script.R

Execution end time

2025-07-22T10:38:21 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 24.04.2 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz UTC
date 2025-07-22
pandoc 3.1.3 @ /usr/bin/ (via rmarkdown)
quarto 1.7.32 @ /usr/local/bin/quarto

R Packages

Package Version Attached Source
cli 3.6.5 No CRAN (R 4.5.1)
digest 0.6.37 No CRAN (R 4.5.1)
dplyr 1.1.4 Yes CRAN (R 4.5.1)
evaluate 1.0.4 No CRAN (R 4.5.1)
fastmap 1.2.0 No CRAN (R 4.5.1)
generics 0.1.4 No CRAN (R 4.5.1)
glue 1.8.0 No CRAN (R 4.5.1)
htmltools 0.5.8.1 No CRAN (R 4.5.1)
jsonlite 2.0.0 No CRAN (R 4.5.1)
knitr 1.50 No CRAN (R 4.5.1)
lattice 0.22-7 No CRAN (R 4.5.1)
lifecycle 1.0.4 No CRAN (R 4.5.1)
magrittr 2.0.3 No CRAN (R 4.5.1)
Matrix 1.7-3 No CRAN (R 4.5.1)
pillar 1.11.0 No CRAN (R 4.5.1)
pkgconfig 2.0.3 No CRAN (R 4.5.1)
png 0.1-8 No CRAN (R 4.5.1)
R6 2.6.1 No CRAN (R 4.5.1)
Rcpp 1.1.0 No CRAN (R 4.5.1)
reticulate 1.43.0 No CRAN (R 4.5.1)
rlang 1.1.6 No CRAN (R 4.5.1)
rmarkdown 2.29 No CRAN (R 4.5.1)
sessioninfo 1.2.3 No any (@1.2.3)
tibble 3.3.0 No CRAN (R 4.5.1)
tidyselect 1.2.1 No CRAN (R 4.5.1)
vctrs 0.6.5 No CRAN (R 4.5.1)
xfun 0.52 No CRAN (R 4.5.1)
yaml 2.3.10 No 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/27.2.12479018
ANDROID_NDK_HOME /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_LATEST_HOME /usr/local/lib/android/sdk/ndk/28.2.13676358
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
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_5a4ca78f-e154-4df6-87f1-e5afcaa372e4
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_5a4ca78f-e154-4df6-87f1-e5afcaa372e4
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 16441811601
GITHUB_RUN_NUMBER 812
GITHUB_SERVER_URL https://github.com
GITHUB_SHA 6eb73b606ea939a85901f3320548bfe06c401240
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_5a4ca78f-e154-4df6-87f1-e5afcaa372e4
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_5a4ca78f-e154-4df6-87f1-e5afcaa372e4
GITHUB_TRIGGERING_ACTOR pawelru
GITHUB_WORKFLOW Build & Deploy Website
GITHUB_WORKFLOW_REF pharmaverse/examples/.github/workflows/docs.yaml@refs/heads/main
GITHUB_WORKFLOW_SHA 6eb73b606ea939a85901f3320548bfe06c401240
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/1.23.10/x64
GOROOT_1_24_X64 /opt/hostedtoolcache/go/1.24.4/x64
GRADLE_HOME /usr/share/gradle-8.14.3
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS 3650
HOMEBREW_NO_AUTO_UPDATE 1
ImageOS ubuntu24
ImageVersion 20250710.1.0
INVOCATION_ID 6165b5d2b5ce4b70b9b4e1cd9aec02bb
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 9:10232
LANG C.UTF-8
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_PS22023d013946_1753180697 YES
PROCESSX_PS2219629ed94f_1753180697 YES
PWD /tmp/RtmpC8uUws/file22021a00ce3
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_FILE dummy.qmd
QUARTO_FILTER_DEPENDENCY_FILE /tmp/quarto-sessionb5270cd55ced47e4/84d73a3456156a4e/28572ca62bae80ac
QUARTO_PRINT_STACK true
QUARTO_PROFILE
QUARTO_PROJECT_DIR /tmp/RtmpC8uUws/file22021a00ce3
QUARTO_PROJECT_ROOT /tmp/RtmpC8uUws/file22021a00ce3
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/RtmpNKJuGQ
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 1000048020
RUNNER_OS Linux
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_59516ab8-472c-4458-a94b-de011812465b
RUNNER_WORKSPACE /home/runner/work/examples
SED /usr/bin/sed
SGX_AESM_ADDR 1
SHELL /bin/bash
SHLVL 3
SYSTEMD_EXEC_PID 1889
TAR /usr/bin/tar
TERM dumb
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT /usr/local/share/vcpkg
WHIRL_LOG_MSG /tmp/RtmpC8uUws/file22021a00ce3/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 letter
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 dummy-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
width 80