Package check result: NOTE Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Jeroen Ooms ’ Found the following (possibly) invalid URLs: URL: https://github.com/r-lib/gert/issues From: DESCRIPTION man/gert-package.Rd Status: Error Message: Timeout was reached [github.com]: Connection timed out after 60002 milliseconds Changes to worse in reverse depends: Package: btw Check: tests New result: ERROR Running ‘testthat.R’ [43s/27s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(btw) > > local_reproducible_output() > > test_check("btw") Starting 2 test processes. Saving _problems/test-btw_this-1.R Saving _problems/test-tool-docs-1.R [ FAIL 2 | WARN 0 | SKIP 49 | PASS 853 ] == Skipped tests (49) ========================================================== * On CRAN (32): 'test-btw.R:7:1', 'test-clipboard.R:1:1', 'test-edit_btw_md.R:1:1', 'test-edit_btw_md.R:27:1', 'test-edit_btw_md.R:46:1', 'test-edit_btw_md.R:64:1', 'test-edit_btw_md.R:86:1', 'test-tool-env.R:15:1', 'test-tool-files.R:164:1', 'test-tool-git.R:1:1', 'test-tool-git.R:67:1', 'test-tool-git.R:107:1', 'test-tool-git.R:132:1', 'test-tool-git.R:166:1', 'test-tool-git.R:191:1', 'test-tool-git.R:214:1', 'test-tool-git.R:345:1', 'test-tool-ide.R:1:1', 'test-tool-pkg-devtools-covr.R:295:1', 'test-tool-search-packages.R:42:3', 'test-tool-search-packages.R:55:3', 'test-tool-session-info.R:3:1', 'test-tool-session-info.R:40:1', 'test-tool-run.R:108:1', 'test-tool-web.R:23:3', 'test-tool-web.R:54:3', 'test-tool-web.R:107:3', 'test-tool-web.R:128:3', 'test-tool-web.R:164:3', 'test-tool-web.R:206:1', 'test-tool-web.R:229:3', 'test-utils-md.R:1:1' * On Linux (17): 'test-btw.R:2:3', 'test-btw_client.R:29:5', 'test-btw_client.R:99:3', 'test-btw_client.R:253:5', 'test-btw_client.R:264:5', 'test-btw_client.R:346:5', 'test-btw_client.R:385:5', 'test-tool-env-df.R:1:1', 'test-tool-env.R:2:3', 'test-tool-files.R:19:3', 'test-tool-files.R:79:3', 'test-tool-ide.R:177:3', 'test-tool-ide.R:199:3', 'test-tool-docs-news.R:148:3', 'test-tool-search-packages.R:23:3', 'test-tool-search-packages.R:72:3', 'test-utils.R:7:3' == Failed tests ================================================================ -- Error ('test-btw_this.R:1:1'): (code run outside of `test_that()`) ---------- Error in `httr2::req_perform(req, path = x$desttmp)`: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [api.github.com]: Connection timed out after 5002 milliseconds Backtrace: x 1. \-btw:::use_latest_pandoc() at test-btw_this.R:1:1 2. +-base::suppressMessages(pandoc::pandoc_available_releases()[1]) at ./helpers.R:10:5 3. | \-base::withCallingHandlers(...) 4. \-pandoc::pandoc_available_releases() 5. \-pandoc:::pandoc_releases() 6. +-rlang::env_cache(the, "pandoc_releases", default_cache()) 7. | \-rlang::env_poke(env, nm, default) 8. \-pandoc (local) default_cache() 9. \-pandoc:::fetch_gh_releases() 10. \-gh::gh(...) 11. \-gh:::gh_make_request(req) 12. \-httr2::req_perform(req, path = x$desttmp) 13. \-httr2:::handle_resp(req, resp, error_call = error_call) 14. \-rlang::cnd_signal(resp) -- Error ('test-tool-docs.R:1:1'): (code run outside of `test_that()`) --------- Error in `httr2::req_perform(req, path = x$desttmp)`: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [api.github.com]: Connection timed out after 5002 milliseconds Backtrace: x 1. \-btw:::use_latest_pandoc() at test-tool-docs.R:1:1 2. +-base::suppressMessages(pandoc::pandoc_available_releases()[1]) at ./helpers.R:10:5 3. | \-base::withCallingHandlers(...) 4. \-pandoc::pandoc_available_releases() 5. \-pandoc:::pandoc_releases() 6. +-rlang::env_cache(the, "pandoc_releases", default_cache()) 7. | \-rlang::env_poke(env, nm, default) 8. \-pandoc (local) default_cache() 9. \-pandoc:::fetch_gh_releases() 10. \-gh::gh(...) 11. \-gh:::gh_make_request(req) 12. \-httr2::req_perform(req, path = x$desttmp) 13. \-httr2:::handle_resp(req, resp, error_call = error_call) 14. \-rlang::cnd_signal(resp) [ FAIL 2 | WARN 0 | SKIP 49 | PASS 853 ] Error: ! Test failures. Execution halted Ran 8/8 deferred expressions Package: dpkg Check: examples New result: ERROR Running examples in ‘dpkg-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: stow_gh_release > ### Title: download a github release asset to the 'stow' R user directory > ### Aliases: stow_gh_release stow stow_url > > ### ** Examples > > Sys.setenv(R_USER_DATA_DIR = tempfile("stow")) > # get by using URL > stow("https://github.com/geomarker-io/appc/releases/download/v0.1.0/nei_2020.rds", + overwrite = TRUE) |> + readRDS() Error in `httr2::req_perform()`: ! Failed to perform HTTP request. Caused by error in `curl::curl_fetch_disk()`: ! Timeout was reached [github.com]: Connection timed out after 10003 milliseconds Backtrace: ▆ 1. ├─base::readRDS(...) 2. └─dpkg::stow(...) 3. └─dpkg::stow_url(url = uri, overwrite = overwrite) 4. └─httr2::req_perform(httr2::request(url), path = dest_path) 5. └─httr2:::handle_resp(req, resp, error_call = error_call) 6. └─rlang::cnd_signal(resp) Execution halted Package: packager Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘An_Introduction_to_packager.Rasciidoc’ using rasciidoc Warning in run_knit(file_name, knit = knit, envir = envir, write_to_disk = write_to_disk) : Setting option knit to TRUE based on the file contents! processing file: /home/hornik/tmp/CRAN_recheck/packager.Rcheck/vign_test/packager/vignettes/An_Introduction_to_packager.Rasciidoc Package: theorytools Check: examples New result: ERROR Running examples in ‘theorytools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download_theory > ### Title: Download FAIR Theory > ### Aliases: download_theory > > ### ** Examples > > download_theory(id = "https://github.com/cjvanlissa/tripartite_model.git", + path = file.path(tempdir(), "tripartite_git")) Error in git_or_zenodo(id) : Not a valid 'Git' or 'Zenodo' archive. Calls: download_theory -> git_or_zenodo Execution halted Package: worcs Check: tests New result: ERROR Running ‘testthat.R’ [32s/163s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > 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") v Creating manuscript files. v Creating manuscript files. v Creating manuscript files. v Creating preregistration files. v Creating preregistration files. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Linking to libgit2 v1.9.2, ssh support: YES Global config: /home/hornik/.gitconfig Default user: yourname v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd14367b854c0". v Storing original data in 'dat.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Creating a codebook in 'codebook_dat.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. processing file: manuscript.Rmd output file: manuscript.knit.md /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/lib/R/Library/4.6/x86_64-linux-gnu/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/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: manuscript.html Output created: manuscript.md v Setting active project to "". processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md processing file: test.Rmd output file: test.knit.md [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: test.html Output created: test.md v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Creating a codebook in 'codebook_iris.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Storing value labels in 'value_labels_iris.yml'. 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'. x Checksum for file '/home/hornik/tmp/scratch/RtmpG15qEq/saveload/iris.csv' did not match the checksum on record (in '.worcs'). This means that the file has changed since the checksum was stored. v Loading original data from 'iris.csv'. v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Storing value labels in 'value_labels_iris.yml'. 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 Updating '.gitignore'. v Storing value labels in 'value_labels_iris.yml'. v Storing original data in 'iris.csv' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Creating a codebook in 'codebook_iris.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Storing value labels in 'value_labels_iris.yml'. v Storing original data in 'cars.csv' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |=================================== | 50% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Creating a codebook in 'codebook_cars.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Loading original data from 'iris.csv'. v Loading synthetic data from 'synthetic_cars.csv'. v Loading original data from 'iris.csv'. v Loading synthetic data from 'synthetic_cars.csv'. v Storing original data in 'df.csv' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Storing value labels in 'value_labels_df.yml'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/savedat22bd14321080758". v Creating manuscript files. v Storing original data in 'df1.csv' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Creating a codebook in 'codebook_df1.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Storing original data in 'df2.csv' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Creating a codebook in 'codebook_df2.Rmd'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. v Setting active project to "". v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd1435c551580". v Adding recipe to '.worcs'. v Creating first commit (committing README.md). v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/zip". v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd1435c551580". v Setting active project to "". v Adding recipe to '.worcs'. i Your analysis might not reproduce because worcs could not identify associated data sources. v Adding recipe to '.worcs'. i Your analysis might not reproduce because worcs could not identify associated data sources. 'Rscript' should not be used without a path -- see par. 1.6 of the manual v Storing original data in 'dat.dat' and updating the checksum in '.worcs'. v Updating '.gitignore'. v Storing value labels in 'value_labels_dat.yml'. v Loading original data from 'dat.dat'. x No valid codebook found. v Loading original data from 'dat.dat'. x No valid codebook found. v Loading original data from 'dat.dat'. x No valid codebook found. v Loading original data from 'dat.dat'. x No valid codebook found. x Checksum for file '/home/hornik/tmp/scratch/RtmpG15qEq/save_expression/dat.dat' did not match the checksum on record (in '.worcs'). This means that the file has changed since the checksum was stored. v Loading original data from 'dat.dat'. x No valid codebook found. v Storing original data in 'dat.dat' and updating the checksum in '.worcs'. v Generating synthetic data for public use. Ensure that no identifying information is included. | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in... v Updating '.gitignore'. v Storing value labels in 'value_labels_dat.yml'. v Loading original data from 'dat.dat'. x No valid codebook found. v Loading synthetic data from 'synthetic_dat.dat'. x No valid codebook found. | | | 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% Loading required package: targets v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd14349efdec5". x Creating manuscript files. v Adding recipe to '.worcs'. v Wrote _targets.R v Added targets to project. v Setting recipe to targets::tar_make(). v Adding rmarkdown manuscript to targets pipeline. v Adding targets to rmarkdown manuscript. v Creating directory './R/' for targets scripts. v Initializing 'targets' for a Make-like pipeline. + data dispatched ✔ data completed [6ms, 1.74 kB] + model dispatched ✔ model completed [2ms, 107 B] + manuscript dispatched Quitting from manuscript.Rmd:6-15 [setup] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! targets data store ../_targets not found. Utility functions like tar_read() and tar_load() require a pre-existing targets data store (default: _targets/) created by tar_make(), tar_make_clustermq(), or tar_make_future(). Details: https://books.ropensci.org/targets/data.html --- Backtrace: ▆ 1. └─targets::tar_load(model) 2. └─targets::tar_assert_store(store = store) 3. └─targets::tar_assert_path(...) 4. └─targets::tar_throw_validate(...) 5. └─targets::tar_error(...) 6. └─rlang::abort(message = message, class = class, call = tar_envir_base) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ✖ manuscript errored ✖ errored pipeline [398ms, 2 completed, 0 skipped] processing file: manuscript.Rmd output file: manuscript.knit.md /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/lib/R/Library/4.6/x86_64-linux-gnu/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/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Preview created: manuscript.html Output created: manuscript.md # 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" + data dispatched ✔ data completed [7ms, 1.74 kB] + model dispatched ✔ model completed [2ms, 107 B] + manuscript dispatched [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. ✔ manuscript completed [514ms, 9.65 kB] ✔ ended pipeline [700ms, 3 completed, 0 skipped] v Setting active project to "". v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd143729df719". v Writing '_targets.Rmd'. v Creating manuscript files. v Adding recipe to '.worcs'. v Added targets to project. v Setting recipe to targets::tar_make(). v Creating directory './R/' for targets scripts. v Initializing 'targets' for a Make-like pipeline. processing file: _targets.Rmd output file: _targets.knit.md /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/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --syntax-highlighting=none --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/RtmpG15qEq/rmarkdown-str2bd14340985937.html Output created: _targets.html i Your analysis might not reproduce because worcs could not identify associated data sources. processing file: _targets.Rmd output file: _targets.knit.md /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/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --syntax-highlighting=none --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/RtmpG15qEq/rmarkdown-str2bd143273bdc5.html Output created: _targets.html v Setting active project to "". Missing value imputation by random forests 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% v Setting active project to "/home/hornik/tmp/scratch/RtmpG15qEq/aaa2bd1437361c8d3". x Creating manuscript files. v Adding recipe to '.worcs'. v Creating preregistration files. v Creating first commit (committing README.md). v Setting active project to "". [ FAIL 1 | WARN 11 | SKIP 1 | PASS 179 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-can_clone.R:10:3'): gert can clone repos ─────────────────────── Error in `libgit2::git_clone`: failed to connect to github.com: Connection timed out Backtrace: ▆ 1. ├─gert::git_clone(...) at test-can_clone.R:10:3 2. └─gert:::raise_libgit2_error(...) [ FAIL 1 | WARN 11 | SKIP 1 | PASS 179 ] Error: ! Test failures. Execution halted