* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck’ * using R Under development (unstable) (2025-03-19 r88007) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ottrpal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ottrpal’ version ‘2.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] OK * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘ottrpal’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘CODE_OF_CONDUCT.md’ ‘CONTRIBUTING.md’ ‘SECURITY.md’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: authorize.Rd: oauth2.0_token Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [4s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [43s/79s] ERROR Running ‘testthat.R’ [43s/79s] 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(ottrpal) Use the authorize() function to begin. This gives the package the proper credentials to run. > > test_check("ottrpal") processing file: parent_doc.Rmd output file: parent_doc.knit.md /usr/bin/pandoc +RTS -K512m -RTS parent_doc.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output parent_doc.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 --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str32180475e0c8c7.html Output created: parent_doc.html trying URL 'https://github.com/jhudsl/OTTR_Template/archive/refs/heads/main.zip' downloaded 30.3 MB ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/01-intro.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/02-chapter_of_course.Rmd Testing: https://www.linkedin.com Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org Testing: https://docs.google.com/presentation/d/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ/edit#slide=id.gcc4fbee202_0_141 Testing: https://www.ottrproject.org/getting_started.html Testing: https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image Testing: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://rmarkdown.rstudio.com/lesson-3.html Testing: https://yihui.org Testing: https://yihui.org Testing: https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html Testing: https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html Testing: https://github.com/jhudsl/OTTR_Template Testing: https://jhudatascience.org/OTTR_Template/ Testing: https://tips.uark.edu/using-blooms-taxonomy/ Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/References.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/index.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_ch1.md No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/url_test_error.md Testing: https://notawebsiteaaaaaaa.com 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/url_checks.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): urls, urls_status, file i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/fhdsl/OTTR_Quarto/archive/refs/heads/main.zip' downloaded 3.4 MB ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/404.qmd Testing: https://github.com/fhdsl/OTTR_Quarto/issues/new ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/conclusion.qmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/first-section-new-chapter.qmd Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org Testing: https://docs.google.com/presentation/d/1Dw_rBb1hySN_76xh9-x5J2dWF_das9BAUjQigf2fN-E/edit#slide=id.g252f18e2576_1_0 Testing: https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image Testing: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://rmarkdown.rstudio.com/lesson-3.html Testing: https://yihui.org Testing: https://yihui.org Testing: https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/index.qmd Testing: https://itcr.cancer.gov/) called the Informatics Technology for Cancer Research Education Resource. This material was created by the ITCR Training Network (ITN) which is a collaborative effort of researchers around the United States to support cancer informatics and data science training through resources, technology, and events. This initiative is funded by the following grant: [National Cancer Institute (NCI Testing: https://www.ottrproject.org/ Testing: https://leanpub.com/ Testing: https://www.coursera.org/) (but it is not available for free on Coursera Testing: https://github.com/fhdsl/OTTR_Quarto ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/intro.qmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/manuscript/Conclusion.md Testing: http://hutchdatascience.org/OTTR_Quarto/conclusion.html ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/manuscript/Introduction-to-the-Course.md Testing: http://hutchdatascience.org/OTTR_Quarto/intro.html ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/manuscript/New-Chapter.md Testing: http://hutchdatascience.org/OTTR_Quarto/third-section-new-chapter.html ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/references.qmd Testing: (https://ieeexplore.ieee.org/document/6773024 Testing: (https://mind.oxfordjournals.org/content/LIX/236/433 Testing: (https://www.cs.virginia.edu/~robins/Turing_Paper_1936.pdf Testing: (https://dl.acm.org/doi/10.1145/358198.358210 Testing: (https://research.google.com/archive/gfs-sosp2003.pdf ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/url_test_error.md Testing: https://notawebsiteaaaaaaa.com 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/check_reports/url_checks.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): urls, urls_status, file i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/jhudsl/OTTR_Template_Website/archive/refs/heads/main.zip' downloaded 9.5 MB ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/contact.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/editing.Rmd Testing: https://www.ottrproject.org/editing_website.html Testing: https://fontawesome.com/ Testing: https://www.w3schools.com/bootstrap/bootstrap_ref_comp_glyphs.asp ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/git_actions.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/hosting.Rmd Testing: https://username.github.io/repository_name/ Testing: https://pages.github.com/ ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/index.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/setup.Rmd Testing: https://github.com/jhudsl/OTTR_Template_Website Testing: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/style.Rmd Testing: https://bookdown.org/yihui/blogdown/themes.html Testing: https://www.w3schools.com/css/ Testing: https://htmlcolorcodes.com/ Testing: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf Testing: https://favicon.io/favicon-converter/ ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/url_test_error.md Testing: https://notawebsiteaaaaaaa.com 13 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/check_reports/url_checks.tsv Rows: 13 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): urls, urls_status, file i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/fhdsl/OTTR_Quarto_Website/archive/refs/heads/main.zip' downloaded 9.4 MB ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/contact.qmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/editing.qmd Testing: https://www.ottrproject.org/editing_website.html Testing: https://fontawesome.com/ Testing: https://www.w3schools.com/bootstrap/bootstrap_ref_comp_glyphs.asp ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/git_actions.qmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/hosting.qmd Testing: https://username.github.io/repository_name/ Testing: https://pages.github.com/ ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/index.qmd Testing: https://github.com/fhdsl/OTTR_Quarto Testing: https://www.ottrproject.org/ ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/setup.qmd Testing: https://github.com/jhudsl/OTTR_Template_Website Testing: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/style.qmd Testing: https://bookdown.org/yihui/blogdown/themes.html Testing: https://www.w3schools.com/css/ Testing: https://htmlcolorcodes.com/ Testing: https://quarto.org/docs/websites/#workflow Testing: https://favicon.io/favicon-converter/ ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/url_test_error.md Testing: https://notawebsiteaaaaaaa.com 15 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/check_reports/url_checks.tsv Rows: 15 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): urls, urls_status, file i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. 1 trying URL 'https://github.com/jhudsl/OTTR_Template/archive/refs/heads/main.zip' Content type 'application/zip' length 31811169 bytes (30.3 MB) ================================================== downloaded 30.3 MB ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/01-intro.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/02-chapter_of_course.Rmd Testing: https://www.linkedin.com Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org Testing: https://docs.google.com/presentation/d/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ/edit#slide=id.gcc4fbee202_0_141 Testing: https://www.ottrproject.org/getting_started.html Testing: https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image Testing: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://rmarkdown.rstudio.com/lesson-3.html Testing: https://yihui.org Testing: https://yihui.org Testing: https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html Testing: https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html Testing: https://github.com/jhudsl/OTTR_Template Testing: https://jhudatascience.org/OTTR_Template/ Testing: https://tips.uark.edu/using-blooms-taxonomy/ Testing: https://www.youtube.com/embed/VOCYL-FNbr0 Testing: https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview Testing: https://yihui.org ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/References.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/index.Rmd No URLs found ##### Testing URLs from file: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_ch1.md No URLs found 0 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/url_checks.tsv 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/spell_check_results.tsv Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_ch1.md Checking question: First question to as ... in quiz: quiz_ch1.md Checking question: Question example wit ... in quiz: quiz_ch1.md Checking question: Second question to a ... in quiz: quiz_ch1.md Checking question: A more complicated e ... in quiz: quiz_ch1.md Checking question: A question in which ... in quiz: quiz_ch1.md No question errors to report! 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/question_error_report.tsv --2025-03-20 16:47:17-- https://raw.githubusercontent.com/jhudsl/OTTR_Template/refs/heads/main/.github/workflows/check-url.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 4064 (4.0K) [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd/.github/workflows/check-url.yml’ 0K ... 100% 57.1M=0s 2025-03-20 16:47:18 (57.1 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd/.github/workflows/check-url.yml’ saved [4064/4064] --2025-03-20 16:47:18-- https://raw.githubusercontent.com/jhudsl/OTTR_Template/refs/heads/main/.github/workflows/pull_request.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected. 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HTTP request sent, awaiting response... 200 OK Length: 198 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/dictionary.txt’ 0K 100% 7.23M=0s 2025-03-20 16:47:31 (7.23 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/dictionary.txt’ saved [198/198] --2025-03-20 16:47:31-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/resources/ignore-urls.txt Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 44 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/ignore-urls.txt’ 0K 100% 3.41M=0s 2025-03-20 16:47:31 (3.41 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/ignore-urls.txt’ saved [44/44] --2025-03-20 16:47:31-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/resources/exclude_files.txt Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 99 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/exclude_files.txt’ 0K 100% 6.07M=0s 2025-03-20 16:47:31 (6.07 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/exclude_files.txt’ saved [99/99] --2025-03-20 16:47:31-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/_site.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 602 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/_site.yml’ 0K 100% 41.3M=0s 2025-03-20 16:47:31 (41.3 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/_site.yml’ saved [602/602] --2025-03-20 16:47:32-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/styles.css Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 624 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/styles.css’ 0K 100% 43.0M=0s 2025-03-20 16:47:33 (43.0 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/styles.css’ saved [624/624] --2025-03-20 16:47:33-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/.github/workflows/render-site.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2922 (2.9K) [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/.github/workflows/render-site.yml’ 0K .. 100% 41.5M=0s 2025-03-20 16:47:33 (41.5 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/.github/workflows/render-site.yml’ saved [2922/2922] --2025-03-20 16:47:33-- https://raw.githubusercontent.com/jhudsl/OTTR_Template_Website/refs/heads/main/resources/header.html Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 335 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/header.html’ 0K 100% 12.6M=0s 2025-03-20 16:47:33 (12.6 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/rmd_web/resources/header.html’ saved [335/335] Rendering: rmd_web/index.Rmd /usr/bin/pandoc +RTS -K512m -RTS index.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output index.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str32180426d36ffa.html --variable navbar=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804527f76e8.html Rendering: rmd_web/page1.Rmd /usr/bin/pandoc +RTS -K512m -RTS page1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output page1.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str3218041bd3b929.html --variable navbar=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804145ce6c5.html Output created: docs/index.html --2025-03-20 16:47:33-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/.github/workflows/check-url.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 4064 (4.0K) [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/check-url.yml’ 0K ... 100% 57.9M=0s 2025-03-20 16:47:34 (57.9 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/check-url.yml’ saved [4064/4064] --2025-03-20 16:47:34-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/.github/workflows/pull_request.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 7532 (7.4K) [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/pull_request.yml’ 0K ....... 100% 65.2M=0s 2025-03-20 16:47:34 (65.2 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/pull_request.yml’ saved [7532/7532] --2025-03-20 16:47:34-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/.github/workflows/delete-preview.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 644 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/delete-preview.yml’ 0K 100% 36.9M=0s 2025-03-20 16:47:34 (36.9 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/delete-preview.yml’ saved [644/644] --2025-03-20 16:47:34-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/config_automation.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 682 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/config_automation.yml’ 0K 100% 42.3M=0s 2025-03-20 16:47:34 (42.3 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/config_automation.yml’ saved [682/682] --2025-03-20 16:47:34-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/resources/dictionary.txt Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 202 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/dictionary.txt’ 0K 100% 16.2M=0s 2025-03-20 16:47:34 (16.2 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/dictionary.txt’ saved [202/202] --2025-03-20 16:47:34-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/resources/ignore-urls.txt Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 44 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/ignore-urls.txt’ 0K 100% 1.68M=0s 2025-03-20 16:47:35 (1.68 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/ignore-urls.txt’ saved [44/44] --2025-03-20 16:47:35-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/resources/exclude_files.txt Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.109.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 99 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/exclude_files.txt’ 0K 100% 7.34M=0s 2025-03-20 16:47:35 (7.34 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/resources/exclude_files.txt’ saved [99/99] --2025-03-20 16:47:35-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/_quarto.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.111.133, 185.199.110.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 534 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/_quarto.yml’ 0K 100% 25.1M=0s 2025-03-20 16:47:35 (25.1 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/_quarto.yml’ saved [534/534] --2025-03-20 16:47:35-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/styles.css Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.111.133, 185.199.110.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 624 [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/styles.css’ 0K 100% 42.2M=0s 2025-03-20 16:47:35 (42.2 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/styles.css’ saved [624/624] --2025-03-20 16:47:35-- https://raw.githubusercontent.com/fhdsl/OTTR_Quarto_Website/refs/heads/main/.github/workflows/render-site.yml Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.108.133, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2467 (2.4K) [text/plain] Saving to: ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/render-site.yml’ 0K .. 100% 40.4M=0s 2025-03-20 16:47:35 (40.4 MB/s) - ‘/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/quarto_web/.github/workflows/render-site.yml’ saved [2467/2467] pandoc  to: html output-file: index.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en name: OTTR Quarto Website output_dir: docs navbar: left: href: index.html Output created: index.html Checking question: First question to as ... in quiz: NA Checking question: Example without choo ... in quiz: NA Checking question: Question example wit ... in quiz: NA Checking question: A more complicated e ... in quiz: NA Checking question: It would be a shame ... in quiz: NA Checking question: What a shame if we p ... in quiz: NA Checking question: Shame shame if we sa ... in quiz: NA Checking question: What if we don't put ... in quiz: NA Checking question: What if only give co ... in quiz: NA Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/ottrpal/extdata/quizzes/quiz_bad.md Checking question: It would be a shame ... in quiz: quiz_bad.md Checking question: What a shame if we p ... in quiz: quiz_bad.md Checking question: Shame shame if we sa ... in quiz: quiz_bad.md Checking question: What if we don't put ... in quiz: quiz_bad.md Checking question: What if only give co ... in quiz: quiz_bad.md Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/ottrpal/extdata/quizzes/quiz_good.md Checking question: First question to as ... in quiz: quiz_good.md Checking question: Example without choo ... in quiz: quiz_good.md Checking question: Question example wit ... in quiz: quiz_good.md Checking question: A more complicated e ... in quiz: quiz_good.md Question error report saved to:/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/ottrpal/extdata/quizzes/question_error_report.tsv Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_ch1.md Checking question: First question to as ... in quiz: quiz_ch1.md Checking question: Question example wit ... in quiz: quiz_ch1.md Checking question: Second question to a ... in quiz: quiz_ch1.md Checking question: A more complicated e ... in quiz: quiz_ch1.md Checking question: A question in which ... in quiz: quiz_ch1.md No question errors to report! 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/question_error_report.tsv Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_bad.md Checking question: It would be a shame ... in quiz: quiz_bad.md Checking question: What a shame if we p ... in quiz: quiz_bad.md Checking question: Shame shame if we sa ... in quiz: quiz_bad.md Checking question: What if we don't put ... in quiz: quiz_bad.md Checking question: What if only give co ... in quiz: quiz_bad.md Checking quiz: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/quiz_ch1.md Checking question: First question to as ... in quiz: quiz_ch1.md Checking question: Question example wit ... in quiz: quiz_ch1.md Checking question: Second question to a ... in quiz: quiz_ch1.md Checking question: A more complicated e ... in quiz: quiz_ch1.md Checking question: A question in which ... in quiz: quiz_ch1.md Question error report saved to:/srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/quizzes/question_error_report.tsv 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/question_error_report.tsv Rendering book in directory './OTTR_Template-main' processing file: index.Rmd output file: index.knit.md processing file: 01-intro.Rmd Error in loadNamespace(x) : there is no package called 'devtools' Calls: local ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Quitting from 01-intro.Rmd:17-19 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `loadNamespace()`: ! there is no package called 'devtools' --- Backtrace: ▆ 1. └─base::loadNamespace(x) 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted trying URL 'https://github.com/jhudsl/OTTR_Template_Website/archive/refs/heads/main.zip' downloaded 9.5 MB Rendering: ./OTTR_Template_Website-main/contact.Rmd /usr/bin/pandoc +RTS -K512m -RTS contact.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output contact.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804847ec43.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804e235039.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/editing.Rmd /usr/bin/pandoc +RTS -K512m -RTS editing.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output editing.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804628f46b6.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804255e9f5a.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/git_actions.Rmd /usr/bin/pandoc +RTS -K512m -RTS git_actions.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output git_actions.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str32180448e93da6.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str3218045f2b6c5e.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/hosting.Rmd /usr/bin/pandoc +RTS -K512m -RTS hosting.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hosting.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str3218046633dfe8.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str32180417bf19b3.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/index.Rmd /usr/bin/pandoc +RTS -K512m -RTS index.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output index.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str32180464e78b12.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804314c13.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/setup.Rmd /usr/bin/pandoc +RTS -K512m -RTS setup.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output setup.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804c0f3c43.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804213846af.html --include-in-header resources/header.html Rendering: ./OTTR_Template_Website-main/style.Rmd /usr/bin/pandoc +RTS -K512m -RTS style.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output style.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 --variable bs3=TRUE --standalone --section-divs --template /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str3218041fc8b382.html --variable navbar=1 --variable theme=cosmo --css styles.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5QJq5A/working_dir/RtmpmHM6qI/rmarkdown-str321804294fdf79.html --include-in-header resources/header.html Output created: docs/index.html trying URL 'https://github.com/fhdsl/OTTR_Quarto/archive/refs/heads/main.zip' downloaded 3.4 MB  [1/6] index.qmd  [2/6] intro.qmd  processing file: intro.qmd Error in loadNamespace(x) : there is no package called 'devtools' Calls: .main ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart  Quitting from intro.qmd:20-22 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `loadNamespace()`: ! there is no package called 'devtools' --- Backtrace: ▆ 1. └─base::loadNamespace(x) 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted trying URL 'https://github.com/fhdsl/OTTR_Quarto_Website/archive/refs/heads/main.zip' downloaded 9.4 MB  [1/7] contact.qmd  [2/7] hosting.qmd  processing file: hosting.qmd output file: hosting.knit.md  [3/7] setup.qmd  processing file: setup.qmd output file: setup.knit.md  [4/7] editing.qmd  processing file: editing.qmd output file: editing.knit.md  [5/7] style.qmd  processing file: style.qmd output file: style.knit.md  [6/7] index.qmd  processing file: index.qmd output file: index.knit.md  [7/7] git_actions.qmd  processing file: git_actions.qmd output file: git_actions.knit.md  Output created: docs/index.html trying URL 'https://github.com/jhudsl/OTTR_Template/archive/refs/heads/main.zip' downloaded 30.3 MB 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template-main/check_reports/spell_check_results.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): word, file dbl (1): lines i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/fhdsl/OTTR_Quarto/archive/refs/heads/main.zip' downloaded 3.4 MB 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto-main/check_reports/spell_check_results.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): word, file dbl (1): lines i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/jhudsl/OTTR_Template_Website/archive/refs/heads/main.zip' downloaded 9.5 MB 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Template_Website-main/check_reports/spell_check_results.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): word, file dbl (1): lines i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. trying URL 'https://github.com/fhdsl/OTTR_Quarto_Website/archive/refs/heads/main.zip' downloaded 9.4 MB 1 Saved to: /srv/hornik/tmp/CRAN_pretest/ottrpal.Rcheck/tests/testthat/OTTR_Quarto_Website-main/check_reports/spell_check_results.tsv Rows: 1 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): word, file dbl (1): lines i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. [ FAIL 2 | WARN 4 | SKIP 1 | PASS 41 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-main-check.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-rendering.R:5:3'): Rmd Rendering ─────────────────────────────── Error in `Rscript_render(f, render_args, render_meta, add1, add2)`: Failed to compile 01-intro.Rmd Backtrace: ▆ 1. └─ottrpal::setup_ottr_template(dir = ".", type = "rmd") at test-rendering.R:5:3 2. └─bookdown::render_book(output_dir) 3. └─bookdown:::render_new_session(...) 4. └─bookdown:::Rscript_render(...) ── Error ('test-rendering.R:26:3'): Quarto Rendering ─────────────────────────── Error in `quarto::quarto_render(output_dir, as_job = FALSE)`: x Error running quarto cli. Caused by error: ! System command 'quarto' failed Backtrace: ▆ 1. └─ottrpal::setup_ottr_template(dir = ".", type = "quarto") at test-rendering.R:26:3 2. └─quarto::quarto_render(output_dir, as_job = FALSE) 3. └─quarto:::quarto_run(args, echo = TRUE, quarto_bin = quarto_bin) 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7. └─value[[3L]](cond) 8. └─cli::cli_abort(msg, call = .call, parent = e) 9. └─rlang::abort(...) [ FAIL 2 | WARN 4 | SKIP 1 | PASS 41 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character 😱 (U+1F631) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘OTTR_Quarto-main’ ‘OTTR_Quarto-main.zip’ ‘OTTR_Template-main’ ‘OTTR_Template-main.zip’ ‘ottrpal-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 3 NOTEs