* using log directory ‘/data/localhost/ripley/R/packages/tests-noLD/spinebil.Rcheck’ * using R Under development (unstable) (2026-10-28 r90779) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-28 19:25:22 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘spinebil/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spinebil’ version ‘1.0.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘spinebil’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [20s/69s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [161s/229s] ERROR Error(s) in re-building vignettes: --- re-building ‘more_descriptives.qmd’ using html  processing file: more_descriptives.qmd  Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100% Progress: 100% Progress: 100% Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100%  Progress: 100% Progress: 100% Progress: 100% Progress: 100%  Progress: 100% Progress: 100%  Progress: 100% Progress: ──────────── 100% Progress: ──────────── 100%  Progress: ──────────── 100% Progress: ───────────────────────── 100% Progress: ───────────────────────── 100% Progress: ───────────────────────── 100%  Progress: ───────────────────────── 100% Progress: ───────────────────────── 100%  Progress: ───────────────────────── 100% Progress: ───────────────────────── 100% Progress: ───────────────────────── 100% Progress: 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──────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100%  Progress: ──────────────────────────────────────────────────────────────── 100%output file: more_descriptives.knit.md pandoc  to: html output-file: more_descriptives.html standalone: true embed-resources: true wrap: none default-image-extension: png css: - >- /data/localhost/ripley/R/test-dev/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css metadata document-css: false lang: en minimal: true theme: none title: Exploring Potential of Functions to be used for Projection Pursuit vignette: | %\VignetteIndexEntry{More Descriptive Analysis of Projection Pursuit Indices} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8} Output created: more_descriptives.html --- finished re-building ‘more_descriptives.qmd’ --- re-building ‘ppi_diagnostics.qmd’ using html  processing file: ppi_diagnostics.qmd Error in `dplyr::summarise()`: ℹ In argument: `intermediate_scags(...)`. ℹ In group 1: `Var1 = V2`, `Var2 = V1`. Caused by error in `colnames<-`: ! attempt to set 'colnames' on an object with less than two dimensions Backtrace: ▆ 1. ├─spinebil::profile_rotation(d, index_list, index_labels, n = 50) 2. │ └─spinebil (local) idx(dprj) 3. │ └─cassowaryr::calc_scags_wide(as.data.frame(mat), index_name) 4. │ └─... %>% dplyr::ungroup() 5. ├─dplyr::ungroup(.) 6. ├─dplyr::summarise(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ ├─base::withCallingHandlers(...) 10. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask) 11. │ └─base::lapply(.x, .f, ...) 12. │ └─dplyr (local) FUN(X[[i]], ...) 13. │ └─mask$eval_all_summarise(quo) 14. │ └─dplyr (local) eval() 15. ├─cassowaryr:::intermediate_scags(...) 16. │ └─cassowaryr::calc_scags(x, y, scags, out.rm, euclid) 17. │ └─cassowaryr:::original_and_robust(x, y) 18. │ └─cassowaryr::scree(new_x, new_y) 19. │ └─alphahull::delvor(xy) 20. │ └─interp::tri.mesh(X) 21. │ └─base::`colnames<-`(...) 22. │ └─base::stop("attempt to set 'colnames' on an object with less than two dimensions") 23. └─base::.handleSimpleError(...) 24. └─dplyr (local) h(simpleError(msg, call)) 25. └─dplyr (local) handler(cnd) 26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)  Quitting from ppi_diagnostics.qmd:279-287 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: ℹ In argument: `intermediate_scags(...)`. ℹ In group 1: `Var1 = V2`, `Var2 = V1`. Caused by error in `colnames<-`: ! attempt to set 'colnames' on an object with less than two dimensions --- Backtrace: ▆ 1. ├─spinebil::profile_rotation(d, index_list, index_labels, n = 50) 2. │ └─spinebil (local) idx(dprj) 3. │ └─cassowaryr::calc_scags_wide(as.data.frame(mat), index_name) 4. │ └─... %>% dplyr::ungroup() 5. ├─dplyr::ungroup(.) 6. ├─dplyr::summarise(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ ├─base::withCallingHandlers(...) 10. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask) 11. │ └─base::lapply(.x, .f, ...) 12. │ └─dplyr (local) FUN(X[[i]], ...) 13. │ └─mask$eval_all_summarise(quo) 14. │ └─dplyr (local) eval() 15. └─cassowaryr:::intermediate_scags(...) 16. └─cassowaryr::calc_scags(x, y, scags, out.rm, euclid) 17. └─cassowaryr:::original_and_robust(x, y) 18. └─cassowaryr::scree(new_x, new_y) 19. └─alphahull::delvor(xy) 20. └─interp::tri.mesh(X) 21. └─base::`colnames<-`(...) 22. └─base::stop("attempt to set 'colnames' on an object with less than two dimensions") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted WARN: Error encountered when rendering files Error: processing vignette 'ppi_diagnostics.qmd' failed with diagnostics: ! Error running quarto CLI from R. Caused by error in `quarto_render()`: ✖ Error returned by quarto CLI. ----------------------------- processing file: ppi_diagnostics.qmd Error in `dplyr::summarise()`: ℹ In argument: `intermediate_scags(...)`. ℹ In group 1: `Var1 = V2`, `Var2 = V1`. Caused by error in `colnames<-`: ! attempt to set 'colnames' on an object with less than two dimensions Backtrace: ▆ 1. ├─spinebil::profile_rotation(d, index_list, index_labels, n = 50) 2. │ └─spinebil (local) idx(dprj) 3. │ └─cassowaryr::calc_scags_wide(as.data.frame(mat), index_name) 4. │ └─... %>% dplyr::ungroup() 5. ├─dplyr::ungroup(.) 6. ├─dplyr::summarise(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ ├─base::withCallingHandlers(...) 10. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask) 11. │ └─base::lapply(.x, .f, ...) 12. │ └─dplyr (local) FUN(X[[i]], ...) 13. │ └─mask$eval_all_summarise(quo) 14. │ └─dplyr (local) eval() 15. ├─cassowaryr:::intermediate_scags(...) 16. │ └─cassowaryr::calc_scags(x, y, scags, out.rm, euclid) 17. │ └─cassowaryr:::original_and_robust(x, y) 18. │ └─cassowaryr::scree(new_x, new_y) 19. │ └─alphahull::delvor(xy) 20. │ └─interp::tri.mesh(X) 21. │ └─base::`colnames<-`(...) 22. │ └─base::stop("attempt to set 'colnames' on an object with less than two dimensions") 23. └─base::.handleSimpleError(...) 24. └─dplyr (local) h(simpleError(msg, call)) 25. └─dplyr (local) handler(cnd) 26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Quitting from ppi_diagnostics.qmd:279-287 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: ℹ In argument: `intermediate_scags(...)`. ℹ In group 1: `Var1 = V2`, `Var2 = V1`. Caused by error in `colnames<-`: ! attempt to set 'colnames' on an object with less than two dimensions --- Backtrace: ▆ 1. ├─spinebil::profile_rotation(d, index_list, index_labels, n = 50) 2. │ └─spinebil (local) idx(dprj) 3. │ └─cassowaryr::calc_scags_wide(as.data.frame(mat), index_name) 4. │ └─... %>% dplyr::ungroup() 5. ├─dplyr::ungroup(.) 6. ├─dplyr::summarise(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ ├─base::withCallingHandlers(...) 10. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask) 11. │ └─base::lapply(.x, .f, ...) 12. │ └─dplyr (local) FUN(X[[i]], ...) 13. │ └─mask$eval_all_summarise(quo) 14. │ └─dplyr (local) eval() 15. └─cassowaryr:::intermediate_scags(...) 16. └─cassowaryr::calc_scags(x, y, scags, out.rm, euclid) 17. └─cassowaryr:::original_and_robust(x, y) 18. └─cassowaryr::scree(new_x, new_y) 19. └─alphahull::delvor(xy) 20. └─interp::tri.mesh(X) 21. └─base::`colnames<-`(...) 22. └─base::stop("attempt to set 'colnames' on an object with less than two dimensions") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted WARN: Error encountered when rendering files Caused by error in `processx::run()`: ! System command 'quarto' failed --- failed re-building ‘ppi_diagnostics.qmd’ --- re-building ‘spinebil.qmd’ using html  processing file: spinebil.qmd output file: spinebil.knit.md pandoc  to: html output-file: spinebil.html standalone: true embed-resources: true wrap: none default-image-extension: png css: - >- /data/localhost/ripley/R/test-dev/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css metadata document-css: false lang: en minimal: true theme: none title: An introduction to the spinebil package vignette: | %\VignetteIndexEntry{An introduction to the spinebil package} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8} Output created: spinebil.html --- finished re-building ‘spinebil.qmd’ SUMMARY: processing the following file failed: ‘ppi_diagnostics.qmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-noLD/spinebil.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:00.39, 200.95 + 11.39