script.R

Execution end time

2025-09-06T10:32:10 Coordinated Universal Time

Path to script

/home/runner/work/examples/examples/logging/script.R

Summary

success

Script

# file: script.R
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

file_path <- "script.log"

average_mpg <- mtcars %>%
  group_by(cyl) %>%
  summarise(average_mpg = mean(mpg, na.rm = TRUE))

model <- lm(mpg ~ wt, data = mtcars)
summary(model)

Call:
lm(formula = mpg ~ wt, data = mtcars)

Residuals:
    Min      1Q  Median      3Q     Max 
-4.5432 -2.3647 -0.1252  1.4096  6.8727 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  37.2851     1.8776  19.858  < 2e-16 ***
wt           -5.3445     0.5591  -9.559 1.29e-10 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 3.046 on 30 degrees of freedom
Multiple R-squared:  0.7528,    Adjusted R-squared:  0.7446 
F-statistic: 91.38 on 1 and 30 DF,  p-value: 1.294e-10

# log file path: script.log

Session info

Platform

Setting	Value
version	R version 4.5.1 (2025-06-13)
os	Ubuntu 24.04.3 LTS
system	x86_64, linux-gnu
ui	X11
language	(EN)
collate	C.UTF-8
ctype	C.UTF-8
tz	UTC
date	2025-09-06
pandoc	3.1.3 @ /usr/bin/ (via rmarkdown)
quarto	1.7.34 @ /usr/local/bin/quarto

R packages used directly

Package	Version	Source
dplyr	1.1.4	CRAN (R 4.5.1)
knitr	1.50	CRAN (R 4.5.1)
rmarkdown	2.29	CRAN (R 4.5.1)
sessioninfo	1.2.3	any (@1.2.3)

R packages used indirectly

Package	Version	Source
cli	3.6.5	CRAN (R 4.5.1)
digest	0.6.37	CRAN (R 4.5.1)
evaluate	1.0.5	CRAN (R 4.5.1)
fastmap	1.2.0	CRAN (R 4.5.1)
generics	0.1.4	CRAN (R 4.5.1)
glue	1.8.0	CRAN (R 4.5.1)
htmltools	0.5.8.1	CRAN (R 4.5.1)
jsonlite	2.0.0	CRAN (R 4.5.1)
lattice	0.22-7	CRAN (R 4.5.1)
lifecycle	1.0.4	CRAN (R 4.5.1)
magrittr	2.0.3	CRAN (R 4.5.1)
Matrix	1.7-3	CRAN (R 4.5.1)
pillar	1.11.0	CRAN (R 4.5.1)
pkgconfig	2.0.3	CRAN (R 4.5.1)
png	0.1-8	CRAN (R 4.5.1)
R6	2.6.1	CRAN (R 4.5.1)
Rcpp	1.1.0	CRAN (R 4.5.1)
reticulate	1.43.0	CRAN (R 4.5.1)
rlang	1.1.6	CRAN (R 4.5.1)
tibble	3.3.0	CRAN (R 4.5.1)
tidyselect	1.2.1	CRAN (R 4.5.1)
vctrs	0.6.5	CRAN (R 4.5.1)
xfun	0.53	CRAN (R 4.5.1)
yaml	2.3.10	CRAN (R 4.5.1)

Environment variables

Variable	Value
_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/27.3.13750724
ANDROID_NDK_HOME	/usr/local/lib/android/sdk/ndk/27.3.13750724
ANDROID_NDK_LATEST_HOME	/usr/local/lib/android/sdk/ndk/28.2.13676358
ANDROID_NDK_ROOT	/usr/local/lib/android/sdk/ndk/27.3.13750724
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
CALLR_IS_RUNNING	true
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
DOTNET_MULTILEVEL_LOOKUP	0
DOTNET_NOLOGO	1
DOTNET_SKIP_FIRST_TIME_EXPERIENCE	1
EDGEWEBDRIVER	/usr/local/share/edge_driver
EDITOR	vi
ENABLE_RUNNER_TRACING	true
GECKOWEBDRIVER	/usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX	/usr/local
GITHUB_ACTION	__quarto-dev_quarto-actions_2
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
GITHUB_ACTIONS	true
GITHUB_ACTOR	pawelru
GITHUB_ACTOR_ID	12943682
GITHUB_API_URL	https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV	/home/runner/work/_temp/_runner_file_commands/set_env_a2d16531-d3a8-4c2b-9680-3f30e07a63ea
GITHUB_EVENT_NAME	schedule
GITHUB_GRAPHQL_URL	https://api.github.com/graphql
GITHUB_HEAD_REF
GITHUB_JOB	build-deploy
GITHUB_OUTPUT	/home/runner/work/_temp/_runner_file_commands/set_output_a2d16531-d3a8-4c2b-9680-3f30e07a63ea
GITHUB_REF	refs/heads/main
GITHUB_REF_NAME	main
GITHUB_REF_PROTECTED	true
GITHUB_REF_TYPE	branch
GITHUB_REPOSITORY	pharmaverse/examples
GITHUB_REPOSITORY_ID	655720846
GITHUB_REPOSITORY_OWNER	pharmaverse
GITHUB_REPOSITORY_OWNER_ID	84541169
GITHUB_RETENTION_DAYS	90
GITHUB_RUN_ATTEMPT	1
GITHUB_RUN_ID	17513347478
GITHUB_RUN_NUMBER	884
GITHUB_SERVER_URL	https://github.com
GITHUB_SHA	9273fa9fbdce2649c89dd9d6f4d73efe8d02f2fc
GITHUB_STATE	/home/runner/work/_temp/_runner_file_commands/save_state_a2d16531-d3a8-4c2b-9680-3f30e07a63ea
GITHUB_STEP_SUMMARY	/home/runner/work/_temp/_runner_file_commands/step_summary_a2d16531-d3a8-4c2b-9680-3f30e07a63ea
GITHUB_TRIGGERING_ACTOR	pawelru
GITHUB_WORKFLOW	Build & Deploy Website
GITHUB_WORKFLOW_REF	pharmaverse/examples/.github/workflows/docs.yaml@refs/heads/main
GITHUB_WORKFLOW_SHA	9273fa9fbdce2649c89dd9d6f4d73efe8d02f2fc
GITHUB_WORKSPACE	/home/runner/work/examples/examples
GOROOT_1_22_X64	/opt/hostedtoolcache/go/1.22.12/x64
GOROOT_1_23_X64	/opt/hostedtoolcache/go/1.23.12/x64
GOROOT_1_24_X64	/opt/hostedtoolcache/go/1.24.6/x64
GRADLE_HOME	/usr/share/gradle-9.0.0
HOME	/home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS	3650
HOMEBREW_NO_AUTO_UPDATE	1
ImageOS	ubuntu24
ImageVersion	20250831.1.0
INVOCATION_ID	ba57f85b86cb46de9c43115d1d108feb
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	9:14094
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LN_S	ln -s
LOGNAME	runner
MAKE	make
MEMORY_PRESSURE_WATCH	/sys/fs/cgroup/system.slice/hosted-compute-agent.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
PIPX_BIN_DIR	/opt/pipx_bin
PIPX_HOME	/opt/pipx
PKGCACHE_HTTP_VERSION	2
POWERSHELL_DISTRIBUTION_CHANNEL	GitHub-Actions-ubuntu24
PROCESSX_PS23af985944e_1757154726	YES
PROCESSX_PS23c570427552_1757154727	YES
PWD	/tmp/Rtmp3lJgEC/file23af17427d3
QUARTO_DENO	/opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_FILE	dummy.qmd
QUARTO_FILTER_DEPENDENCY_FILE	/tmp/quarto-session10d8d790bb8d2d75/ad1c9024b779d578/7ba6093a33a07bca
QUARTO_PRINT_STACK	true
QUARTO_PROFILE
QUARTO_PROJECT_DIR	/tmp/Rtmp3lJgEC/file23af17427d3
QUARTO_PROJECT_ROOT	/tmp/Rtmp3lJgEC/file23af17427d3
QUARTO_R	/opt/R/4.5.1/lib/R/bin
QUARTO_ROOT	/
R_ARCH
R_BROWSER	xdg-open
R_BZIPCMD	/usr/bin/bzip2
R_DOC_DIR	/opt/R/4.5.1/lib/R/doc
R_GZIPCMD	/usr/bin/gzip
R_HOME	/opt/R/4.5.1/lib/R
R_INCLUDE_DIR	/opt/R/4.5.1/lib/R/include
R_LIB_FOR_PAK	/opt/R/4.5.1/lib/R/site-library
R_LIBS_SITE	/opt/R/4.5.1/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/Rtmpc9SJc1
R_SHARE_DIR	/opt/R/4.5.1/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 1000062617
RUNNER_OS	Linux
RUNNER_TEMP	/home/runner/work/_temp
RUNNER_TOOL_CACHE	/opt/hostedtoolcache
RUNNER_TRACKING_ID	github_65a93089-db04-43bb-a2bb-28cedf9cbcda
RUNNER_WORKSPACE	/home/runner/work/examples
SED	/usr/bin/sed
SGX_AESM_ADDR	1
SHELL	/bin/bash
SHLVL	3
SYSTEMD_EXEC_PID	1893
TAR	/usr/bin/tar
TERM	dumb
TZ	UTC
USER	runner
VCPKG_INSTALLATION_ROOT	/usr/local/share/vcpkg
WHIRL_LOG_MSG	/tmp/Rtmp3lJgEC/file23af17427d3/log_msg.json
XDG_CONFIG_HOME	/home/runner/.config
XDG_RUNTIME_DIR	/run/user/1001

Options

Option	Value
add.smooth	TRUE
ambiguousMethodSelection	function (cond) , NULL
bitmapType	cairo
browser	xdg-open
browserNLdisabled	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), }, }
catch.script.errors	FALSE
CBoundsCheck	FALSE
check.bounds	FALSE
citation.bibtex.max	1
continue	+
contrasts	contr.treatment, contr.poly
defaultPackages	datasets , utils , grDevices, graphics , stats , methods
demo.ask	default
deparse.cutoff	60
device	function (width = 7, height = 7, ...) , {, grDevices::pdf(NULL, width, height, ...), }
device.ask.default	FALSE
digits	7
dplyr.show_progress	TRUE
dvipscmd	dvips
echo	FALSE
editor	vi
encoding	native.enc
example.ask	default
expressions	5000
help.search.types	vignette, demo , help
help.try.all.packages	FALSE
htmltools.preserve.raw	TRUE
HTTPUserAgent	R/4.5.1 R (4.5.1 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions
internet.info	2
keep.parse.data	TRUE
keep.parse.data.pkgs	FALSE
keep.source	FALSE
keep.source.pkgs	FALSE
knitr.in.progress	TRUE
locatorBell	TRUE
mailer	mailto
matprod	default
max.contour.segments	25000
max.print	99999
menu.graphics	TRUE
na.action	na.omit
Ncpus	1
nwarnings	50
OutDec	.
pager	/opt/R/4.5.1/lib/R/bin/pager
papersize	a4
PCRE_limit_recursion	NA
PCRE_study	FALSE
PCRE_use_JIT	TRUE
pdfviewer	/usr/bin/xdg-open
pkgType	source
printcmd	/usr/bin/lpr
prompt	>
repos	https://cran.rstudio.com
rlang_trace_top_env	<environment: R_GlobalEnv>
scipen	0
show.coef.Pvalues	TRUE
show.error.messages	TRUE
show.signif.stars	TRUE
showErrorCalls	TRUE
showNCalls	50
showWarnCalls	FALSE
str	no, 3, 4, 99, TRUE, function (x, ...) , format(x, trim = TRUE, drop0trailing = TRUE, ...)
str.dendrogram.last	`
texi2dvi	/usr/bin/texi2dvi
tikzMetricsDictionary	logging-tikzDictionary
timeout	60
try.outFile	3
ts.eps	1e-05
ts.S.compat	FALSE
unzip	/usr/bin/unzip
useFancyQuotes	FALSE
verbose	FALSE
warn	0
warning.length	1000
warnPartialMatchArgs	FALSE
warnPartialMatchAttr	FALSE
warnPartialMatchDollar	FALSE
whirl.verbosity_level	minimal
width	80