CRAN Package Check Results for Package worcs

Last updated on 2024-11-29 09:49:30 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.15	10.97	205.33	216.30	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.15	8.88	151.35	160.23	OK
r-devel-linux-x86_64-fedora-clang	0.1.15			363.99	OK
r-devel-linux-x86_64-fedora-gcc	0.1.15			478.03	OK
r-devel-windows-x86_64	0.1.15	14.00	253.00	267.00	OK
r-patched-linux-x86_64	0.1.15	12.96	197.93	210.89	ERROR
r-release-linux-x86_64	0.1.15	11.13	195.26	206.39	OK
r-release-macos-arm64	0.1.15			134.00	OK
r-release-macos-x86_64	0.1.15			191.00	OK
r-release-windows-x86_64	0.1.15	15.00	249.00	264.00	OK
r-oldrel-macos-arm64	0.1.15			165.00	OK
r-oldrel-macos-x86_64	0.1.15			263.00	OK
r-oldrel-windows-x86_64	0.1.15	19.00	289.00	308.00	OK

Check Details

Version: 0.1.15
Check: tests
Result: ERROR Running ‘testthat.R’ [48s/64s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(worcs) <1b>[0;34mWelcome to WORCS: Workflow for Open Reproducible Code in Science. Please read the tutorial before using this package, and consider citing it: Van Lissa and colleagues (2020) <doi:10.3233/DS-210031><1b>[0m > > test_check("worcs") /usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md /usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --highlight-style pygments --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax | | | 0% | 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|=============================================== | 67% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% ▶ dispatched target data ● completed target data [0.016 seconds, 1.742 kilobytes] ▶ dispatched target model ● completed target model [0.005 seconds, 107 bytes] ▶ dispatched target manuscript Quitting from lines 7-15 [setup] (manuscript.Rmd) ▶ recorded workspace manuscript ✖ errored target manuscript ✖ errored pipeline [0.63 seconds] /usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md /usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --highlight-style pygments --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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. # 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", cue = tar_cue(mode = 'always')) )[1] "_targets.yaml" "manuscript.Rmd" "manuscript.md" "manuscript_files" ▶ dispatched target data ● completed target data [0.014 seconds, 1.742 kilobytes] ▶ dispatched target model ● completed target model [0.005 seconds, 107 bytes] ▶ dispatched target manuscript ● completed target manuscript [0.956 seconds, 9.647 kilobytes] ▶ ended pipeline [1.102 seconds] /usr/bin/pandoc +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 /home/hornik/tmp/scratch/RtmpNeCBY1/rmarkdown-str4e33518fcfe36.html /usr/bin/pandoc +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 /home/hornik/tmp/scratch/RtmpNeCBY1/rmarkdown-str4e33538e00960.html Variables to impute: Petal.Length, Sepal.Width, Petal.Width, Species, Sepal.Length 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% iter 4 | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 0 | PASS 180 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-can_clone.R:10:3'): gert can clone repos ─────────────────────── <GIT_ERROR/libgit2_error/error/condition> Error in `libgit2::git_clone`: SSL error: 0xffff8880 - SSL - A fatal alert message was received from our peer Backtrace: ▆ 1. ├─gert::git_clone(...) at test-can_clone.R:10:3 2. └─gert:::raise_libgit2_error(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 180 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.15
Check: tests
Result: ERROR Running ‘testthat.R’ [46s/63s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(worcs) <1b>[0;34mWelcome to WORCS: Workflow for Open Reproducible Code in Science. Please read the tutorial before using this package, and consider citing it: Van Lissa and colleagues (2020) <doi:10.3233/DS-210031><1b>[0m > > test_check("worcs") /usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md /usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --highlight-style pygments --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax | | | 0% | 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|=============================================== | 67% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% ▶ dispatched target data ● completed target data [0.015 seconds, 1.743 kilobytes] ▶ dispatched target model ● completed target model [0.005 seconds, 108 bytes] ▶ dispatched target manuscript Quitting from lines 7-15 [setup] (manuscript.Rmd) ▶ recorded workspace manuscript ✖ errored target manuscript ✖ errored pipeline [0.54 seconds] /usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md /usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --highlight-style pygments --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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. # 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", cue = tar_cue(mode = 'always')) )[1] "_targets.yaml" "manuscript.Rmd" "manuscript.md" "manuscript_files" ▶ dispatched target data ● completed target data [0.014 seconds, 1.743 kilobytes] ▶ dispatched target model ● completed target model [0.004 seconds, 108 bytes] ▶ dispatched target manuscript ● completed target manuscript [0.946 seconds, 9.647 kilobytes] ▶ ended pipeline [1.082 seconds] /usr/bin/pandoc +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/scratch/RtmpOTJPNO/rmarkdown-strbe79c63d87c64.html /usr/bin/pandoc +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/scratch/RtmpOTJPNO/rmarkdown-strbe79c4b58cc15.html Variables to impute: Petal.Length, Sepal.Width, Petal.Width, Species, Sepal.Length 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% iter 4 | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 0 | PASS 180 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-can_clone.R:10:3'): gert can clone repos ─────────────────────── <GIT_ERROR/libgit2_error/error/condition> Error in `libgit2::git_clone`: SSL error: 0xffff8880 - SSL - A fatal alert message was received from our peer Backtrace: ▆ 1. ├─gert::git_clone(...) at test-can_clone.R:10:3 2. └─gert:::raise_libgit2_error(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 180 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64