Validation Report - checkmate@2.3.2
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 checkmate
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 370 |
| has_vignettes | 4 |
| export_help | 370 |
| has_website | TRUE |
| has_maintainer | Michel Lang michellang@gmail.com |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/mllg/checkmate |
| has_bug_reports_url | 1 |
| downloads_1yr | 3198654 |
| reverse_dependencies | 492 |
| has_examples | 1 |
| dependencies | 2 |
| license | BSD_3_clause + file LICENSE |
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 | backports (>= 1.1.0) | Imports |
| 2 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 492 reverse dependencies:
accessibility, ADImpute, adproclus, aeddo, aldvmm, amt, ao, aopdata, APCtools, arealDB, aslib, autocogs, autoslider.core, autothresholdr, babelmixr2, baRulho, base64url, BatchExperiments, BatchJobs, batchtools, BayesFBHborrow, BayesFM, BayesianMCPMod, BBmisc, bbotk, Bchron, beaver, BioTIMEr, bonsaiforest, boostrq, bootGOF, botor, brclimr, brpop, bsitar, bssm, carbonr, causalPAF, causalweight, CDMConnector, censobr, cfr, chevron, chimeraviz, chooseGCM, cito, cleanepi, cleanr, clustree, cmaesr, CodelistGenerator, codified, CohortAlgebra, CohortConstructor, CohortExplorer, CohortGenerator, CohortSurvival, CohortSymmetry, cointReg, ColOpenData, comorbidity, conogive, CoreGx, CornerstoneR, cosimmr, counterfactuals, CrossClustering, crosstable, crumble, cucumber, cusum, cvms, cyclestreets, cypress, dapper, DatabaseConnector, dataverse, DCCA, DEFormats, deident, detrendr, diffuStats, discharge, DiscreteDatasets, DiscreteFDR, DiscreteFWER, DiscreteTests, diseasystore, distfromq, distillML, document, DoubleML, DrugExposureDiagnostics, DtD, DTSg, dunlin, dynamite, eatRep, eatTools, ebvcube, ecostate, ecpc, ecr, EFAfactors, EFAtools, EGM, enderecobr, epichains, epicmodel, epiCo, epidatr, EpiNow2, epiparameter, epiregulon, epiregulon.extra, eplusr, epwshiftr, exampletestr, FACT, fail, farff, fastLogisticRegressionWrap, fastVoteR, FCO, FDX, FeatureExtraction, ffscrapr, fHMM, filesstrings, finalsize, fitbitr, fixtuRes, flacco, flipdownr, fmeffects, forestplot, formatdown, formatters, fritools, fritools2, funStatTest, fuseMLR, FuzzyDBScan, gDRcore, gDRimport, gDRstyle, gDRutils, geboes.score, genomicInstability, geocodebr, ggbrain, ggparty, ggplot2.utils, ggPMX, glmSparseNet, Gmisc, gofreg, GRaNIE, grapherator, graphite, grattan, GreedyExperimentalDesign, gridstackeR, groupdata2, gtfs2emis, gtfs2gps, gtfstools, GTFSwizard, hdf5r.Extra, hdflex, hdm, hermes, hetu, HicAggR, hidradenitis, highs, holiglm, HospitalNetwork, htmlTable, hubUtils, HyMETT, IBMPopSim, icecream, icmstate, icpack, ie2misc, igvShiny, ijtiff, imaginator, iml, injurytools, inlcolor, inldata, inlpubs, innsight, install.load, ipeaplot, itsdm, ivo.table, IxPopDyMod, katdetectr, kgen, KMunicate, lazysql, ldaPrototype, leafdown, learnr, limorhyde2, linelist, listdown, llama, lmtp, localICE, longmixr, loo, lotri, maicplus, mallet, maraca, marginaleffects, markmyassignment, matchedcc, matrixprofiler, MBNMAdose, MBNMAtime, mcboost, mcMST, mcparallelDo, mcradds, mctq, md4r, melt, metaRange, metR, midfieldr, miesmuschel, mifa, miniPCH, mlms, mlr, mlr3, mlr3batchmark, mlr3benchmark, mlr3cluster, mlr3db, mlr3fairness, mlr3fda, mlr3filters, mlr3fselect, mlr3hyperband, mlr3inferr, mlr3learners, mlr3mbo, mlr3measures, mlr3misc, mlr3oml, mlr3pipelines, mlr3resampling, mlr3spatial, mlr3spatiotempcv, mlr3summary, mlr3superlearner, mlr3torch, mlr3tuning, mlr3tuningspaces, mlr3viz, mlrCPO, mlrintermbo, mlrMBO, mmrm, modelsummary, monolix2rx, MOSClip, MplusAutomation, MSstats, MSstatsConvert, MSstatsLiP, MSstatsPTM, MSstatsTMT, mvMAPIT, nandb, nat.utils, nestcolor, NetCoupler, NetworkInference, ngsReports, nlmixr2est, nlmixr2extra, nlmixr2lib, nonmem2rx, npi, nseq, oaii, OBIC, occumb, ODEnetwork, ODEsensitivity, oeli, OhdsiShinyAppBuilder, ohun, OmnipathR, OncoBayes2, oncomsm, ontologics, openFDA, OpenML, opentripplanner, optimizeR, Orcs, ordbetareg, otpr, ox, packager, packcircles, pammtools, panstarrs, paradox, parallelMap, ParamHelpers, PaRe, parsermd, pdfminer, PharmacoGx, phers, photosynthesis, pipenostics, pixiedust, PKbioanalysis, PKNCA, pmcalibration, pmwg, portvine, posterior, priorityelasticnet, prioritylasso, priorsense, ProteoDisco, proverbs, psborrow2, pulsar, pushoverr, pvda, pxweb, qpmadr, QTLExperiment, quest, quid, r5r, radous, random.cdisc.data, rasciidoc, rATTAINS, RBesT, RBPcurve, RDML, reactable.extras, rearrr, redcapAPI, REDCapR, REDCapTidieR, replacer, RestRserve, ResultModelManager, retel, rflsgen, Rigma, rJavaEnv, rjstat, rlistings, rminizinc, robnptests, ROI, ROI.plugin.qpoases, rollinglda, romic, rosmium, RPhosFate, RprobitB, rrandvec, rsimsum, rsprite2, rsurveycto, rtables, rtables.officer, rush, rwarrior, Rwclust, rxode2, rxode2ll, sacRebleu, SAMprior, sanityTracker, sasr, savvyr, SCDB, scorepeak, scoringutils, SCRIP, scTensor, sdcLog, SeedMaker, segregation, semantic.dashboard, SeqExpMatch, sevenbridges2, shelter, shiny.blueprint, shiny.telemetry, shinydisconnect, shinyMolBio, shinytest2, simfinapi, simIDM, simmr, simPIC, simulist, sjSDM, slickR, smcfcs, smoof, SNPhood, softbib, sorvi, SpaDES.tools, spanishoddata, sparrow, SPAS, spatialDE, SPEI, spINAR, splatter, SqlRender, sspm, SSVS, stabm, str2str, strata, stratallo, strex, summarytools, superspreading, sweidnumbr, tabshiftr, TBox, teal, teal.code, teal.data, teal.modules.clinical, teal.modules.general, teal.reporter, teal.slice, teal.transform, teal.widgets, tealeaves, tern, tern.gee, tern.mmrm, tern.rbmi, TestGenerator, tf, tidier, tidyhte, tidyMC, tidyrates, tidyrules, tidysq, tidystats, tidyUSDA, timeOmics, tna, topiclabels, TreatmentPatterns, treePlotArea, triact, TrialEmulation, TSEAL, tsmp, tspmeta, typetracer, uci, usefun, vaccineff, vvauditor, vvconverter, webmap, WhatsR, xpectr, xportr, zendown, zenstats, zephyr, zFPKM
Namespace
Overall the package has 370 exported objects. 369 are documented:
%??% allMissing anyInfinite
FALSE TRUE TRUE
anyMissing anyNaN asCount
TRUE TRUE TRUE
asInt asInteger assert
TRUE TRUE TRUE
assert_access assert_array assert_atomic
TRUE TRUE TRUE
assert_atomic_vector assert_character assert_choice
TRUE TRUE TRUE
assert_class assert_complex assert_count
TRUE TRUE TRUE
assert_data_frame assert_data_table assert_date
TRUE TRUE TRUE
assert_directory assert_directory_exists assert_disjunct
TRUE TRUE TRUE
assert_double assert_environment assert_factor
TRUE TRUE TRUE
assert_false assert_file assert_file_exists
TRUE TRUE TRUE
assert_flag assert_formula assert_function
TRUE TRUE TRUE
assert_int assert_integer assert_integerish
TRUE TRUE TRUE
assert_list assert_logical assert_matrix
TRUE TRUE TRUE
assert_multi_class assert_named assert_names
TRUE TRUE TRUE
assert_null assert_number assert_numeric
TRUE TRUE TRUE
assert_os assert_path_for_output assert_permutation
TRUE TRUE TRUE
assert_posixct assert_r6 assert_raw
TRUE TRUE TRUE
assert_scalar assert_scalar_na assert_set_equal
TRUE TRUE TRUE
assert_string assert_subset assert_tibble
TRUE TRUE TRUE
assert_true assert_vector assertAccess
TRUE TRUE TRUE
assertArray assertAtomic assertAtomicVector
TRUE TRUE TRUE
assertCharacter assertChoice assertClass
TRUE TRUE TRUE
assertComplex assertCount assertDataFrame
TRUE TRUE TRUE
assertDataTable assertDate assertDirectory
TRUE TRUE TRUE
assertDirectoryExists assertDisjunct assertDouble
TRUE TRUE TRUE
assertEnvironment assertFactor assertFALSE
TRUE TRUE TRUE
assertFile assertFileExists assertFlag
TRUE TRUE TRUE
assertFormula assertFunction assertInt
TRUE TRUE TRUE
assertInteger assertIntegerish assertList
TRUE TRUE TRUE
assertLogical assertMatrix assertMultiClass
TRUE TRUE TRUE
assertNamed assertNames assertNull
TRUE TRUE TRUE
assertNumber assertNumeric assertOS
TRUE TRUE TRUE
assertPathForOutput assertPermutation assertPOSIXct
TRUE TRUE TRUE
assertR6 assertRaw assertScalar
TRUE TRUE TRUE
assertScalarNA assertSetEqual assertString
TRUE TRUE TRUE
assertSubset assertTibble assertTRUE
TRUE TRUE TRUE
assertVector check_access check_array
TRUE TRUE TRUE
check_atomic check_atomic_vector check_character
TRUE TRUE TRUE
check_choice check_class check_complex
TRUE TRUE TRUE
check_count check_data_frame check_data_table
TRUE TRUE TRUE
check_date check_directory_exists check_disjunct
TRUE TRUE TRUE
check_double check_environment check_factor
TRUE TRUE TRUE
check_false check_file_exists check_flag
TRUE TRUE TRUE
check_formula check_function check_int
TRUE TRUE TRUE
check_integer check_integerish check_list
TRUE TRUE TRUE
check_logical check_matrix check_multi_class
TRUE TRUE TRUE
check_named check_names check_null
TRUE TRUE TRUE
check_number check_numeric check_os
TRUE TRUE TRUE
check_path_for_output check_permutation check_posixct
TRUE TRUE TRUE
check_r6 check_raw check_scalar
TRUE TRUE TRUE
check_scalar_na check_set_equal check_string
TRUE TRUE TRUE
check_subset check_tibble check_true
TRUE TRUE TRUE
check_vector checkAccess checkArray
TRUE TRUE TRUE
checkAtomic checkAtomicVector checkCharacter
TRUE TRUE TRUE
checkChoice checkClass checkComplex
TRUE TRUE TRUE
checkCount checkDataFrame checkDataTable
TRUE TRUE TRUE
checkDate checkDirectory checkDirectoryExists
TRUE TRUE TRUE
checkDisjunct checkDouble checkEnvironment
TRUE TRUE TRUE
checkFactor checkFALSE checkFile
TRUE TRUE TRUE
checkFileExists checkFlag checkFormula
TRUE TRUE TRUE
checkFunction checkInt checkInteger
TRUE TRUE TRUE
checkIntegerish checkList checkLogical
TRUE TRUE TRUE
checkMatrix checkMultiClass checkNamed
TRUE TRUE TRUE
checkNames checkNull checkNumber
TRUE TRUE TRUE
checkNumeric checkOS checkPathForOutput
TRUE TRUE TRUE
checkPermutation checkPOSIXct checkR6
TRUE TRUE TRUE
checkRaw checkScalar checkScalarNA
TRUE TRUE TRUE
checkSetEqual checkString checkSubset
TRUE TRUE TRUE
checkTibble checkTRUE checkVector
TRUE TRUE TRUE
expect_access expect_array expect_atomic
TRUE TRUE TRUE
expect_atomic_vector expect_character expect_choice
TRUE TRUE TRUE
expect_class expect_complex expect_count
TRUE TRUE TRUE
expect_data_frame expect_data_table expect_date
TRUE TRUE TRUE
expect_directory expect_directory_exists expect_disjunct
TRUE TRUE TRUE
expect_double expect_environment expect_factor
TRUE TRUE TRUE
expect_file expect_file_exists expect_flag
TRUE TRUE TRUE
expect_formula expect_function expect_int
TRUE TRUE TRUE
expect_integer expect_integerish expect_list
TRUE TRUE TRUE
expect_logical expect_matrix expect_multi_class
TRUE TRUE TRUE
expect_names expect_number expect_numeric
TRUE TRUE TRUE
expect_os expect_path_for_output expect_permutation
TRUE TRUE TRUE
expect_posixct expect_r6 expect_raw
TRUE TRUE TRUE
expect_scalar expect_scalar_na expect_set_equal
TRUE TRUE TRUE
expect_string expect_subset expect_tibble
TRUE TRUE TRUE
makeAssertCollection makeAssertion makeAssertionFunction
TRUE TRUE TRUE
makeExpectation makeExpectationFunction makeTest
TRUE TRUE TRUE
makeTestFunction matchArg qassert
TRUE TRUE TRUE
qassertr qexpect qexpectr
TRUE TRUE TRUE
qtest qtestr register_test_backend
TRUE TRUE TRUE
reportAssertions test_access test_array
TRUE TRUE TRUE
test_atomic test_atomic_vector test_character
TRUE TRUE TRUE
test_choice test_class test_complex
TRUE TRUE TRUE
test_count test_data_frame test_data_table
TRUE TRUE TRUE
test_date test_directory test_directory_exists
TRUE TRUE TRUE
test_disjunct test_double test_environment
TRUE TRUE TRUE
test_factor test_false test_file_exists
TRUE TRUE TRUE
test_flag test_formula test_function
TRUE TRUE TRUE
test_int test_integer test_integerish
TRUE TRUE TRUE
test_list test_logical test_matrix
TRUE TRUE TRUE
test_multi_class test_named test_names
TRUE TRUE TRUE
test_null test_number test_numeric
TRUE TRUE TRUE
test_os test_path_for_output test_permutation
TRUE TRUE TRUE
test_posixct test_r6 test_raw
TRUE TRUE TRUE
test_scalar test_scalar_na test_set_equal
TRUE TRUE TRUE
test_string test_subset test_tibble
TRUE TRUE TRUE
test_true test_vector testAccess
TRUE TRUE TRUE
testArray testAtomic testAtomicVector
TRUE TRUE TRUE
testCharacter testChoice testClass
TRUE TRUE TRUE
testComplex testCount testDataFrame
TRUE TRUE TRUE
testDataTable testDate testDirectory
TRUE TRUE TRUE
testDirectoryExists testDisjunct testDouble
TRUE TRUE TRUE
testEnvironment testFactor testFALSE
TRUE TRUE TRUE
testFile testFileExists testFlag
TRUE TRUE TRUE
testFormula testFunction testInt
TRUE TRUE TRUE
testInteger testIntegerish testList
TRUE TRUE TRUE
testLogical testMatrix testMultiClass
TRUE TRUE TRUE
testNamed testNames testNull
TRUE TRUE TRUE
testNumber testNumeric testOS
TRUE TRUE TRUE
testPathForOutput testPermutation testPOSIXct
TRUE TRUE TRUE
testR6 testRaw testScalar
TRUE TRUE TRUE
testScalarNA testSetEqual testString
TRUE TRUE TRUE
testSubset testTibble testTRUE
TRUE TRUE TRUE
testVector vname wf
TRUE TRUE TRUE
wl
TRUE Examples
There are 64 help pages with examples, from 64 (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 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-16 04:10:31 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
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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_6ba12b84-2f44-4ad5-be34-dae80230865f
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_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_6ba12b84-2f44-4ad5-be34-dae80230865f
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
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GITHUB_RETENTION_DAYS 90
GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13351230359
GITHUB_RUN_NUMBER 93
GITHUB_SERVER_URL https://github.com
GITHUB_SHA b7796ef4941f135c4d61c83d399bb9fa3a477379
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_6ba12b84-2f44-4ad5-be34-dae80230865f
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 b7796ef4941f135c4d61c83d399bb9fa3a477379
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 cea0ff53850b49ce839e8b7d02d05041
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 8:7454
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/RtmpCk6Ofc
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1bc3226168e2_1739679026
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/Rtmp5B51iC
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 9
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_d0120492-4873-4b13-9ede-fb6d0d82420b
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 829
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/1001These 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: 0x560f8f1bb910>
<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: 0x560f8e942528>
<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: 0x560f8e693520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_checkmate_v2.3.2-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