TRUE                    TRUE 
           fslbinv.help           fslchfiletype      fslchfiletype.help 
                   TRUE                    TRUE                    TRUE 
             fslcluster                  fslcmd                  fslcog 
                   TRUE                    TRUE                    TRUE 
                 fslcos             fslcos.help               fslcpgeom 
                   TRUE                    TRUE                    TRUE 
         fslcpgeom.help               fsldilate                  fsldir 
                   TRUE                    TRUE                    TRUE 
                 fsldiv             fsldiv.help                 fsledge 
                   TRUE                    TRUE                    TRUE 
           fsledge.help              fslentropy              fslepi_reg 
                   TRUE                    TRUE                    TRUE 
               fslerode           fslerode.help                  fslexp 
                   TRUE                    TRUE                    TRUE 
            fslexp.help                 fsleyes                 fslfast 
                   TRUE                    TRUE                    TRUE 
         fslfast_nobias                 fslfill            fslfill.help 
                   TRUE                    TRUE                    TRUE 
               fslfill2            fslgetorient             fslgetqform 
                   TRUE                    TRUE                    TRUE 
        fslgetqformcode             fslgetsform         fslgetsformcode 
                   TRUE                    TRUE                    TRUE 
                  fslhd              fslhd.help             fslhd.parse 
                   TRUE                    TRUE                    TRUE 
                fslhelp                fslindex           fslindex.help 
                   TRUE                    TRUE                    TRUE 
                 fsllog             fsllog.help                 fslmask 
                   TRUE                    TRUE                    TRUE 
           fslmask.help                fslmaths           fslmaths.help 
                   TRUE                    TRUE                    TRUE 
                 fslmax                 fslmean                fslmerge 
                   TRUE                    TRUE                    TRUE 
          fslmerge.help                  fslmin                  fslmul 
                   TRUE                    TRUE                    TRUE 
            fslmul.help                  fslnan             fslnan.help 
                   TRUE                    TRUE                    TRUE 
                fslnanm            fslnanm.help                   fslor 
                   TRUE                    TRUE                    TRUE 
              fslorient          fslorient.help                 fslrand 
                   TRUE                    TRUE                    TRUE 
           fslrand.help                fslrandn           fslrandn.help 
                   TRUE                    TRUE                    TRUE 
               fslrange                fslrecip           fslrecip.help 
                   TRUE                    TRUE                    TRUE 
                 fslrem             fslrem.help         fslreorient2std 
                   TRUE                    TRUE                    TRUE 
    fslreorient2std_mat    fslreorient2std.help            fslrobustfov 
                   TRUE                    TRUE                    TRUE 
      fslrobustfov.help                  fslroi             fslroi_time 
                   TRUE                    TRUE                    TRUE 
                  fslsd                  fslsin             fslsin.help 
                   TRUE                    TRUE                    TRUE 
          fslslicetimer               fslsmooth       fslsmooth_in_mask 
                   TRUE                    TRUE                    TRUE 
         fslsmooth.help                fslsplit           fslsplit.help 
                   TRUE                    TRUE                    TRUE 
                 fslsqr             fslsqr.help                 fslsqrt 
                   TRUE                    TRUE                    TRUE 
           fslsqrt.help                fslstats           fslstats.help 
                   TRUE                    TRUE                    TRUE 
                 fslsub             fslsub.help                 fslsub2 
                   TRUE                    TRUE                    TRUE 
           fslsub2.help                  fslsum              fslswapdim 
                   TRUE                    TRUE                    TRUE 
        fslswapdim.help                  fsltan             fsltan.help 
                   TRUE                    TRUE                    TRUE 
              fslthresh          fslthresh.help                  fslval 
                   TRUE                    TRUE                    TRUE 
            fslval.help              fslversion                 fslview 
                   TRUE                    TRUE                    TRUE 
           fslview.help                  fslvol               fslvolume 
                   TRUE                    TRUE                    TRUE 
                 fslxor                 get_fsl     get_mridefacer_mask 
                   TRUE                    TRUE                    TRUE 
    get_quickshear_mask                 get.fsl           get.fsloutput 
                   TRUE                    TRUE                    TRUE 
             get.imgext                getForms                have_fsl 
                   TRUE                    TRUE                    TRUE 
               have.fsl              invert_xfm                  is_rpi 
                   TRUE                    TRUE                    TRUE 
                 is.rpi                 mcflirt            mcflirt.help 
                   TRUE                    TRUE                    TRUE 
                melodic            melodic.help      mid_sagittal_align 
                   TRUE                    TRUE                    TRUE 
         mni_face_fname               mni_fname                 mni_img 
                   TRUE                    TRUE                    TRUE 
             mridefacer           parse_avscale              probtrackx 
                   TRUE                    TRUE                    TRUE 
quickshear_deface_image      read_cluster_table                read_xfm 
                   TRUE                    TRUE                    TRUE 
                readrpi      reverse_rpi_orient reverse_rpi_orient_file 
                   TRUE                    TRUE                    TRUE 
             rpi_orient         rpi_orient_file           run_first_all 
                   TRUE                    TRUE                    TRUE 
     run_first_all.help                   susan              susan.help 
                   TRUE                    TRUE                    TRUE 
                  topup                 xfibres 
                   TRUE                    TRUE 

Examples

There are 203 help pages with examples, from 203 (100.00 %).

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 2025-03-17 03:31:29 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_35de53e0-bba8-48db-994a-b6d141992fd4
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_35de53e0-bba8-48db-994a-b6d141992fd4
GITHUB_PATH             /home/runner/work/_temp/_runner_file_commands/add_path_35de53e0-bba8-48db-994a-b6d141992fd4
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           13890865743
GITHUB_RUN_NUMBER       137
GITHUB_SERVER_URL       https://github.com
GITHUB_SHA              4202376d670fac0a022e165ebfa1ebb3b5c6ee5f
GITHUB_STATE            /home/runner/work/_temp/_runner_file_commands/save_state_35de53e0-bba8-48db-994a-b6d141992fd4
GITHUB_STEP_SUMMARY     /home/runner/work/_temp/_runner_file_commands/step_summary_35de53e0-bba8-48db-994a-b6d141992fd4
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     4202376d670fac0a022e165ebfa1ebb3b5c6ee5f
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           8c2fa24f222040819c358512a4892c23
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          8:6807
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/RtmpvFsviq
POWERSHELL_DISTRIBUTION_CHANNEL
                        GitHub-Actions-ubuntu24
PROCESSX_PS1dd9528b1342_1742182285
                        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/RtmpyWOv29
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-1000000515
RUNNER_OS               Linux
RUNNER_PERFLOG          /home/runner/perflog
RUNNER_TEMP             /home/runner/work/_temp
RUNNER_TOOL_CACHE       /opt/hostedtoolcache
RUNNER_TRACKING_ID      github_7dcadf91-7a7c-4938-bcc4-8aedfcb81488
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        832
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: 0x55aa0bea7330>
<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: 0x55aa0b543060>
<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: 0x55aa0b382688>


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

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

$tikzMetricsDictionary
[1] "validation_report_fslr_v2.25.3-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