Last updated on 2022-04-24 03:52:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.8 | 10.97 | 142.95 | 153.92 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.8 | 9.37 | 112.58 | 121.95 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.8 | 180.01 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.8 | 176.57 | OK | |||
| r-patched-linux-x86_64 | 0.1.8 | 11.42 | 138.05 | 149.47 | OK | |
| r-release-linux-x86_64 | 0.1.8 | 10.42 | 141.01 | 151.43 | OK | |
| r-release-macos-arm64 | 0.1.8 | OK | ||||
| r-release-macos-x86_64 | 0.1.8 | OK | ||||
| r-release-windows-x86_64 | 0.1.8 | 47.00 | 173.00 | 220.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.8 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.8 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.8 | 22.00 | 145.00 | 167.00 | ERROR |
Version: 0.1.8
Check: examples
Result: ERROR
Running examples in 'worcs-Ex.R' failed
The error most likely occurred in:
> ### Name: cite_all
> ### Title: Comprehensive citation Knit function for 'RStudio'
> ### Aliases: cite_all
>
> ### ** Examples
>
> # NOTE: Do not use this function interactively, as in the example below.
> # Only specify it as custom knit function in an 'R Markdown' file, like so:
> # knit: worcs::cite_all
>
> if (rmarkdown::pandoc_available("1.14")){
+ file_name <- file.path(tempdir(), "citeall.Rmd")
+ loc <- rmarkdown::draft(file_name,
+ template = "github_document",
+ package = "rmarkdown",
+ create_dir = FALSE,
+ edit = FALSE)
+ write(c("", "Optional reference: @reference2020"),
+ file = file_name, append = TRUE)
+ cite_all(file_name)
+ }
Error: only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.8
Check: tests
Result: ERROR
Running 'testthat.R' [21s]
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:10.17605/OSF.IO/ZCVBS><1b>[0m
>
> test_check("worcs")
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating manuscript files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating preregistration files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating preregistration files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mInitializing 'Git' repository.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mWriting '.worcs' file.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCopying standard files.<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mCreating first commit (committing README.md).<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mNot a valid 'Git' remote repository address: https<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mNo valid 'GitHub' address provided. You are working with a local 'Git' repository only.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Seed' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Assault' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'UrbanPop' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;31mX <1b>[0m<1b>[0;30mArgument 'data' has missing values, but no 'missingness_expression' is specified. Listwise deletion is used.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Solar.R' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Temp' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Month' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Day' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;31mX <1b>[0m<1b>[0;30mArgument 'data' has missing values, but no 'missingness_expression' is specified. Listwise deletion is used.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Freq' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'alcgp' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'tobgp' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'y' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'freeny.y' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'stratum' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Year' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Run' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Speed' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'depth' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'stations' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Examination' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mSynthetic variable 'Education' did not have identical classes to its original counterpart. Attempted to convert to its original type. Check the input types of your variables, and check whether the data are synthesized correctly.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mStoring original data in 'iris.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mStoring original data in 'iris.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating D:/temp/RtmpW8214P/saveload/README.md.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mGenerating synthetic data for public use. Ensure that no identifying information is included.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mStoring synthetic data in 'synthetic_iris.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating D:/temp/RtmpW8214P/saveload/README.md.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading synthetic data from 'synthetic_iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mStoring original data in 'iris.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mAppending D:/temp/RtmpW8214P/saveload/README.md.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mCannot find the original data iris.csv, and there is no synthetic version on record.<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mNo valid resource found for these files:
* iris.csv<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mStoring original data in 'iris.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mStoring original data in 'cars.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating D:/temp/RtmpW8214P/saveload2/README.md.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mGenerating synthetic data for public use. Ensure that no identifying information is included.<1b>[0m
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<1b>[0;32mv <1b>[0m<1b>[0;30mStoring synthetic data in 'synthetic_cars.csv' and updating the checksum in '.worcs'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating D:/temp/RtmpW8214P/saveload2/README.md.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mUpdating '.gitignore'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading original data from 'iris.csv'.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mLoading synthetic data from 'synthetic_cars.csv'.<1b>[0m
Missing value imputation by random forests
Variables to impute: Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species
Variables used to impute: Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species
iter 1: .....
iter 2: .....
iter 3: .....
iter 4: .....
iter 5: .....
iter 6: .....
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<1b>[0;32mv <1b>[0m<1b>[0;30mInitializing 'Git' repository.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mWriting '.worcs' file.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCopying standard files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating manuscript files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mCreating preregistration files.<1b>[0m
<1b>[0;32mv <1b>[0m<1b>[0;30mWriting license file.<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mCreating first commit (committing README.md).<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mNot a valid 'Git' remote repository address: bla<1b>[0m
<1b>[0;31mX <1b>[0m<1b>[0;30mNo valid 'GitHub' address provided. You are working with a local 'Git' repository only.<1b>[0m
[ FAIL 6 | WARN 2 | SKIP 1 | PASS 116 ]
== Skipped tests ===============================================================
* Sys.info()["user"] == "Lissa102" is not TRUE (1)
== Failed tests ================================================================
-- Error (test-citations.R:18:5): documents with spaces in names can be rendered --
Error: only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0
Backtrace:
x
1. +-testthat::capture_output(cite_all(file_name)) at test-citations.R:18:4
2. | \-testthat::capture_output_lines(code, print, width = width)
3. | \-testthat:::eval_with_output(code, print = print, width = width)
4. | +-withr::with_output_sink(path, withVisible(code))
5. | | \-base::force(code)
6. | \-base::withVisible(code)
7. \-worcs::cite_all(file_name)
8. \-worcs:::comprehensive_cite(..., citeall = TRUE)
9. +-base::do.call(render, dots)
10. \-rmarkdown `<fn>`(encoding = "UTF-8", input = "D:\\temp\\RtmpW8214P/citeall/test.Rmd")
11. \-rmarkdown:::create_output_format(output_format$name, output_format$options)
12. +-base::do.call(output_format_func, options)
13. \-rmarkdown `<fn>`()
14. \-rmarkdown:::add_math_support(math, NULL, NULL, NULL)
15. \-rmarkdown:::stop2("only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0 ")
-- Error (test-citations.R:52:5): cite_* work with umlaute ---------------------
Error: only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0
Backtrace:
x
1. +-testthat::capture_output(cite_all(file_name)) at test-citations.R:52:4
2. | \-testthat::capture_output_lines(code, print, width = width)
3. | \-testthat:::eval_with_output(code, print = print, width = width)
4. | +-withr::with_output_sink(path, withVisible(code))
5. | | \-base::force(code)
6. | \-base::withVisible(code)
7. \-worcs::cite_all(file_name)
8. \-worcs:::comprehensive_cite(..., citeall = TRUE)
9. +-base::do.call(render, dots)
10. \-rmarkdown `<fn>`(encoding = "UTF-8", input = "D:\\temp\\RtmpW8214P/citeall/test.Rmd")
11. \-rmarkdown:::create_output_format(output_format$name, output_format$options)
12. +-base::do.call(output_format_func, options)
13. \-rmarkdown `<fn>`()
14. \-rmarkdown:::add_math_support(math, NULL, NULL, NULL)
15. \-rmarkdown:::stop2("only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0 ")
-- Error (test-citations.R:95:5): cite_* retain relative paths -----------------
Error: only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0
Backtrace:
x
1. +-testthat::capture_output(cite_all(file_name)) at test-citations.R:95:4
2. | \-testthat::capture_output_lines(code, print, width = width)
3. | \-testthat:::eval_with_output(code, print = print, width = width)
4. | +-withr::with_output_sink(path, withVisible(code))
5. | | \-base::force(code)
6. | \-base::withVisible(code)
7. \-worcs::cite_all(file_name)
8. \-worcs:::comprehensive_cite(..., citeall = TRUE)
9. +-base::do.call(render, dots)
10. \-rmarkdown `<fn>`(encoding = "UTF-8", input = "D:\\temp\\RtmpW8214P/relative/test.Rmd")
11. \-rmarkdown:::create_output_format(output_format$name, output_format$options)
12. +-base::do.call(output_format_func, options)
13. \-rmarkdown `<fn>`()
14. \-rmarkdown:::add_math_support(math, NULL, NULL, NULL)
15. \-rmarkdown:::stop2("only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0 ")
-- Error (test-citations.R:128:5): cite_* retain double @ ----------------------
Error: only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0
Backtrace:
x
1. +-testthat::capture_output(cite_all(file_name)) at test-citations.R:128:4
2. | \-testthat::capture_output_lines(code, print, width = width)
3. | \-testthat:::eval_with_output(code, print = print, width = width)
4. | +-withr::with_output_sink(path, withVisible(code))
5. | | \-base::force(code)
6. | \-base::withVisible(code)
7. \-worcs::cite_all(file_name)
8. \-worcs:::comprehensive_cite(..., citeall = TRUE)
9. +-base::do.call(render, dots)
10. \-rmarkdown `<fn>`(encoding = "UTF-8", input = "D:\\temp\\RtmpW8214P/citeall/test.Rmd")
11. \-rmarkdown:::create_output_format(output_format$name, output_format$options)
12. +-base::do.call(output_format_func, options)
13. \-rmarkdown `<fn>`()
14. \-rmarkdown:::add_math_support(math, NULL, NULL, NULL)
15. \-rmarkdown:::stop2("only `math_method = 'mathjax'` is supported with earlier version than Pandoc 2.0 ")
-- Failure (test-codebook.R:12:5): codebook works for iris ---------------------
file.exists("codebook.md") is not TRUE
`actual`: FALSE
`expected`: TRUE
-- Failure (test-codebook.R:38:5): codebook works for PlantGrowth with missings --
file.exists("codebook.md") is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 6 | WARN 2 | SKIP 1 | PASS 116 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64