script.R

Execution end time

2025-05-24T10:31:30 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 4.5.0 (2025-04-11)
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 2025-05-24
pandoc 3.1.3 @ /usr/bin/ (via rmarkdown)
quarto 1.7.31 @ /usr/local/bin/quarto

R Packages

Package Version Date (UTC) Source
callr 3.7.6 2024-03-25 CRAN (R 4.5.0)
cli 3.6.5 2025-04-23 CRAN (R 4.5.0)
digest 0.6.37 2024-08-19 CRAN (R 4.5.0)
dplyr 1.1.4 2023-11-17 CRAN (R 4.5.0)
evaluate 1.0.3 2025-01-10 CRAN (R 4.5.0)
fastmap 1.2.0 2024-05-15 CRAN (R 4.5.0)
generics 0.1.4 2025-05-09 CRAN (R 4.5.0)
glue 1.8.0 2024-09-30 CRAN (R 4.5.0)
htmltools 0.5.8.1 2024-04-04 CRAN (R 4.5.0)
jsonlite 2.0.0 2025-03-27 CRAN (R 4.5.0)
knitr 1.50 2025-03-16 CRAN (R 4.5.0)
lattice 0.22-6 2024-03-20 CRAN (R 4.5.0)
lifecycle 1.0.4 2023-11-07 CRAN (R 4.5.0)
magrittr 2.0.3 2022-03-30 CRAN (R 4.5.0)
Matrix 1.7-3 2025-03-11 CRAN (R 4.5.0)
pillar 1.10.2 2025-04-05 CRAN (R 4.5.0)
pkgconfig 2.0.3 2019-09-22 CRAN (R 4.5.0)
png 0.1-8 2022-11-29 CRAN (R 4.5.0)
processx 3.8.6 2025-02-21 CRAN (R 4.5.0)
ps 1.9.1 2025-04-12 CRAN (R 4.5.0)
R6 2.6.1 2025-02-15 CRAN (R 4.5.0)
Rcpp 1.0.14 2025-01-12 CRAN (R 4.5.0)
reticulate 1.42.0 2025-03-25 CRAN (R 4.5.0)
rlang 1.1.6 2025-04-11 CRAN (R 4.5.0)
rmarkdown 2.29 2024-11-04 CRAN (R 4.5.0)
sessioninfo 1.2.3 2025-02-05 any (@1.2.3)
tibble 3.2.1 2023-03-20 CRAN (R 4.5.0)
tidyselect 1.2.1 2024-03-11 CRAN (R 4.5.0)
vctrs 0.6.5 2023-12-01 CRAN (R 4.5.0)
whirl 0.2.0 2025-04-15 CRAN (R 4.5.0)
xfun 0.52 2025-04-02 CRAN (R 4.5.0)
yaml 2.3.10 2024-07-26 CRAN (R 4.5.0)

Environment variables

Setting 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/28.1.13356709
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/libplu<br>gin.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_PATH /home/runner/work/_actions/quarto-dev/quarto<br>-actions/v2/render
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_command<br>s/set_env_c3c6240a-48e5-43e7-b239-e53a7396e59<br>2
GITHUB_EVENT_NAME schedule
GITHUB_EVENT_PATH /home/runner/work/_temp/_github_workflow/eve<br>nt.json
GITHUB_GRAPHQL_URL https://api.github.com/graphql
GITHUB_HEAD_REF
GITHUB_JOB build-deploy
GITHUB_OUTPUT /home/runner/work/_temp/_runner_file_command<br>s/set_output_c3c6240a-48e5-43e7-b239-e53a7396<br>e592
GITHUB_PATH /home/runner/work/_temp/_runner_file_command<br>s/add_path_c3c6240a-48e5-43e7-b239-e53a7396e5<br>92
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 15226156413
GITHUB_RUN_NUMBER 753
GITHUB_SERVER_URL https://github.com
GITHUB_SHA 6eb73b606ea939a85901f3320548bfe06c401240
GITHUB_STATE /home/runner/work/_temp/_runner_file_command<br>s/save_state_c3c6240a-48e5-43e7-b239-e53a7396<br>e592
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_command<br>s/step_summary_c3c6240a-48e5-43e7-b239-e53a73<br>96e592
GITHUB_TRIGGERING_ACTOR pawelru
GITHUB_WORKFLOW Build & Deploy Website
GITHUB_WORKFLOW_REF pharmaverse/examples/.github/workflows/docs.<br>yaml@refs/heads/main
GITHUB_WORKFLOW_SHA 6eb73b606ea939a85901f3320548bfe06c401240
GITHUB_WORKSPACE /home/runner/work/examples/examples
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/1.23.9/x64
GRADLE_HOME /usr/share/gradle-8.14
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS 3650
HOMEBREW_NO_AUTO_UPDATE 1
ImageOS ubuntu24
ImageVersion 20250511.1.0
INVOCATION_ID 74f0f497c4ff4385b7bc6ccf3a497600
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 9:14511
LANG C.UTF-8
LD_LIBRARY_PATH /opt/R/4.5.0/lib/R/lib:/usr/local/lib:/usr/l<br>ib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-j<br>dk-amd64/lib/server:/opt/R/4.5.0/lib/R/lib:/u<br>sr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/l<br>ib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R<br>/4.5.0/lib/R/lib:/usr/local/lib:/usr/lib/x86_<br>64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd6<br>4/lib/server
LN_S ln -s
LOGNAME runner
MAKE make
MEMORY_PRESSURE_WATCH /sys/fs/cgroup/system.slice/hosted-compute-a<br>gent.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_<br>bin:/home/runner/.cargo/bin:/home/runner/.con<br>fig/composer/vendor/bin:/usr/local/.ghcup/bin<br>:/home/runner/.dotnet/tools:/usr/local/sbin:/<br>usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/<br>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_PS203c3f81ad19_1748082686 YES
PROCESSX_PS20526a270212_1748082686 YES
PWD /tmp/Rtmp2yVpFl/file203c4277b554
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_FILE dummy.qmd
QUARTO_DOCUMENT_PATH /tmp/Rtmp2yVpFl/file203c4277b554
QUARTO_FILTER_DEPENDENCY_FILE /tmp/quarto-sessionc5e5672f1fdbb36b/6a19dde5<br>8df2bb23/141265f43e06090a
QUARTO_PRINT_STACK true
QUARTO_PROFILE
QUARTO_PROJECT_DIR /tmp/Rtmp2yVpFl/file203c4277b554
QUARTO_PROJECT_ROOT /tmp/Rtmp2yVpFl/file203c4277b554
QUARTO_ROOT /
QUARTO_SHARE_PATH /opt/quarto/share
R_ARCH
R_BROWSER xdg-open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/4.5.0/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/4.5.0/lib/R
R_INCLUDE_DIR /opt/R/4.5.0/lib/R/include
R_LIB_FOR_PAK /opt/R/4.5.0/lib/R/site-library
R_LIBS_SITE /opt/R/4.5.0/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/RtmpAUx3Ve
R_SHARE_DIR /opt/R/4.5.0/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 1000030099
RUNNER_OS Linux
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_62328c0f-94de-4c25-b5ec-f09fb2c52848
RUNNER_WORKSPACE /home/runner/work/examples
SED /usr/bin/sed
SELENIUM_JAR_PATH /usr/share/java/selenium-server.jar
SGX_AESM_ADDR 1
SHELL /bin/bash
SHLVL 3
SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 1882
TAR /usr/bin/tar
TERM dumb
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT /usr/local/share/vcpkg
WHIRL_LOG_MSG /tmp/Rtmp2yVpFl/file203c4277b554/log_msg.jso<br>n
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001

Option settings

Setting 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.unordered contr.treatment
contrasts.ordered contr.poly
defaultPackages1 datasets
defaultPackages2 utils
defaultPackages3 grDevices
defaultPackages4 graphics
defaultPackages5 stats
defaultPackages6 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.types1 vignette
help.search.types2 demo
help.search.types3 help
help.try.all.packages FALSE
htmltools.preserve.raw TRUE
HTTPUserAgent R/4.5.0 R (4.5.0 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/4.5.0/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.CRAN 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.strict.width no
str.digits.d 3
str.vec.len 4
str.list.len 99
str.drop.deparse.attr TRUE
str.formatNum 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