R Under development (unstable) (2025-05-15 r88204 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(worcs) Welcome to WORCS: Workflow for Open Reproducible Code in Science. Run `check_worcs_installation()` to make sure all dependencies are installed. For more information, see the package vignettes () and accompanying paper: Van Lissa and colleagues (2020) () > > test_check("worcs") "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS manuscript.knit.md --to gfm+tex_math_dollars-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\default.md" "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS manuscript.md --to html4 --from gfm+tex_math_dollars --output manuscript.html --embed-resources --standalone --highlight-style pygments --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\preview.html" --variable "github-markdown-css:D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\github.css" --metadata pagetitle=PREVIEW --mathjax | | | 0% | |============== | 20% | |============================ | 40% | 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|=============================================== | 67% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% → de-duplicating _targets/meta/meta → reading _targets/meta/meta → parsing _targets/meta/meta → noting builders and branches → parsing _targets/meta/meta → restricting metadata records → querying 0 local files in _targets/objects → parsing _targets/meta/process + data dispatched ✔ data completed [10ms, 1.74 kB] + model dispatched ✔ model completed [10ms, 107 B] + manuscript dispatched Quitting from manuscript.Rmd:6-15 [setup] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ✖ manuscript errored → de-duplicating _targets/meta/meta ✖ errored pipeline [921ms, 2 completed, 0 skipped] Warning messages: 1: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. 2: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. 3: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS manuscript.knit.md --to gfm+tex_math_dollars-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\default.md" "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS manuscript.md --to html4 --from gfm+tex_math_dollars --output manuscript.html --embed-resources --standalone --highlight-style pygments --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\preview.html" --variable "github-markdown-css:D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\templates\github_document\resources\github.css" --metadata pagetitle=PREVIEW --mathjax # Created by use_targets(). # Follow the comments below to fill in this target script. # Then follow the manual to check and run the pipeline: # https://books.ropensci.org/targets/walkthrough.html#inspect-the-pipeline # Load packages required to define the pipeline: library(targets) # library(tarchetypes) # Load other packages as needed. # Set target options: tar_option_set( packages = c("tibble") # Packages that your targets need for their tasks. # format = "qs", # Optionally set the default storage format. qs is fast. # # Pipelines that take a long time to run may benefit from # optional distributed computing. To use this capability # in tar_make(), supply a {crew} controller # as discussed at https://books.ropensci.org/targets/crew.html. # Choose a controller that suits your needs. For example, the following # sets a controller that scales up to a maximum of two workers # which run as local R processes. Each worker launches when there is work # to do and exits if 60 seconds pass with no tasks to run. # # controller = crew::crew_controller_local(workers = 2, seconds_idle = 60) # # Alternatively, if you want workers to run on a high-performance computing # cluster, select a controller from the {crew.cluster} package. # For the cloud, see plugin packages like {crew.aws.batch}. # The following example is a controller for Sun Grid Engine (SGE). # # controller = crew.cluster::crew_controller_sge( # # Number of workers that the pipeline can scale up to: # workers = 10, # # It is recommended to set an idle time so workers can shut themselves # # down if they are not running tasks. # seconds_idle = 120, # # Many clusters install R as an environment module, and you can load it # # with the script_lines argument. To select a specific verison of R, # # you may need to include a version string, e.g. "module load R/4.3.2". # # Check with your system administrator if you are unsure. # script_lines = "module load R" # ) # # Set other options as needed. ) # Run the R scripts in the R/ folder with your custom functions: tar_source() # tar_source("other_functions.R") # Source other scripts as needed. # Set default priority to 1 to ensure all results are completed before manuscript. tar_option_set(priority = 1) # Replace the target list below with your own: list( tar_target( name = data, command = tibble(x = rnorm(100), y = rnorm(100)) # format = "qs" # Efficient storage for general data objects. ), tar_target( name = model, command = coefficients(lm(y ~ x, data = data)) ), tarchetypes::tar_render(manuscript, "manuscript/manuscript.Rmd", priority = 0, cue = tar_cue(mode = 'always')) # Set priority to 0 to ensure the manuscript is rendered after other results are available )[1] "_targets.yaml" "manuscript.Rmd" "manuscript.md" "manuscript_files" → de-duplicating ../_targets/meta/meta → reading ../_targets/meta/meta → parsing ../_targets/meta/meta → noting builders and branches → parsing ../_targets/meta/meta → restricting metadata records → querying 0 local files in ../_targets/objects → parsing ../_targets/meta/process + data dispatched ✔ data completed [10ms, 1.74 kB] + model dispatched ✔ model completed [0ms, 107 B] + manuscript dispatched ✔ manuscript completed [950ms, 5.55 kB] → de-duplicating ../_targets/meta/meta ✔ ended pipeline [1.3s, 3 completed, 0 skipped] Warning messages: 1: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. 2: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. 3: Effective 2025-04-08 (targets version 1.10.1.9013), the `priority` argument is deprecated in tar_target(), tar_target_raw(), and tar_option_set(). The targets package has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which does not support custom user-specified priorities. User-specified priorities no longer have a reliable effect on execution order. "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2025_05_16_10_50_17_6032\RtmpUrqLki\rmarkdown-str2c5842e3426f4.html" "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2025_05_16_10_50_17_6032\RtmpUrqLki\rmarkdown-str2c5843a33cd2.html" Variables to impute: Sepal.Length, Petal.Length, Species, Petal.Width, Sepal.Width Variables used to impute: Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species iter 1 | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% iter 2 | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% iter 3 | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 0 | PASS 180 ] > > proc.time() user system elapsed 24.73 4.93 76.65