Validation Report - bupaR@0.5.4
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 bupaR
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | FALSE |
| exported_namespace | 106 |
| has_vignettes | 0 |
| export_help | 106 |
| has_website | TRUE |
| has_maintainer | Gert Janssenswillen gert.janssenswillen@uhasselt.be |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_source_control | https://github.com/bupaverse/bupaR/ |
| has_bug_reports_url | 0 |
| downloads_1yr | 17169 |
| reverse_dependencies | 11 |
| has_examples | 0.8735632 |
| dependencies | 19 |
| license | MIT + 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 | magrittr | Imports |
| 2 | dplyr | Imports |
| 3 | data.table | Imports |
| 4 | shiny | Imports |
| 5 | miniUI | Imports |
| 6 | pillar | Imports |
| 7 | purrr | Imports |
| 8 | tidyr | Imports |
| 9 | tibble | Imports |
| 10 | glue | Imports |
| 11 | forcats | Imports |
| 12 | rlang (>= 1.0.0) | Imports |
| 13 | cli (>= 3.2.0) | Imports |
| 14 | eventdataR (>= 0.2.0) | Imports |
| 15 | stringr | Imports |
| 16 | stringi | Imports |
| 17 | lubridate | Imports |
| 18 | lifecycle | Imports |
| 19 | ggplot2 | Imports |
Package dependencies
Reverse dependencies
Overall the package has 11 reverse dependencies:
bupaverse, daqapo, edeaR, heuristicsmineR, processanimateR, processcheckR, processmapR, processmonitR, processpredictR, psmineR, xesreadR
Namespace
Overall the package has 106 exported objects. 105 are documented:
%>% act_collapse
FALSE TRUE
act_recode act_unite
TRUE TRUE
activities activities_to_eventlog
TRUE TRUE
activity_id activity_instance_id
TRUE TRUE
activity_labels activitylog
TRUE TRUE
add_end_activity add_start_activity
TRUE TRUE
arrange assign_instance_id
TRUE TRUE
case_id case_labels
TRUE TRUE
case_list cases
TRUE TRUE
convert_timestamps count
TRUE TRUE
detect_resource_inconsistencies dmy
TRUE TRUE
dmy_h dmy_hm
TRUE TRUE
dmy_hms durations
TRUE TRUE
eventlog events_to_activitylog
TRUE TRUE
fill filter
TRUE TRUE
filter_attributes first_n
TRUE TRUE
fix_resource_inconsistencies group_by
TRUE TRUE
group_by_activity group_by_activity_instance
TRUE TRUE
group_by_case group_by_ids
TRUE TRUE
group_by_resource group_by_resource_activity
TRUE TRUE
ieventlog is.activitylog
TRUE TRUE
is.eventlog is.grouped_activitylog
TRUE TRUE
is.grouped_eventlog is.grouped_log
TRUE TRUE
is.log isimple_eventlog
TRUE TRUE
last_n lifecycle_id
TRUE TRUE
lifecycle_labels lifecycles
TRUE TRUE
mapping mdy
TRUE TRUE
mdy_h mdy_hm
TRUE TRUE
mdy_hms mutate
TRUE TRUE
n_activities n_activity_instances
TRUE TRUE
n_cases n_events
TRUE TRUE
n_resources n_traces
TRUE TRUE
re_map rename
TRUE TRUE
resource_id resource_labels
TRUE TRUE
resources sample_n
TRUE TRUE
scale_color_continuous_bupaR scale_color_discrete_bupaR
TRUE TRUE
scale_color_gradient_bupaR scale_color_gradient2_bupaR
TRUE TRUE
scale_fill_continuous_bupaR scale_fill_discrete_bupaR
TRUE TRUE
scale_fill_gradient_bupaR scale_fill_gradient2_bupaR
TRUE TRUE
select select_ids
TRUE TRUE
set_activity_id set_activity_instance_id
TRUE TRUE
set_case_id set_lifecycle_id
TRUE TRUE
set_resource_id set_timestamp
TRUE TRUE
simple_eventlog slice
TRUE TRUE
slice_activities slice_events
TRUE TRUE
slice_sample standardize_lifecycle
TRUE TRUE
summarise timestamp
TRUE TRUE
timestamps to_activitylog
TRUE TRUE
to_eventlog trace_list
TRUE TRUE
traces ungroup
TRUE TRUE
ungroup_eventlog unite
TRUE TRUE
ymd ymd_h
TRUE TRUE
ymd_hm ymd_hms
TRUE TRUE Examples
There are 76 help pages with examples, from 87 (87.36 %).
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 | 2025-02-15 04:55:36 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
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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
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BUNDLE_EXT linux-amd64.deb
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CI true
CONDA /usr/share/miniconda
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DOTNET_MULTILEVEL_LOOKUP
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GITHUB_HEAD_REF
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GITHUB_REF refs/heads/main
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_f8c509ad-0cb5-478b-b30f-5ae6b6902174
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA 0c0fc0bc0d98c42191882830260da9dad887eea6
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
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HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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INVOCATION_ID 5c7bed78c97148e29cb0b195c5a78088
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
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JOURNAL_STREAM 8:8239
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
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MEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=
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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
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PIPX_BIN_DIR /opt/pipx_bin
PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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PROCESSX_PS1ccd331588f4_1739595331
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
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R_PAPERSIZE letter
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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/RtmpiDohSl
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 8
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RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_4fe491a9-475c-47ca-863f-ba9d90fd5980
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
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STATS_TRP true
STATS_UE true
STATS_V3PS true
STATS_VMD true
STATS_VMFE true
SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 830
TAR /usr/bin/tar
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
/usr/local/share/vcpkg
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/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: 0x564592fc3910>
<environment: namespace:cli>
$catch.script.errors
[1] FALSE
$CBoundsCheck
[1] FALSE
$check.bounds
[1] FALSE
$citation.bibtex.max
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$continue
[1] "+ "
$contrasts
unordered ordered
"contr.treatment" "contr.poly"
$covr.record_tests
[1] TRUE
$defaultPackages
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$demo.ask
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$deparse.cutoff
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$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x564592fc0f38>
<environment: namespace:knitr>
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$digits
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$dvipscmd
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$echo
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$example.ask
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$expressions
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$help.search.types
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$locatorBell
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$mailer
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$matprod
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$max.print
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$PCRE_limit_recursion
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$pdfviewer
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$pkgType
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$printcmd
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$prompt
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$repos
CRAN
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$rl_word_breaks
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$rlang_trace_top_env
<environment: R_GlobalEnv>
$scipen
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$show.coef.Pvalues
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
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$showErrorCalls
[1] TRUE
$showNCalls
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$str
$str$strict.width
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$str$digits.d
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$str$vec.len
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$str$list.len
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$str$deparse.lines
NULL
$str$drop.deparse.attr
[1] TRUE
$str$formatNum
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x56459249b520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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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
$unzip
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$useFancyQuotes
[1] FALSE
$verbose
[1] FALSE
$warn
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$warning.length
[1] 1000
$warnPartialMatchArgs
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$warnPartialMatchAttr
[1] FALSE
$warnPartialMatchDollar
[1] FALSE
$width
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