Package: hockeystick Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘usinghockeystick.qmd’ using html  processing file: usinghockeystick.qmd trying URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' Error in `download.file()`: ! cannot open URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' Backtrace: ▆ 1. └─hockeystick::get_carbon() 2. └─utils::download.file(file_url, dl)  Quitting from usinghockeystick.qmd:15-21 [carbon] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `download.file()`: ! cannot open URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' --- Backtrace: ▆ 1. └─hockeystick::get_carbon() 2. └─utils::download.file(file_url, dl) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted WARN: Error encountered when rendering files Error: processing vignette 'usinghockeystick.qmd' failed with diagnostics: ! Error running quarto CLI from R. Caused by error in `quarto_render()`: ✖ Error returned by quarto CLI. ----------------------------- processing file: usinghockeystick.qmd trying URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' Error in `download.file()`: ! cannot open URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' Backtrace: ▆ 1. └─hockeystick::get_carbon() 2. └─utils::download.file(file_url, dl) Quitting from usinghockeystick.qmd:15-21 [carbon] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `download.file()`: ! cannot open URL 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv' --- Backtrace: ▆ 1. └─hockeystick::get_carbon() 2. └─utils::download.file(file_url, dl) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted WARN: Error encountered when rendering files Caused by error: ! System command 'quarto' failed --- failed re-building ‘usinghockeystick.qmd’ SUMMARY: processing the following file failed: ‘usinghockeystick.qmd’ Error: Vignette re-building failed. Execution halted Package: OlinkAnalyze Check: tests New result: ERROR Running ‘testthat.R’ [161s/164s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OlinkAnalyze) > > test_check("OlinkAnalyze") Variables and covariates converted from character to factors: Site ANOVA model fit to each assay: NPX~Site Variables and covariates converted from character to factors: Time ANOVA model fit to each assay: NPX~Time Variables and covariates converted from character to factors: Site, Time ANOVA model fit to each assay: NPX~Site*Time Variables and covariates converted from character to factors: Site Means estimated for each assay from ANOVA model: NPX~Site Variables and covariates converted from character to factors: Time Means estimated for each assay from ANOVA model: NPX~Time 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 ANOVA model fit to each assay: NPX~treatment2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment1 ANOVA model fit to each assay: NPX~treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 Means estimated for each assay from ANOVA model: NPX~treatment2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 Means estimated for each assay from ANOVA model: NPX~treatment2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using max LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using plate LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using plate LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using plate LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 0 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Site Kruskal model fit to each assay: NPX~Site Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Time Friedman model fit to each assay: NPX~Time Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Site Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Time Pairwise comparisons for Friedman test using paired Wilcoxon signed-rank test were performed 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables converted from character to factors: treatment2 Kruskal model fit to each assay: NPX~treatment2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables converted from character to factors: treatment2 Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables and covariates converted from character to factors: Treatment, Time ANOVA model fit to each assay: NPX~Treatment*Time Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables and covariates converted from character to factors: Treatment, Time Means estimated for each assay from ANOVA model: NPX~Treatment*Time Saving _problems/test-Olink_ordinalRegression-27.R Random assignment of SAMPLES to plates Assigning subjects to plates . Random assignment of SUBJECTS to plates `study` column detected in manifest. Optional study argument is set to "study". Assigning subjects to plates. Keeping studies together during randomization. Testing with 0 empty well(s) in the plate. . study1 successful! Testing with 0 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 1 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 2 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 3 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 4 empty well(s) in the plate. . study2 successful! Random assignment of SUBJECTS to plates Totally included 4 empty well(s) in first and/or intermediate plate(s) to accomplish the randomization. Please try another seed or increase the number of iterations if there are indications that another randomization might leave fewer empty wells. `study` column detected in manifest. Optional study argument is set to "study". Assigning subjects to plates. Multi-study project detected. Studies will be kept together during randomization. Random assignment of SAMPLES to plates by study Assigning subjects to plates . Random assignment of SUBJECTS to plates Random assignment of SAMPLES to plates Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Treatment T-test is performed on Treated - Untreated. Variable converted from character to factor: Time Paired t-test is performed on Baseline - Week.6. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Time Variable converted from character to factor: treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. T-test is performed on control - treated. Target 96 data in wide form detected. Multiple quantification columns detected (NPX, PCNormalizedNPX, Count). NPX will be used for downstream analysis. i Outdated Data Analysis Reference ID and Software Version combination detected. > Re-export data using Panel Archive Version 1.5.0+ in NPX Map and use the newest version of the Fixed LOD file when calculating LOD (Version 6+). ! Failure to re-export may result in incorrect PC normalization across lots and Fixed LOD calculations. QUANT data detected. Some downstream functions may not be supported. 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Bridge normalization will be performed! Assay(s) from the following input dataset have been excluded from normalization: * 20200001: OID01216 and OID01217 i Were marked as "EXCLUDED". Bridge normalization will be performed! Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Treatment Mann-Whitney U Test is performed on Treated - Untreated. Variable converted from character to factor: Time Paired Mann-Whitney U Test is performed on Baseline - Week.6. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Time Variable converted from character to factor: treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Mann-Whitney U Test is performed on control - treated. [ FAIL 1 | WARN 0 | SKIP 41 | PASS 565 ] ══ Skipped tests (41) ══════════════════════════════════════════════════════════ • On CRAN (14): 'test-Olink_boxplot.R:1:1', 'test-Olink_plate_randomizer.R:63:3', 'test-Read_NPX_data.R:1:1', 'test-Volcano_plot.R:17:3', 'test-dist_plot.R:23:3', 'test-linear_mixed_model.R:1:1', 'test-npxProcessing.R:141:1', 'test-olink_Pathway_Enrichment.R:1:1', 'test-olink_Pathway_Heatmap.R:1:1', 'test-olink_Pathway_Visualization.R:1:1', 'test-olink_bridgeability_plot.R:6:5', 'test-olink_bridgeability_plot.R:93:5', 'test-olink_qc_plot.R:21:3', 'test-pca_plot.R:2:1' • file.exists(test_path("data", "example_3k_data.rds")) is not TRUE (22): 'test-olink_normalization.R:450:5', 'test-olink_normalization.R:496:5', 'test-olink_normalization.R:869:5', 'test-olink_normalization.R:934:5', 'test-olink_normalization.R:989:5', 'test-olink_normalization_product.R:7:5', 'test-olink_normalization_product.R:129:5', 'test-olink_normalization_product.R:335:5', 'test-olink_normalization_product.R:467:5', 'test-olink_normalization_product.R:599:5', 'test-olink_normalization_product.R:670:5', 'test-olink_normalization_product.R:956:5', 'test-olink_normalization_product.R:1147:5', 'test-olink_normalization_utils.R:327:5', 'test-olink_normalization_utils.R:3478:5', 'test-olink_normalization_utils.R:3609:5', 'test-olink_normalization_utils.R:3901:5', 'test-olink_normalization_utils.R:3973:5', 'test-olink_normalization_utils.R:4022:5', 'test-olink_normalization_utils.R:4197:5', 'test-olink_normalization_utils.R:5243:5', 'test-olink_normalization_utils.R:6688:5' • file.exists(test_path("data", "example_HT_data.rds")) is not TRUE (1): 'test-olink_normalization_product.R:881:5' • file.exists(test_path("data", "ref_results_norm.rds")) is not TRUE (4): 'test-olink_normalization.R:17:5', 'test-olink_normalization.R:125:5', 'test-olink_normalization.R:237:5', 'test-olink_normalization.R:349:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Olink_ordinalRegression.R:17:3'): (code run outside of `test_that()`) ── Error in ``contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])`: contrasts can be applied only to factors with 2 or more levels Backtrace: ▆ 1. ├─... %>% select(-id) at test-Olink_ordinalRegression.R:17:3 2. ├─dplyr::select(., -id) 3. ├─dplyr::arrange(., id, contrast) 4. ├─dplyr::mutate(., id = as.character(OlinkID)) 5. ├─OlinkAnalyze::olink_ordinalRegression_posthoc(...) 6. │ ├─base::withCallingHandlers(...) 7. │ └─... %>% dplyr::mutate(term = paste(effect, collapse = ":")) 8. ├─dplyr::mutate(., term = paste(effect, collapse = ":")) 9. ├─dplyr::ungroup(.) 10. ├─dplyr::do(...) 11. ├─dplyr:::do.grouped_df(...) 12. │ └─rlang::eval_tidy(args[[1]], mask) 13. ├─base::data.frame(...) 14. ├─emmeans::emmeans(...) 15. │ └─emmeans:::.chk.list(object, ...) 16. └─ordinal::clm(as.formula(formula_string), data = .) 17. └─ordinal:::get_clmDesign(fullmf, terms.list, contrasts) 18. └─ordinal:::get_clmDM(...) 19. ├─stats::model.matrix(...) 20. └─stats::model.matrix.default(...) 21. └─stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) [ FAIL 1 | WARN 0 | SKIP 41 | PASS 565 ] Error: ! Test failures. Execution halted Package: usedthese Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘multipage.Rmd’ using rmarkdown Quitting from multipage.Rmd:25-28 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map()`: ℹ In index: 15. Caused by error in `open.connection()`: ! cannot open the connection --- Backtrace: ▆ 1. └─usedthese::used_there("https://www.quantumjitter.com/project/") 2. └─usedthese:::extract_usage(get_links(html, url, num_links)) 3. ├─tidyr::extract(...) 4. ├─tidyr::separate_longer_delim(...) 5. │ └─tidyr:::check_data_frame(data) 6. │ └─base::is.data.frame(x) 7. ├─purrr::list_rbind(...) 8. │ └─purrr:::check_list_of_data_frames(x) 9. │ └─vctrs::obj_check_list(x, call = error_call) 10. ├─purrr::list_flatten(...) 11. │ └─vctrs (local) is_node(x) 12. └─purrr::map(...) 13. └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 14. ├─purrr:::with_indexed_errors(...) 15. │ └─base::withCallingHandlers(...) 16. ├─purrr:::call_with_cleanup(...) 17. └─usedthese (local) .f(.x[[i]], ...) 18. ├─dplyr::mutate(...) 19. ├─rvest::html_table(html_element(read_html(x), ".usedthese")) 20. ├─rvest::html_element(read_html(x), ".usedthese") 21. ├─xml2::read_html(x) 22. └─xml2:::read_html.default(x) 23. ├─base::suppressWarnings(...) 24. │ └─base::withCallingHandlers(...) 25. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 26. └─xml2:::read_xml.character(...) 27. └─xml2:::read_xml.connection(...) 28. ├─base::open(x, "rb") 29. └─base::open.connection(x, "rb") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'multipage.Rmd' failed with diagnostics: ℹ In index: 15. Caused by error in `open.connection()`: ! cannot open the connection --- failed re-building ‘multipage.Rmd’ --- re-building ‘usedthese.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘usedthese.Rmd’ SUMMARY: processing the following file failed: ‘multipage.Rmd’ Error: Vignette re-building failed. Execution halted Package: vroom Check: compiled code Old result: NOTE File ‘vroom/libs/vroom.so’: Found non-API calls to R: ‘ATTRIB’, ‘SETLENGTH’, ‘SET_TRUELENGTH’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. New result: WARNING File ‘vroom/libs/vroom.so’: Found non-API calls to R: ‘ATTRIB’, ‘SETLENGTH’, ‘SET_TRUELENGTH’ These entry points may be removed soon: ‘SET_TRUELENGTH’, ‘SETLENGTH’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.