* using log directory 'd:/Rcompile/CRANpkg/local/4.0/worcs.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'worcs/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'worcs' version '0.1.8' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'worcs' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [5s] 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... [22s] ERROR Running 'testthat.R' [21s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(worcs) Welcome 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)  > > test_check("worcs") v Creating manuscript files. v Creating preregistration files. v Creating preregistration files. v Initializing 'Git' repository. v Writing '.worcs' file. v Copying standard files. X Creating first commit (committing README.md). X Not a valid 'Git' remote repository address: https X No valid 'GitHub' address provided. You are working with a local 'Git' repository only. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% v Synthetic 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. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. | | | 0% | |====== | 8% | |============ | 17% | |================== | 25% | |======================= | 33% | |============================= | 42% | |=================================== | 50% | |========================================= | 58% | |=============================================== | 67% | |==================================================== | 75% | |========================================================== | 83% | |================================================================ | 92% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |========== | 14% | |==================== | 29% | |============================== | 43% | |======================================== | 57% | |================================================== | 71% | |============================================================ | 86% | |======================================================================| 100% | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% X Argument 'data' has missing values, but no 'missingness_expression' is specified. Listwise deletion is used. | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. v Synthetic 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. v Synthetic 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. | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% X Argument 'data' has missing values, but no 'missingness_expression' is specified. Listwise deletion is used. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |========== | 14% | |==================== | 29% | |============================== | 43% | |======================================== | 57% | |================================================== | 71% | |============================================================ | 86% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% v Synthetic 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. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% v Synthetic 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. | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% v Synthetic 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. | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% v Synthetic 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. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |========== | 14% | |==================== | 29% | |============================== | 43% | |======================================== | 57% | |================================================== | 71% | |============================================================ | 86% | |======================================================================| 100% v Synthetic 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. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% v Synthetic 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. v Synthetic 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. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |= | 2% | |== | 3% | |=== | 5% | |===== | 7% | |====== | 8% | |======= | 10% | |======== | 11% | |========= | 13% | |========== | 15% | |=========== | 16% | |============= | 18% | |============== | 20% | |=============== | 21% | |================ | 23% | |================= | 25% | |================== | 26% | |==================== | 28% | |===================== | 30% | |====================== | 31% | |======================= | 33% | |======================== | 34% | |========================= | 36% | |========================== | 38% | |============================ | 39% | |============================= | 41% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 48% | |================================== | 49% | |==================================== | 51% | |===================================== | 52% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |========================================= | 59% | |========================================== | 61% | |============================================ | 62% | |============================================= | 64% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 69% | |================================================= | 70% | |================================================== | 72% | |==================================================== | 74% | |===================================================== | 75% | |====================================================== | 77% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 82% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================= | 93% | |=================================================================== | 95% | |==================================================================== | 97% | |===================================================================== | 98% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Loading original data from 'iris.csv'. v Loading original data from 'iris.csv'. v Loading original data from 'iris.csv'. v Loading original data from 'iris.csv'. v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Creating D:/temp/RtmpC27fLx/saveload/README.md. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% v Storing synthetic data in 'synthetic_iris.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Updating D:/temp/RtmpC27fLx/saveload/README.md. v Updating '.gitignore'. v Loading original data from 'iris.csv'. v Loading synthetic data from 'synthetic_iris.csv'. v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Appending D:/temp/RtmpC27fLx/saveload/README.md. v Updating '.gitignore'. X Cannot find the original data iris.csv, and there is no synthetic version on record. X No valid resource found for these files: * iris.csv v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Storing original data in 'cars.csv' and updating the checksum in '.worcs'. v Creating D:/temp/RtmpC27fLx/saveload2/README.md. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |=================================== | 50% | |======================================================================| 100% v Storing synthetic data in 'synthetic_cars.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Updating D:/temp/RtmpC27fLx/saveload2/README.md. v Updating '.gitignore'. v Loading original data from 'iris.csv'. v Loading synthetic data from 'synthetic_cars.csv'. 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: ..... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% v Initializing 'Git' repository. v Writing '.worcs' file. v Copying standard files. v Creating manuscript files. v Creating preregistration files. v Writing license file. X Creating first commit (committing README.md). X Not a valid 'Git' remote repository address: bla X No valid 'GitHub' address provided. You are working with a local 'Git' repository only. [ 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 ``(encoding = "UTF-8", input = "D:\\temp\\RtmpC27fLx/citeall/test.Rmd") 11. \-rmarkdown:::create_output_format(output_format$name, output_format$options) 12. +-base::do.call(output_format_func, options) 13. \-rmarkdown ``() 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 ``(encoding = "UTF-8", input = "D:\\temp\\RtmpC27fLx/citeall/test.Rmd") 11. \-rmarkdown:::create_output_format(output_format$name, output_format$options) 12. +-base::do.call(output_format_func, options) 13. \-rmarkdown ``() 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 ``(encoding = "UTF-8", input = "D:\\temp\\RtmpC27fLx/relative/test.Rmd") 11. \-rmarkdown:::create_output_format(output_format$name, output_format$options) 12. +-base::do.call(output_format_func, options) 13. \-rmarkdown ``() 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 ``(encoding = "UTF-8", input = "D:\\temp\\RtmpC27fLx/citeall/test.Rmd") 11. \-rmarkdown:::create_output_format(output_format$name, output_format$options) 12. +-base::do.call(output_format_func, options) 13. \-rmarkdown ``() 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [19s] OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs